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Posted to commits@taverna.apache.org by st...@apache.org on 2016/09/07 12:14:15 UTC
[1/3] incubator-taverna-plugin-bioinformatics git commit: Removed (c)
Univ of Manchester LGPL license header
Repository: incubator-taverna-plugin-bioinformatics
Updated Branches:
refs/heads/master 39d65baec -> 33e003af2
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
index 13c7791..cacde0b 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryXMLHandler.java,v $
- * Revision $Revision: 1.6 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:45:18 $
- * by $Author: davidwithers $
- * Created on 28-Apr-2006
- *****************************************************************/
package org.biomart.martservice.query;
import java.util.List;
@@ -40,7 +7,7 @@ import org.jdom.Namespace;
/**
* Utility class for serializing <code>Query</code> classes to XML.
- *
+ *
* @author David Withers
*/
public class QueryXMLHandler {
@@ -63,18 +30,18 @@ public class QueryXMLHandler {
public static final String UNIQUE_ROWS_ATTRIBUTE = "uniqueRows";
public static final String VERSION_ATTRIBUTE = "softwareVersion";
-
+
public static final String FORMATTER_ATTRIBUTE = "formatter";
-
+
public static final String HEADER_ATTRIBUTE = "header";
-
+
public static final String REQUEST_ID_ATTRIBUTE = "requestId";
public static final String SCHEMA_ATTRIBUTE = "virtualSchemaName";
/**
* Converts a <code>Query</code> to an XML element.
- *
+ *
* @param query
* the <code>Query</code> to serialize
* @param namespace
@@ -94,16 +61,16 @@ public class QueryXMLHandler {
queryElement.setAttribute(UNIQUE_ROWS_ATTRIBUTE, String.valueOf(query.getUniqueRows()));
String softwareVersion = query.getSoftwareVersion();
if (softwareVersion != null) {
- queryElement.setAttribute(VERSION_ATTRIBUTE, softwareVersion);
+ queryElement.setAttribute(VERSION_ATTRIBUTE, softwareVersion);
}
String formatter = query.getFormatter();
if (formatter != null) {
- queryElement.setAttribute(FORMATTER_ATTRIBUTE, formatter);
- queryElement.setAttribute(HEADER_ATTRIBUTE, "1");
+ queryElement.setAttribute(FORMATTER_ATTRIBUTE, formatter);
+ queryElement.setAttribute(HEADER_ATTRIBUTE, "1");
}
String requestId = query.getRequestId();
if (requestId != null) {
- queryElement.setAttribute(REQUEST_ID_ATTRIBUTE, requestId);
+ queryElement.setAttribute(REQUEST_ID_ATTRIBUTE, requestId);
}
for (Dataset dataset : query.getDatasets()) {
queryElement.addContent(datasetToElement(dataset, namespace));
@@ -117,7 +84,7 @@ public class QueryXMLHandler {
/**
* Converts a <code>Dataset</code> to an XML element.
- *
+ *
* @param dataset
* the <code>Dataset</code> to serialize
* @param namespace
@@ -142,7 +109,7 @@ public class QueryXMLHandler {
/**
* Converts a <code>Link</code> to an XML element.
- *
+ *
* @param link
* the <code>Link</code> to serialize
* @param namespace
@@ -160,7 +127,7 @@ public class QueryXMLHandler {
/**
* Converts an <code>Attribute</code> to an XML element.
- *
+ *
* @param attribute
* the <code>Attribute</code> to serialize
* @param namespace
@@ -181,7 +148,7 @@ public class QueryXMLHandler {
/**
* Converts a <code>Filter</code> to an XML element.
- *
+ *
* @param filter
* the <code>Filter</code> to serialize
* @param namespace
@@ -214,7 +181,7 @@ public class QueryXMLHandler {
/**
* Creates a <code>Query</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @param namespace
@@ -247,7 +214,7 @@ public class QueryXMLHandler {
/**
* Creates a <code>Dataset</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @param namespace
@@ -272,7 +239,7 @@ public class QueryXMLHandler {
/**
* Creates a <code>Filter</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @return a deserialized <code>Filter</code>
@@ -300,7 +267,7 @@ public class QueryXMLHandler {
/**
* Creates an <code>Attribute</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @return a deserialized <code>Attribute</code>
@@ -317,7 +284,7 @@ public class QueryXMLHandler {
/**
* Creates an <code>Link</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @return a deserialized <code>Link</code>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java
index abf963d..66eceab 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartDatasetTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:14 $
- * by $Author: davidwithers $
- * Created on 4 Aug 2006
*****************************************************************/
package org.biomart.martservice;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java
index 5766d60..115136a 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartRegistryTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:14 $
- * by $Author: davidwithers $
- * Created on 4 Aug 2006
*****************************************************************/
package org.biomart.martservice;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java
index d938440..e90ca0a 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceUtilsTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/02/22 18:31:56 $
- * by $Author: davidwithers $
- * Created on 22 Feb 2007
*****************************************************************/
package org.biomart.martservice;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java
index 4c4dded..7cadce6 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceXMLHandlerTest.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/04 14:16:00 $
- * by $Author: davidwithers $
- * Created on 02-Jun-2006
*****************************************************************/
package org.biomart.martservice;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java
index aa5ad8a..3546160 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartURLLocationTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:14 $
- * by $Author: davidwithers $
- * Created on 02-Jun-2006
*****************************************************************/
package org.biomart.martservice;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java
index c22d8e2..0c86d0a 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentEventTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:15 $
- * by $Author: davidwithers $
- * Created on 06-Jun-2006
*****************************************************************/
package org.biomart.martservice.config.event;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java
index 2236f37..45c6bb7 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceIconsTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:16 $
- * by $Author: davidwithers $
- * Created on 24-Aug-2006
*****************************************************************/
package org.biomart.martservice.config.ui;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java
index 5ac4c9e..c717127 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: AttributeTest.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:43:40 $
- * by $Author: davidwithers $
- * Created on 02-May-2006
*****************************************************************/
package org.biomart.martservice.query;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java
index 374ce5d..22f901c 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: DatasetTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:10 $
- * by $Author: davidwithers $
- * Created on 03-May-2006
*****************************************************************/
package org.biomart.martservice.query;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java
index 2d0be4e..5961226 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: FilterTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:10 $
- * by $Author: davidwithers $
- * Created on 03-May-2006
*****************************************************************/
package org.biomart.martservice.query;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java
index b2b93cc..4b17984 100644
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java
+++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java
@@ -1,35 +1,4 @@
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryTest.java,v $
- * Revision $Revision: 1.3 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/01 12:11:30 $
- * by $Author: davidwithers $
- * Created on 03-May-2006
*****************************************************************/
package org.biomart.martservice.query;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
index 803fde3..653571b 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.actions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
index 865c1f1..283e933 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.actions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java
index 8e02195..eeb3753 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.edits;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java
index e13c208..586d6cf 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java
@@ -1,25 +1,3 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
package net.sf.taverna.t2.activities.biomoby.edits;
import java.util.ArrayList;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java
index 43bc61f..7ff5e4d 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.edits;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java
index fea1860..2d0232d 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java
@@ -1,25 +1,3 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
package net.sf.taverna.t2.activities.biomoby.edits;
import java.util.ArrayList;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java
index a80c5fb..7e02e16 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomoby.servicedescriptions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
index 4ceed9b..6fe4099 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.view;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
index 0e6ea55..86b0591 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.view;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
index 91d4cd6..dc07ba2 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.view;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
index 5179642..9032f02 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
@@ -1,23 +1,4 @@
/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
*
*/
package net.sf.taverna.t2.activities.biomoby.view;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
index d4e85f9..dab657f 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab.actions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
index 560562b..5895e1c 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab.actions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
index 594a7a2..bc3ede4 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
@@ -1,55 +1,6 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MissingSoaplabException.java,v $
- * Revision $Revision: 1.3 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/11/19 17:33:04 $
- * by $Author: anenadic $
- * Created on 4 Sep 2006
*****************************************************************/
package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
index f9d273b..29ee07f 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
index 47f994c..4bf3672 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
@@ -1,55 +1,6 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: SoaplabCategory.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/09/04 13:40:38 $
- * by $Author: sowen70 $
- * Created on 4 Sep 2006
*****************************************************************/
package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
index fe428ec..b9127f1 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
@@ -1,55 +1,6 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: SoaplabScavengerAgent.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/09/04 13:40:37 $
- * by $Author: sowen70 $
- * Created on 4 Sep 2006
*****************************************************************/
package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
index 6dbd2b0..008093c 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab.views;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
index 3b7986d..659f402 100644
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
+++ b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab.views;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java b/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
index 039cc18..58fc6ba 100644
--- a/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
+++ b/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab.views;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java
index ba9cce6..8a7f7e1 100644
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java
+++ b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java
index 53091e1..f345557 100644
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java
+++ b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java
index fa6bdec..126f5b6 100644
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java
+++ b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java
index 3c62c9d..16f79a1 100644
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java
+++ b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java
index 69b910e..c8177ec 100644
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java
+++ b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java b/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java
index 3dc9ec3..fa8b8f4 100644
--- a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java
+++ b/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java b/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java
index e0b0dca..c18a4b0 100644
--- a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java
+++ b/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.soaplab;
[3/3] incubator-taverna-plugin-bioinformatics git commit: Removed (c)
Univ of Manchester LGPL license header
Posted by st...@apache.org.
Removed (c) Univ of Manchester LGPL license header
These were part of Software Grant to ASF filed 2015-02-23
and can thus be relicensed to Apache license 2.0
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/33e003af
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/33e003af
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/33e003af
Branch: refs/heads/master
Commit: 33e003af24b7bf088692ef0578a650b7b6066f52
Parents: 39d65ba
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed Sep 7 13:13:37 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed Sep 7 13:13:37 2016 +0100
----------------------------------------------------------------------
.../BiomartActivityConfigurationAction.java | 18 ---
.../actions/BiomartConfigurationPanel.java | 18 ---
.../BiomartActivityIcon.java | 18 ---
.../BiomartServiceDescription.java | 18 ---
.../views/BiomartActivityContextualView.java | 18 ---
.../views/BiomartActivityViewFactory.java | 18 ---
.../TestBiomartActivityContextualView.java | 18 ---
.../t2/activities/biomart/BiomartActivity.java | 18 ---
.../BiomartActivityConfigurationBean.java | 18 ---
.../biomart/BiomartActivityFactory.java | 18 ---
.../biomart/BiomartActivityHealthChecker.java | 18 ---
.../biomart/BiomartActivityFactoryTest.java | 18 ---
.../org/biomart/martservice/DatasetLink.java | 33 ------
.../org/biomart/martservice/MartDataset.java | 33 ------
.../java/org/biomart/martservice/MartQuery.java | 65 +++--------
.../org/biomart/martservice/MartRegistry.java | 39 +------
.../org/biomart/martservice/MartService.java | 83 +++++---------
.../martservice/MartServiceException.java | 43 +-------
.../biomart/martservice/MartServiceUtils.java | 59 +++-------
.../martservice/MartServiceXMLHandler.java | 53 ++-------
.../biomart/martservice/MartURLLocation.java | 71 ++++--------
.../org/biomart/martservice/ResultReceiver.java | 47 ++------
.../martservice/ResultReceiverException.java | 43 +-------
.../config/QueryConfigController.java | 69 +++---------
.../martservice/config/QueryConfigUtils.java | 77 ++++---------
.../config/event/QueryComponentAdapter.java | 51 ++-------
.../config/event/QueryComponentEvent.java | 45 +-------
.../config/event/QueryComponentListener.java | 51 ++-------
.../config/ui/ConfigDisplayObject.java | 49 ++-------
.../martservice/config/ui/ExpandableBox.java | 37 +------
.../martservice/config/ui/MartServiceIcons.java | 35 +-----
.../ui/MartServiceQueryConfigUIFactory.java | 33 ------
.../martservice/config/ui/MinimalLayout.java | 45 +-------
.../martservice/config/ui/QueryComponent.java | 75 ++++---------
.../config/ui/QueryConfigUIFactory.java | 73 ++++---------
.../biomart/martservice/query/Attribute.java | 33 ------
.../org/biomart/martservice/query/Dataset.java | 77 ++++---------
.../org/biomart/martservice/query/Filter.java | 67 +++---------
.../org/biomart/martservice/query/Link.java | 57 ++--------
.../org/biomart/martservice/query/Query.java | 109 +++++++------------
.../martservice/query/QueryListener.java | 51 ++-------
.../martservice/query/QueryXMLHandler.java | 69 +++---------
.../biomart/martservice/MartDatasetTest.java | 31 ------
.../biomart/martservice/MartRegistryTest.java | 31 ------
.../martservice/MartServiceUtilsTest.java | 31 ------
.../martservice/MartServiceXMLHandlerTest.java | 31 ------
.../martservice/MartURLLocationTest.java | 31 ------
.../config/event/QueryComponentEventTest.java | 31 ------
.../config/ui/MartServiceIconsTest.java | 31 ------
.../martservice/query/AttributeTest.java | 31 ------
.../biomart/martservice/query/DatasetTest.java | 31 ------
.../biomart/martservice/query/FilterTest.java | 31 ------
.../biomart/martservice/query/QueryTest.java | 31 ------
.../actions/MobyObjectDetailsAction.java | 19 ----
.../biomoby/actions/MobyParserAction.java | 19 ----
.../edits/AddBiomobyCollectionDataTypeEdit.java | 19 ----
.../edits/AddBiomobyConsumingServiceEdit.java | 22 ----
.../biomoby/edits/AddMobyParseDatatypeEdit.java | 19 ----
.../biomoby/edits/AddUpstreamObjectEdit.java | 22 ----
.../BiomobyServiceProvider.java | 18 ---
.../BiomobyObjectActivityContextualView.java | 19 ----
...mobyObjectActivityContextualViewFactory.java | 19 ----
.../view/MobyParseDatatypeContextualView.java | 19 ----
.../MobyParseDatatypeContextualViewFactory.java | 19 ----
.../SoaplabActivityConfigurationAction.java | 18 ---
.../actions/SoaplabConfigurationPanel.java | 18 ---
.../MissingSoaplabException.java | 49 ---------
.../SoaplabActivityIcon.java | 18 ---
.../servicedescriptions/SoaplabCategory.java | 49 ---------
.../SoaplabScavengerAgent.java | 49 ---------
.../views/SoaplabActivityContextualView.java | 18 ---
.../views/SoaplabActivityViewFactory.java | 18 ---
.../TestSoaplabActivityContextualView.java | 18 ---
.../sf/taverna/t2/activities/soaplab/Soap.java | 18 ---
.../t2/activities/soaplab/SoaplabActivity.java | 18 ---
.../SoaplabActivityConfigurationBean.java | 18 ---
.../soaplab/SoaplabActivityFactory.java | 18 ---
.../soaplab/SoaplabActivityHealthChecker.java | 18 ---
.../SoaplabActivityConfigurationBeanTest.java | 18 ---
.../activities/soaplab/SoaplabActivityTest.java | 18 ---
80 files changed, 341 insertions(+), 2483 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
index ad290f0..6df1af9 100644
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart.actions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
index 4d0a118..06d1a6a 100644
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart.actions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
index 845665e..4affb62 100644
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart.servicedescriptions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
index 7508b4d..0114053 100644
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
@@ -1,21 +1,3 @@
-/* Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart.servicedescriptions;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
index eacf193..c6c2bd9 100644
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart.views;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
index 4a866bc..1836dfc 100644
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart.views;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
index 8ad6242..f8d5c9b 100644
--- a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
+++ b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.biomart.views;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java
index 7e87939..13fc4f2 100644
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java
+++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java
index 91cc323..da71551 100644
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java
+++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java
index 4aaf043..a4b8877 100644
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java
+++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java
index 8e48635..7fb67a6 100644
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java
+++ b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java b/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java
index 78ed2f6..eec2c46 100644
--- a/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java
+++ b/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java
@@ -1,22 +1,4 @@
/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
******************************************************************************/
package net.sf.taverna.t2.activities.biomart;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java
index e5dccd4..65330cf 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: DatasetLink.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 12-Apr-2006
- *****************************************************************/
package org.biomart.martservice;
import java.util.Comparator;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java
index 8c0f584..6090dcf 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartDataset.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/04 14:17:19 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
package org.biomart.martservice;
import java.util.Comparator;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java
index 9f75566..fe4be71 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartQuery.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 08-May-2006
- *****************************************************************/
package org.biomart.martservice;
import java.util.ArrayList;
@@ -50,7 +17,7 @@ import org.ensembl.mart.lib.config.DatasetConfig;
/**
* Class for creating queries to send to a BioMart web service.
- *
+ *
* @author David Withers
*/
public class MartQuery {
@@ -98,7 +65,7 @@ public class MartQuery {
/**
* Returns the martDataset.
- *
+ *
* @return the martDataset.
*/
public MartDataset getMartDataset() {
@@ -107,7 +74,7 @@ public class MartQuery {
/**
* Sets the martDataset.
- *
+ *
* @param martDataset
* the martDataset to set.
*/
@@ -117,7 +84,7 @@ public class MartQuery {
/**
* Returns the martService.
- *
+ *
* @return the martService.
*/
public MartService getMartService() {
@@ -126,7 +93,7 @@ public class MartQuery {
/**
* Sets the martService.
- *
+ *
* @param martService
* the martService to set.
*/
@@ -136,7 +103,7 @@ public class MartQuery {
/**
* Returns the query.
- *
+ *
* @return the query.
*/
public Query getQuery() {
@@ -145,7 +112,7 @@ public class MartQuery {
/**
* Sets the query.
- *
+ *
* @param query
* the query to set.
*/
@@ -156,7 +123,7 @@ public class MartQuery {
/**
* Adds the ID that links the specified dataset to the initial dataset.
- *
+ *
* @param datasetName
* the dataset
* @param linkId
@@ -168,7 +135,7 @@ public class MartQuery {
/**
* Removes a dataset and any datasets linked to it.
- *
+ *
* @param datasetName
* the dataset to remove
*/
@@ -192,7 +159,7 @@ public class MartQuery {
/**
* Changes the ID that links a dataset. This method performs no function,
* nor does it throw an exception, if the specified dataset does not exist.
- *
+ *
* @param datasetName
* the dataset
* @param linkId
@@ -218,7 +185,7 @@ public class MartQuery {
/**
* Returns the Datasets that this Query contains in the order specified by
* the links.
- *
+ *
* @return the Datasets that this Query contains in the order specified by
* the links
*/
@@ -257,7 +224,7 @@ public class MartQuery {
/**
* Returns all the Attributes from all the Datasets in this Query in the
* order specified by the links.
- *
+ *
* @return all the Attributes from all the Datasets in this Query in the
* order specified by the links
*/
@@ -278,7 +245,7 @@ public class MartQuery {
/**
* Adds an Attribute to the Dataset with the given datasetName. If the Query
* has no Dataset with the given datasetName then a new Dataset is created.
- *
+ *
* @param datasetName
* the name of the Dataset to add the Attribute to
* @param attribute
@@ -300,7 +267,7 @@ public class MartQuery {
/**
* Removes an Attribute from its containing Dataset.
- *
+ *
* @param attribute
*/
public void removeAttribute(Attribute attribute) {
@@ -320,7 +287,7 @@ public class MartQuery {
/**
* Adds a Filter to the Dataset with the given datasetName. If the Query has
* no Dataset with the given datasetName then a new Dataset is created.
- *
+ *
* @param datasetName
* the name of the Dataset to add the Filter to
* @param filter
@@ -342,7 +309,7 @@ public class MartQuery {
/**
* Removes a Filter from its containing Dataset.
- *
+ *
* @param filter
*/
public void removeFilter(Filter filter) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java
index 93bf04d..85df4ae 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartRegistry.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
package org.biomart.martservice;
import java.util.ArrayList;
@@ -38,7 +5,7 @@ import java.util.List;
/**
* The MartRegistry returned by a BioMart web service.
- *
+ *
* @author David Withers
*/
public class MartRegistry {
@@ -46,7 +13,7 @@ public class MartRegistry {
/**
* Returns the martURLLocations.
- *
+ *
* @return the martURLLocations.
*/
public MartURLLocation[] getMartURLLocations() {
@@ -56,7 +23,7 @@ public class MartRegistry {
/**
* Adds a martURLLocation to the registry.
- *
+ *
* @param martURLLocations
* the martURLLocations to add.
*/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java
index c02bbb5..c6f4de1 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartService.java,v $errors/failure.html
- * Revision $Revision: 1.7 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/08/11 12:48:29 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
package org.biomart.martservice;
import java.io.File;
@@ -63,7 +30,7 @@ import org.xml.sax.InputSource;
/**
* A class for interacting with a BioMart web service.
- *
+ *
* @author David Withers
*/
public class MartService {
@@ -102,10 +69,10 @@ public class MartService {
/**
* Constructs an instance of a <code>MartService</code> with the specified
* location.
- *
+ *
* The location must be the URL of a valid BioMart MartService, e.g.
* http://www.biomart.org/biomart/martservice
- *
+ *
* @param location
* the URL of the MartService
*/
@@ -117,10 +84,10 @@ public class MartService {
* Returns a <code>MartService</code> for the specified location. If a
* <code>MartService</code> does not exist for the location a new one is
* constructed.
- *
+ *
* The location must be the URL of a valid BioMart MartService, e.g.
* http://www.biomart.org/biomart/martservice
- *
+ *
* @param location
* the URL of the MartService
*/
@@ -133,7 +100,7 @@ public class MartService {
/**
* Returns the requestId.
- *
+ *
* @return the requestId
*/
public String getRequestId() {
@@ -142,7 +109,7 @@ public class MartService {
/**
* Sets the requestId.
- *
+ *
* @param requestId
* the new requestId
*/
@@ -152,7 +119,7 @@ public class MartService {
/**
* Returns the cacheDirectory.
- *
+ *
* @return the cacheDirectory
*/
public File getCacheDirectory() {
@@ -161,7 +128,7 @@ public class MartService {
/**
* Sets the cacheDirectory.
- *
+ *
* @param cacheDirectory
* the new cacheDirectory
*/
@@ -171,7 +138,7 @@ public class MartService {
/**
* Returns the URL of the MartService.
- *
+ *
* @return the URL of the MartService
*/
public String getLocation() {
@@ -191,7 +158,7 @@ public class MartService {
/**
* Returns the MartRegistry for this MartService.
- *
+ *
* @return the MartRegistry for this MartService
* @throws MartServiceException
* if the MartService returns an error or is unavailable
@@ -214,7 +181,7 @@ public class MartService {
/**
* Returns all the datasets available from this MartService.
- *
+ *
* @return all the datasets available from this MartService.
* @throws MartServiceException
* if the MartService returns an error or is unavailable
@@ -230,7 +197,7 @@ public class MartService {
/**
* Returns the datasets belonging to the virtualSchema.
- *
+ *
* @param virtualSchema
* the virtual schema to include datasets from.
* @return the datasets belonging to the virtualSchema.
@@ -252,7 +219,7 @@ public class MartService {
/**
* Returns the datasets specified by martURLLocation.
- *
+ *
* @param martURLLocation
* where to find the datasets.
* @return the datasets specified by martURLLocation.
@@ -271,7 +238,7 @@ public class MartService {
/**
* Returns the dataset specified by a virtualSchema and a dataset name.
- *
+ *
* @param virtualSchema
* the virtualSchema containing the dataset
* @param datasetName
@@ -295,7 +262,7 @@ public class MartService {
/**
* Returns the configuration for a dataset.
- *
+ *
* @param dataset
* the dataset to get the configuration for
* @return the configuration for a dataset
@@ -398,7 +365,7 @@ public class MartService {
/**
* Returns the importables for a dataset.
- *
+ *
* @param dataset
* @return the importables for a dataset
* @throws MartServiceException
@@ -420,7 +387,7 @@ public class MartService {
/**
* Returns the exportables for a dataset.
- *
+ *
* @param dataset
* @return the exportables for a dataset
* @throws MartServiceException
@@ -443,10 +410,10 @@ public class MartService {
/**
* Sends a <code>Query</code> to the MartService and returns the results
* of executing the query.
- *
+ *
* The results are returned as an array of lists; one list for each
* attribute specified in the query.
- *
+ *
* @param query
* the query to execute
* @return the results of executing the query
@@ -462,12 +429,12 @@ public class MartService {
* Sends a <code>Query</code> to the MartService and writes the results to
* the <code>ResultReceiver</code> as each line of the result stream is
* read.
- *
+ *
* @param query
* @param resultReceiver
* @throws MartServiceException
* if the MartService returns an error or is unavailable
- * @throws ResultReceiverException
+ * @throws ResultReceiverException
* if the ResultReceiver cannot receive the result
* @see ResultReceiver
*/
@@ -478,7 +445,7 @@ public class MartService {
/**
* Returns a list of datasets that can be linked to the specified dataset.
- *
+ *
* @param martDataset
* @return datasets that can be linked to the specified dataset
* @throws MartServiceException
@@ -520,7 +487,7 @@ public class MartService {
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#equals(java.lang.Object)
*/
public boolean equals(Object obj) {
@@ -538,7 +505,7 @@ public class MartService {
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#hashCode()
*/
public int hashCode() {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java
index f1f0639..a6adb3b 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java
@@ -1,41 +1,8 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceException.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:05 $
- * by $Author: davidwithers $
- * Created on 05-May-2006
- *****************************************************************/
package org.biomart.martservice;
/**
* Thrown when a MartService is inaccessable or returns an error.
- *
+ *
* @author David Withers
*/
public class MartServiceException extends Exception {
@@ -43,7 +10,7 @@ public class MartServiceException extends Exception {
/**
* Constructs a new exception with no detail message.
- *
+ *
*/
public MartServiceException() {
super();
@@ -51,7 +18,7 @@ public class MartServiceException extends Exception {
/**
* Constructs a new exception with the specified detail message.
- *
+ *
* @param message
* the detail message
* @param cause
@@ -64,7 +31,7 @@ public class MartServiceException extends Exception {
/**
* Constructs a new exception with the specified detail message and cause.
- *
+ *
* @param message
* the detail message
*/
@@ -74,7 +41,7 @@ public class MartServiceException extends Exception {
/**
* Constructs a new exception with the specified cause.
- *
+ *
* @param cause
* the cause (a null value is permitted, and indicates that the
* cause is nonexistent or unknown)
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java
index cdcb400..9319cee 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceUtils.java,v $
- * Revision $Revision: 1.12 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/07/31 15:06:49 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
package org.biomart.martservice;
import java.io.BufferedReader;
@@ -73,7 +40,7 @@ import org.xml.sax.InputSource;
/**
* Utility class for interacting with a BioMart web service.
- *
+ *
* @author David Withers
*/
public class MartServiceUtils {
@@ -110,7 +77,7 @@ public class MartServiceUtils {
/**
* Sends a registry request to the Biomart webservice and constructs a
* MartRegistry from the XML returned by the webservice.
- *
+ *
* @param martServiceLocation
* the URL of the Biomart webservice
* @return a MartRegistry
@@ -197,7 +164,7 @@ public class MartServiceUtils {
* Sends a datasets request to the Biomart webservice and constructs an
* array of MartDataset from the tab separated rows of data returned by the
* webservice.
- *
+ *
* @param martServiceLocation
* the URL of the Biomart webservice
* @param mart
@@ -245,7 +212,7 @@ public class MartServiceUtils {
/**
* Sends a configuration request to the Biomart webservice and constructs a
* DatasetConfig from the XML returned by the webservice.
- *
+ *
* @param martServiceLocation
* the URL of the Biomart webservice
* @param dataset
@@ -320,7 +287,7 @@ public class MartServiceUtils {
* Sends a query to the Biomart webservice and constructs an array of List
* of String results from the tab separated rows of data returned by the
* webservice.
- *
+ *
* @param martServiceLocation
* the URL of the Biomart webservice
* @param query
@@ -435,7 +402,7 @@ public class MartServiceUtils {
}
}
-
+
// private static String getLocation(MartURLLocation martUrlLocation) {
// StringBuffer location = new StringBuffer("http://");
// location.append(martUrlLocation.getHost());
@@ -443,7 +410,7 @@ public class MartServiceUtils {
// location.append(martUrlLocation.getPath());
// return location.toString();
// }
-
+
private static int getAttributeCount(List<Attribute> attributeList) {
int result = 0;
for (Attribute attribute : attributeList) {
@@ -526,10 +493,10 @@ public class MartServiceUtils {
} else if ("XLS".equals(formatter)) {
mimeType = "'application/excel'";
}
-
+
return mimeType;
}
-
+
private static List<String>[] tabSeparatedReaderToResults(Reader reader,
int resultsCount) throws IOException {
List<String>[] results = new List[resultsCount];
@@ -550,7 +517,7 @@ public class MartServiceUtils {
private static Object[] readResult(InputStream inputStream, String formatter) throws IOException {
Object[] result = new Object[1];
-
+
if (getMimeTypeForFormatter(formatter).contains("application/")) {
result[0] = IOUtils.toByteArray(inputStream);
} else {
@@ -558,7 +525,7 @@ public class MartServiceUtils {
}
return result;
}
-
+
private static MartDataset[] tabSeparatedReaderToDatasets(Reader reader,
MartURLLocation martURLLocation) throws IOException {
List<MartDataset> datasetList = new ArrayList<MartDataset>();
@@ -606,7 +573,7 @@ public class MartServiceUtils {
/**
* Creates an XML string from a query
- *
+ *
* @param query
* @return an XML string
*/
@@ -644,7 +611,7 @@ public class MartServiceUtils {
}
/**
- *
+ *
* @param client
*/
public static void setProxy(HttpClient client) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java
index e8a5189..c4d3982 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceXMLHandler.java,v $
- * Revision $Revision: 1.4 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 28-Apr-2006
- *****************************************************************/
package org.biomart.martservice;
import java.util.Iterator;
@@ -43,7 +10,7 @@ import org.jdom.Namespace;
/**
* Utility class for serializing mart service classes to XML.
- *
+ *
* @author David Withers
*/
public class MartServiceXMLHandler {
@@ -105,7 +72,7 @@ public class MartServiceXMLHandler {
/**
* Converts a <code>MartService</code> to an XML element.
- *
+ *
* @param martService
* the <code>MartService</code> to serialize
* @param namespace
@@ -122,7 +89,7 @@ public class MartServiceXMLHandler {
/**
* Creates a <code>MartService</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @return a deserialized <code>MartService</code>
@@ -134,7 +101,7 @@ public class MartServiceXMLHandler {
/**
* Converts a <code>MartDataset</code> to an XML element.
- *
+ *
* @param dataset
* the <code>MartDataset</code> to serialize
* @param namespace
@@ -167,7 +134,7 @@ public class MartServiceXMLHandler {
/**
* Creates a <code>MartDataset</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @param namespace
@@ -197,7 +164,7 @@ public class MartServiceXMLHandler {
/**
* Creates a <code>MartRegistry</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @param namespace
@@ -236,7 +203,7 @@ public class MartServiceXMLHandler {
/**
* Converts a <code>MartURLLocation</code> to an XML element.
- *
+ *
* @param location
* the <code>MartURLLocation</code> to serialize
* @param namespace
@@ -283,7 +250,7 @@ public class MartServiceXMLHandler {
/**
* Creates a <code>MartURLLocation</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @return a deserialized <code>MartURLLocation</code>
@@ -320,7 +287,7 @@ public class MartServiceXMLHandler {
/**
* Creates a <code>MartQuery</code> from an XML element.
- *
+ *
* @param element
* the <code>Element</code> to deserialize
* @param namespace
@@ -354,7 +321,7 @@ public class MartServiceXMLHandler {
/**
* Converts a <code>MartQuery</code> to an XML element.
- *
+ *
* @param martQuery
* the <code>MartQuery</code> to serialize
* @param namespace
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java
index 476956d..6a15aa1 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartURLLocation.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/04 14:15:59 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
package org.biomart.martservice;
import org.ensembl.mart.lib.config.MartLocation;
@@ -38,7 +5,7 @@ import org.ensembl.mart.lib.config.MartLocation;
/**
* The MartURLLocation contained by the MartRegistry returned by a BioMart web
* service.
- *
+ *
* @author David Withers
*/
public class MartURLLocation implements MartLocation {
@@ -90,7 +57,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns true if the default flag is set.
- *
+ *
* @return true if the default flag is set
*/
public boolean isDefault() {
@@ -99,7 +66,7 @@ public class MartURLLocation implements MartLocation {
/**
* Sets the default flag.
- *
+ *
* @param defaultValue
* the value of the default flag
*/
@@ -109,7 +76,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns the displayName.
- *
+ *
* @return the displayName.
*/
public String getDisplayName() {
@@ -118,7 +85,7 @@ public class MartURLLocation implements MartLocation {
/**
* Sets the displayName.
- *
+ *
* @param displayName
* the displayName to set.
*/
@@ -128,7 +95,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns the host.
- *
+ *
* @return the host.
*/
public String getHost() {
@@ -137,7 +104,7 @@ public class MartURLLocation implements MartLocation {
/**
* Sets the host.
- *
+ *
* @param host
* the host to set.
*/
@@ -183,7 +150,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns the name
- *
+ *
* @return the name.
*/
public String getName() {
@@ -192,7 +159,7 @@ public class MartURLLocation implements MartLocation {
/**
* Sets the name.
- *
+ *
* @param name
* the name to set.
*/
@@ -220,7 +187,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns the port.
- *
+ *
* @return the port.
*/
public int getPort() {
@@ -229,7 +196,7 @@ public class MartURLLocation implements MartLocation {
/**
* Sets the port.
- *
+ *
* @param port
* the port to set.
*/
@@ -239,7 +206,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns the serverVirtualSchema.
- *
+ *
* @return the serverVirtualSchema.
*/
public String getServerVirtualSchema() {
@@ -248,7 +215,7 @@ public class MartURLLocation implements MartLocation {
/**
* Sets the serverVirtualSchema.
- *
+ *
* @param serverVirtualSchema
* the serverVirtualSchema to set.
*/
@@ -258,7 +225,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns the virtualSchema.
- *
+ *
* @return the virtualSchema.
*/
public String getVirtualSchema() {
@@ -267,7 +234,7 @@ public class MartURLLocation implements MartLocation {
/**
* Sets the virtualSchema.
- *
+ *
* @param virtualSchema
* the virtualSchema to set.
*/
@@ -277,7 +244,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns true if the location is visible.
- *
+ *
* @return Returns the visible.
*/
public boolean isVisible() {
@@ -294,7 +261,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns true if this location is redirected.
- *
+ *
* @return the redirect
*/
public boolean isRedirect() {
@@ -310,7 +277,7 @@ public class MartURLLocation implements MartLocation {
/*
* (non-Javadoc)
- *
+ *
* @see org.ensembl.mart.lib.config.MartLocation#getType()
*/
public String getType() {
@@ -319,7 +286,7 @@ public class MartURLLocation implements MartLocation {
/**
* Returns the display name.
- *
+ *
* @return the display name
*/
public String toString() {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java
index cc1d062..952899c 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java
@@ -1,61 +1,28 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ResultReceiver.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/07/31 15:06:49 $
- * by $Author: davidwithers $
- * Created on Jan 18, 2008
- *****************************************************************/
package org.biomart.martservice;
/**
* An interface for receiving results of a Query.
- *
+ *
* @author David Withers
*/
public interface ResultReceiver {
/**
* Receives a single row from the results of executing a Query.
- *
+ *
* This method will be called frequently and should not block.
- *
+ *
* @param resultRow
*/
public void receiveResult(Object[] resultRow, long index) throws ResultReceiverException;
-
+
/**
* Receives an error for a single row from the results of executing a Query.
- *
+ *
* This method will be called frequently and should not block.
- *
+ *
* @param resultRow
*/
public void receiveError(String errorMessage, long index) throws ResultReceiverException;
-
+
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java
index c3498e6..6386c9b 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java
@@ -1,40 +1,7 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ResultReceiverException.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:47:57 $
- * by $Author: davidwithers $
- * Created on 05-May-2006
- *****************************************************************/
package org.biomart.martservice;
/**
- *
+ *
* @author David Withers
*/
public class ResultReceiverException extends Exception {
@@ -42,7 +9,7 @@ public class ResultReceiverException extends Exception {
/**
* Constructs a new exception with no detail message.
- *
+ *
*/
public ResultReceiverException() {
super();
@@ -50,7 +17,7 @@ public class ResultReceiverException extends Exception {
/**
* Constructs a new exception with the specified detail message.
- *
+ *
* @param message
* the detail message
* @param cause
@@ -63,7 +30,7 @@ public class ResultReceiverException extends Exception {
/**
* Constructs a new exception with the specified detail message and cause.
- *
+ *
* @param message
* the detail message
*/
@@ -73,7 +40,7 @@ public class ResultReceiverException extends Exception {
/**
* Constructs a new exception with the specified cause.
- *
+ *
* @param cause
* the cause (a null value is permitted, and indicates that the
* cause is nonexistent or unknown)
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java
index 450b2ba..bd44a7f 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryConfigController.java,v $
- * Revision $Revision: 1.4 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:57 $
- * by $Author: davidwithers $
- * Created on 27-Mar-2006
- *****************************************************************/
package org.biomart.martservice.config;
import java.util.HashMap;
@@ -52,7 +19,7 @@ import org.ensembl.mart.lib.config.FilterDescription;
/**
* Controls the interaction between graphical <code>QueryComponent</code>s
* and <code>Query</code>s.
- *
+ *
* @author David Withers
*/
public class QueryConfigController {
@@ -77,7 +44,7 @@ public class QueryConfigController {
/**
* Constructs an instance of a <code>QueryConfigController</code>.
- *
+ *
* @param martQuery
*/
public QueryConfigController(MartQuery martQuery) {
@@ -97,7 +64,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#finalize()
*/
protected void finalize() throws Throwable {
@@ -107,7 +74,7 @@ public class QueryConfigController {
/**
* Returns the <code>MartQuery</code> under control.
- *
+ *
* @return the <code>MartQuery</code> under control
*/
public MartQuery getMartQuery() {
@@ -116,7 +83,7 @@ public class QueryConfigController {
/**
* Removes a <code>QueryComponent</code> from the controller.
- *
+ *
* @param queryComponent
* the <code>QueryComponent</code> to remove
*/
@@ -126,11 +93,11 @@ public class QueryConfigController {
/**
* Registers a <code>QueryComponent</code> with the controller.
- *
+ *
* If the <code>Query</code> already contains an <code>Attribute</code>
* or <code>Filter</code> with the corresponding name the
* <code>QueryComponent</code> is set as selected.
- *
+ *
* @param queryComponent
* the <code>QueryComponent</code> to register
*/
@@ -182,7 +149,7 @@ public class QueryConfigController {
* Returns the <code>Attribute</code> mapped to the
* <code>QueryComponent</code>. If no <code>Attribute</code> is mapped
* a new <code>Attribute</code> is created and added to the map.
- *
+ *
* @param queryComponent
* @return
*/
@@ -205,7 +172,7 @@ public class QueryConfigController {
* Returns the <code>Filter</code> mapped to the
* <code>QueryComponent</code>. If no <code>Filter</code> is mapped a
* new <code>Filter</code> is created and added to the map.
- *
+ *
* @param queryComponent
* @return
*/
@@ -250,7 +217,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void attributeAdded(QueryComponentEvent event) {
@@ -264,7 +231,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void attributeRemoved(QueryComponentEvent event) {
@@ -278,7 +245,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void filterAdded(QueryComponentEvent event) {
@@ -292,7 +259,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void filterRemoved(QueryComponentEvent event) {
@@ -306,7 +273,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterChanged(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void filterChanged(QueryComponentEvent event) {
@@ -320,7 +287,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.biomart.martservice.config.event.QueryComponentListener#linkAdded(org.biomart.martservice.config.event.QueryComponentEvent)
*/
public void linkAdded(QueryComponentEvent event) {
@@ -329,7 +296,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.biomart.martservice.config.event.QueryComponentListener#linkRemoved(org.biomart.martservice.config.event.QueryComponentEvent)
*/
public void linkRemoved(QueryComponentEvent event) {
@@ -338,7 +305,7 @@ public class QueryConfigController {
/*
* (non-Javadoc)
- *
+ *
* @see org.biomart.martservice.config.QueryComponentListener#linkChanged(org.biomart.martservice.config.QueryComponentEvent)
*/
public void linkChanged(QueryComponentEvent event) {
@@ -385,4 +352,4 @@ public class QueryConfigController {
}
-}
\ No newline at end of file
+}
[2/3] incubator-taverna-plugin-bioinformatics git commit: Removed (c)
Univ of Manchester LGPL license header
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
index 2bc7d71..8b93922 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryConfigUtils.java,v $
- * Revision $Revision: 1.3 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:57 $
- * by $Author: davidwithers $
- * Created on 30-Mar-2006
- *****************************************************************/
package org.biomart.martservice.config;
import java.awt.Component;
@@ -59,14 +26,14 @@ import org.ensembl.mart.lib.config.Option;
/**
* Utility class for configuration objects.
- *
+ *
* @author David Withers
*/
public abstract class QueryConfigUtils {
public static final String LINE_END = System.getProperty("line.separator");
private static int DISPLAY_WIDTH = 35;
-
+
public static String splitSentence(String sentence) {
return splitSentence(sentence, DISPLAY_WIDTH);
}
@@ -97,7 +64,7 @@ public abstract class QueryConfigUtils {
/**
* Returns name truncated to DISPLAY_WIDTH.
- *
+ *
* @param name
* @return
*/
@@ -111,17 +78,17 @@ public abstract class QueryConfigUtils {
public static List<String> getOutputFormats(AttributePage attributePage) {
List<String> outputFormats = new ArrayList<String>();
-
+
String[] formats = attributePage.getOutFormats().split(",");
for (int i = 0; i < formats.length; i++) {
outputFormats.add(formats[i]);
}
return outputFormats;
}
-
+
/**
* Returns true if filterDescription has no options.
- *
+ *
* @param filterDescription
* @return true if filterDescription has no options
*/
@@ -132,7 +99,7 @@ public abstract class QueryConfigUtils {
/**
* Returns true if filterDescription has options and at least one option
* also has options.
- *
+ *
* @param filterDescription
* @return true if filterDescription has options and at least one option
* also has options
@@ -150,7 +117,7 @@ public abstract class QueryConfigUtils {
/**
* Returns true if filterDescription has options and the first option has a
* type equal to "boolean".
- *
+ *
* @param filterDescription
* @return true if filterDescription has options and the first option has a
* type equal to "boolean"
@@ -168,7 +135,7 @@ public abstract class QueryConfigUtils {
/**
* Returns true if filterDescription has options and the first option has a
* value equal to null.
- *
+ *
* @param filterDescription
* @return true if filterDescription has options and the first option has a
* value equal to null
@@ -249,7 +216,7 @@ public abstract class QueryConfigUtils {
/**
* Returns the dataset referenced by a configuration object or null if the
* configuration object does not reference a dataset.
- *
+ *
* @param martService
* the MartService to fetch the referenced dataset from
* @param referencedFromDataset
@@ -286,7 +253,7 @@ public abstract class QueryConfigUtils {
/**
* Returns the filter description referenced by the filter description.
- *
+ *
* @param martService
* the MartService to fetch the referenced filter description
* from
@@ -322,7 +289,7 @@ public abstract class QueryConfigUtils {
/**
* Returns the filter description referenced by the attribute description.
- *
+ *
* @param martService
* the MartService to fetch the referenced filter description
* from
@@ -422,7 +389,7 @@ public abstract class QueryConfigUtils {
/**
* Returns true if the internal name of the configuration object contains a
* '.' character.
- *
+ *
* @param bnco
* the configuration object
* @return true if the internal name of the configuration object contains a
@@ -431,7 +398,7 @@ public abstract class QueryConfigUtils {
public static boolean isReference(BaseNamedConfigurationObject bnco,
String softwareVersion) {
if ("0.5".equals(softwareVersion)) {
- return bnco.getAttribute("pointerDataset") != null
+ return bnco.getAttribute("pointerDataset") != null
&& (bnco.getAttribute("pointerAttribute") != null || bnco.getAttribute("pointerFilter") != null);
} else {
return bnco.getInternalName().indexOf(".") != -1;
@@ -441,7 +408,7 @@ public abstract class QueryConfigUtils {
/**
* Returns true if the internal name of the AttributeDescription has the
* format "[datasetName].[attributeName]".
- *
+ *
* @param attributeDescription
* @return true if the internal name of the AttributeDescription has the
* format "[datasetName].[attributeName]"
@@ -458,7 +425,7 @@ public abstract class QueryConfigUtils {
/**
* Returns true if the internal name of the AttributeDescription has the
* format "[datasetName].filter.[filterName]".
- *
+ *
* @param attributeDescription
* @return true if the internal name of the AttributeDescription has the
* format "[datasetName].filter.[filterName]"
@@ -475,7 +442,7 @@ public abstract class QueryConfigUtils {
// /**
// * Returns the qualified name of the AttributeDescription in the format
// * "[datasetName].[attributeName]".
-// *
+// *
// * @param dataset
// * @param attributeDescription
// * @return true if the qualified name of the AttributeDescription in the
@@ -543,16 +510,16 @@ public abstract class QueryConfigUtils {
* Converts a List of objects to a comma separated string of the objects'
* string representations in the order given by the List's iterator. For
* example:
- *
+ *
* <blockquote>
- *
+ *
* <pre>
* List list = Arrays.toList(new String[] {"one", "two", "three"};
* System.out.println(listToCsv(list));
* </pre>
- *
+ *
* </blockquote> would return the string "one,two,three".
- *
+ *
* @param list
* @return a List of objects to a comma separated string of the object's
* string representations
@@ -571,7 +538,7 @@ public abstract class QueryConfigUtils {
/**
* Returns true iff the 'display' or 'hidden' value of the configuration
* object is not "true".
- *
+ *
* @param bnco
* the configuration object
* @return true iff the 'display' or 'hidden' value of configuration object
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
index 201cc1d..c22d3ff 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
@@ -1,50 +1,17 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentAdapter.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:06 $
- * by $Author: davidwithers $
- * Created on 04-Apr-2006
- *****************************************************************/
package org.biomart.martservice.config.event;
/**
* An abstract adapter class for receiving <code>QueryComponent</code> events.
* The methods in this class are empty. This class exists as convenience for
* creating listener objects.
- *
+ *
* @author David Withers
*/
public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void attributeAdded(QueryComponentEvent event) {
@@ -52,7 +19,7 @@ public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void attributeRemoved(QueryComponentEvent event) {
@@ -60,7 +27,7 @@ public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void filterAdded(QueryComponentEvent event) {
@@ -68,7 +35,7 @@ public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void filterRemoved(QueryComponentEvent event) {
@@ -76,7 +43,7 @@ public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterChanged(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
*/
public void filterChanged(QueryComponentEvent event) {
@@ -84,7 +51,7 @@ public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.biomart.martservice.config.event.QueryComponentListener#linkAdded(org.biomart.martservice.config.event.QueryComponentEvent)
*/
public void linkAdded(QueryComponentEvent event) {
@@ -92,7 +59,7 @@ public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.biomart.martservice.config.event.QueryComponentListener#linkRemoved(org.biomart.martservice.config.event.QueryComponentEvent)
*/
public void linkRemoved(QueryComponentEvent event) {
@@ -100,7 +67,7 @@ public class QueryComponentAdapter implements QueryComponentListener {
/*
* (non-Javadoc)
- *
+ *
* @see org.biomart.martservice.config.QueryComponentListener#linkChanged(org.biomart.martservice.config.QueryComponentEvent)
*/
public void linkChanged(QueryComponentEvent event) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
index 6fc5d18..8364233 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentEvent.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:06 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
package org.biomart.martservice.config.event;
import java.util.EventObject;
@@ -40,7 +7,7 @@ import org.biomart.martservice.MartDataset;
/**
* An event which indicates that a <code>QueryComponent</code> has been
* selected, deselected or its value has been modified.
- *
+ *
* @author David Withers
*/
public class QueryComponentEvent extends EventObject {
@@ -54,7 +21,7 @@ public class QueryComponentEvent extends EventObject {
/**
* Constructs a new <code>QueryComponentEvent</code> instance.
- *
+ *
* @param source
* the source of the event
* @param name
@@ -69,7 +36,7 @@ public class QueryComponentEvent extends EventObject {
/**
* Constructs a new <code>QueryComponentEvent</code> instance.
- *
+ *
* @param source
* the source of the event
* @param name
@@ -90,7 +57,7 @@ public class QueryComponentEvent extends EventObject {
/**
* Returns the name of the attribute or filter affected by this event.
- *
+ *
* @return the name of the attribute or filter affected by this event.
*/
public String getName() {
@@ -100,7 +67,7 @@ public class QueryComponentEvent extends EventObject {
/**
* Returns the dataset containing the attribute or filter affected by this
* event.
- *
+ *
* @return the dataset containing the attribute or filter affected by this
* event.
*/
@@ -110,7 +77,7 @@ public class QueryComponentEvent extends EventObject {
/**
* Returns the value of the filter affected by this event.
- *
+ *
* @return the value of the filter affected by this event.
*/
public String getValue() {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
index af63326..6542da8 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
@@ -1,43 +1,10 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentListener.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:06 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
package org.biomart.martservice.config.event;
import java.util.EventListener;
/**
* The listener interface for receiving QueryComponent events.
- *
+ *
* @author David Withers
*/
public interface QueryComponentListener extends EventListener {
@@ -45,7 +12,7 @@ public interface QueryComponentListener extends EventListener {
/**
* Invoked when a <code>QueryComponent</code> for an attribute is
* selected.
- *
+ *
* @param event the query component event
*/
public void attributeAdded(QueryComponentEvent event);
@@ -53,42 +20,42 @@ public interface QueryComponentListener extends EventListener {
/**
* Invoked when a <code>QueryComponent</code> for an attribute is
* deselected.
- *
+ *
* @param event the query component event
*/
public void attributeRemoved(QueryComponentEvent event);
/**
* Invoked when a <code>QueryComponent</code> for a filter is selected.
- *
+ *
* @param event the query component event
*/
public void filterAdded(QueryComponentEvent event);
/**
* Invoked when a <code>QueryComponent</code> for a filter is deselected.
- *
+ *
* @param event the query component event
*/
public void filterRemoved(QueryComponentEvent event);
/**
* Invoked when a <code>QueryComponent</code> for a filter is changed.
- *
+ *
* @param event the query component event
*/
public void filterChanged(QueryComponentEvent event);
/**
* Invoked when a <code>QueryComponent</code> for a link is selected.
- *
+ *
* @param event the query component event
*/
public void linkAdded(QueryComponentEvent event);
/**
* Invoked when a <code>QueryComponent</code> for a link is deselected.
- *
+ *
* @param event the query component event
*/
public void linkRemoved(QueryComponentEvent event);
@@ -96,7 +63,7 @@ public interface QueryComponentListener extends EventListener {
/**
* Invoked when a <code>QueryComponent</code> for a dataset link id is
* changed.
- *
+ *
* @param event the query component event
*/
public void linkChanged(QueryComponentEvent event);
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
index 89820d3..0e5b1e1 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ConfigDisplayObject.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:09 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
package org.biomart.martservice.config.ui;
import java.awt.Component;
@@ -39,7 +6,7 @@ import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
/**
* An object containing a configuration object and it's graphical component.
- *
+ *
* @author David Withers
*/
public class ConfigDisplayObject {
@@ -50,7 +17,7 @@ public class ConfigDisplayObject {
/**
* Constructs an instance of a <code>ConfigDisplayObject</code> with the
* specified configuration object and a <code>null</code> component.
- *
+ *
* @param configObject
* the configuration object; must not be <code>null</code>
*/
@@ -61,7 +28,7 @@ public class ConfigDisplayObject {
/**
* Constructs an instance of a <code>ConfigDisplayObject</code> with the
* specified configuration object and component.
- *
+ *
* @param configObject
* the configuration object; must not be <code>null</code>
* @param component
@@ -79,7 +46,7 @@ public class ConfigDisplayObject {
/**
* Returns the display name.
- *
+ *
* @return the display name
*/
public String getDisplayName() {
@@ -88,7 +55,7 @@ public class ConfigDisplayObject {
/**
* Returns the internal name.
- *
+ *
* @return the internal name
*/
public String getInternalName() {
@@ -97,7 +64,7 @@ public class ConfigDisplayObject {
/**
* Returns the display name.
- *
+ *
* @return the display name
*/
public String toString() {
@@ -106,7 +73,7 @@ public class ConfigDisplayObject {
/**
* Returns the configuration object.
- *
+ *
* @return the configuration object
*/
public BaseNamedConfigurationObject getConfigObject() {
@@ -115,7 +82,7 @@ public class ConfigDisplayObject {
/**
* Returns the component.
- *
+ *
* @return the component.
*/
public Component getComponent() {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
index d5ff0dd..932ea9d 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ExpandableBox.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:56 $
- * by $Author: davidwithers $
- * Created on Jun 22, 2007
- *****************************************************************/
package org.biomart.martservice.config.ui;
import java.awt.Color;
@@ -52,9 +19,9 @@ import javax.swing.border.LineBorder;
/**
* A component that when collapsed only shows a title and when expanded shows
* the title and contained components.
- *
+ *
* @author David Withers
- *
+ *
*/
public class ExpandableBox extends JPanel {
private static final long serialVersionUID = -5678399632577606442L;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
index 15f294a..33471fa 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceIcons.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:56 $
- * by $Author: davidwithers $
- * Created on 24-Aug-2006
- *****************************************************************/
package org.biomart.martservice.config.ui;
import java.util.HashMap;
@@ -40,7 +7,7 @@ import javax.swing.Icon;
import javax.swing.ImageIcon;
/**
- *
+ *
* @author witherd5
*/
public class MartServiceIcons {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java
index 3531539..2655d7b 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceQueryConfigUIFactory.java,v $
- * Revision $Revision: 1.6 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:46:53 $
- * by $Author: davidwithers $
- * Created on 21-Jun-2007
- *****************************************************************/
package org.biomart.martservice.config.ui;
import java.awt.BorderLayout;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
index 153b982..bf67bdb 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MinimalLayout.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/06/27 12:49:48 $
- * by $Author: davidwithers $
- * Created on 26 Jun 2007
- *****************************************************************/
package org.biomart.martservice.config.ui;
import java.awt.Component;
@@ -42,7 +9,7 @@ import java.awt.LayoutManager;
/**
* A layout manager that lays out components, either horizontally or vertically,
* according to their minimum size.
- *
+ *
* @author David Withers
*/
class MinimalLayout implements LayoutManager {
@@ -64,7 +31,7 @@ class MinimalLayout implements LayoutManager {
/*
* (non-Javadoc)
- *
+ *
* @see java.awt.LayoutManager#removeLayoutComponent(java.awt.Component)
*/
public void removeLayoutComponent(Component comp) {
@@ -72,7 +39,7 @@ class MinimalLayout implements LayoutManager {
/*
* (non-Javadoc)
- *
+ *
* @see java.awt.LayoutManager#layoutContainer(java.awt.Container)
*/
public void layoutContainer(Container parent) {
@@ -98,7 +65,7 @@ class MinimalLayout implements LayoutManager {
/*
* (non-Javadoc)
- *
+ *
* @see java.awt.LayoutManager#addLayoutComponent(java.lang.String,
* java.awt.Component)
*/
@@ -107,7 +74,7 @@ class MinimalLayout implements LayoutManager {
/*
* (non-Javadoc)
- *
+ *
* @see java.awt.LayoutManager#minimumLayoutSize(java.awt.Container)
*/
public Dimension minimumLayoutSize(Container parent) {
@@ -144,7 +111,7 @@ class MinimalLayout implements LayoutManager {
/*
* (non-Javadoc)
- *
+ *
* @see java.awt.LayoutManager#preferredLayoutSize(java.awt.Container)
*/
public Dimension preferredLayoutSize(Container parent) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
index b976684..fdc92c7 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponent.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:56 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
package org.biomart.martservice.config.ui;
import java.awt.event.ItemEvent;
@@ -47,7 +14,7 @@ import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
/**
* Abstract class for creating query configuration UI components.
- *
+ *
* @author David Withers
*/
public abstract class QueryComponent extends JPanel {
@@ -75,7 +42,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Returns the dataset.
- *
+ *
* @return the dataset.
*/
public MartDataset getDataset() {
@@ -84,7 +51,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Sets the dataset.
- *
+ *
* @param dataset
* the dataset to set.
*/
@@ -112,7 +79,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Returns the name.
- *
+ *
* @return the name.
*/
public String getName() {
@@ -141,7 +108,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Returns the value.
- *
+ *
* @return the value.
*/
public String getValue() {
@@ -150,7 +117,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Sets the value.
- *
+ *
* @param value
* the value to set.
*/
@@ -160,7 +127,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Returns the configObject.
- *
+ *
* @return the configObject
*/
public BaseNamedConfigurationObject getConfigObject() {
@@ -169,7 +136,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Sets the configObject.
- *
+ *
* @param configObject
* the configObject to set.
*/
@@ -179,7 +146,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Sets the selected state of this component.
- *
+ *
* @param selected
* <code>true</code> if this component is selected,
* <code>false</code> otherwise
@@ -192,11 +159,11 @@ public abstract class QueryComponent extends JPanel {
/**
* Sets the button used to select/deselect this QueryComponent.
- *
+ *
* This function adds an ItemListener to the button and fires the
* appropriate QueryComponentEvent when the button is selected or
* deselected.
- *
+ *
* @param button
* the button used to select/deselect this QueryComponent.
*/
@@ -229,7 +196,7 @@ public abstract class QueryComponent extends JPanel {
* Adds the specified query component listener to receive query component
* events. If <code>listener</code> is null, no exception is thrown and no
* action is performed.
- *
+ *
* @param listener
* the query component listener
*/
@@ -243,7 +210,7 @@ public abstract class QueryComponent extends JPanel {
* does it throw an exception, if <code>listener</code> was not previously
* added to this component. If <code>listener</code> is null, no exception
* is thrown and no action is performed.
- *
+ *
* @param listener
* the query component listener
*/
@@ -253,7 +220,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an attribute added event.
- *
+ *
* @param event the event to be fired
*/
protected void fireAttributeAdded(QueryComponentEvent event) {
@@ -264,7 +231,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an attribute removed event.
- *
+ *
* @param event the event to be fired
*/
protected void fireAttributeRemoved(QueryComponentEvent event) {
@@ -275,7 +242,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an filter added event.
- *
+ *
* @param event the event to be fired
*/
protected void fireFilterAdded(QueryComponentEvent event) {
@@ -286,7 +253,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an filter removed event.
- *
+ *
* @param event the event to be fired
*/
protected void fireFilterRemoved(QueryComponentEvent event) {
@@ -297,7 +264,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an filter changed event.
- *
+ *
* @param event the event to be fired
*/
protected void fireFilterChanged(QueryComponentEvent event) {
@@ -308,7 +275,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an link added event.
- *
+ *
* @param event the event to be fired
*/
protected void fireLinkAdded(QueryComponentEvent event) {
@@ -319,7 +286,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an link removed event.
- *
+ *
* @param event the event to be fired
*/
protected void fireLinkRemoved(QueryComponentEvent event) {
@@ -330,7 +297,7 @@ public abstract class QueryComponent extends JPanel {
/**
* Fires an link changed event.
- *
+ *
* @param event the event to be fired
*/
protected void fireLinkChanged(QueryComponentEvent event) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
index d0a740a..20ca314 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryConfigUIFactory.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:08 $
- * by $Author: davidwithers $
- * Created on 04-Apr-2006
- *****************************************************************/
package org.biomart.martservice.config.ui;
import java.awt.Component;
@@ -49,7 +16,7 @@ import org.ensembl.mart.lib.config.FilterPage;
/**
* Interface for generating graphical components from <code>DatasetConfig</code>
* objects.
- *
+ *
* @author David Withers
*/
public interface QueryConfigUIFactory {
@@ -62,7 +29,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for a <code>DatasetConfig</code>.
- *
+ *
* @return the generated <code>Component</code>
* @throws MartServiceException
* if the MartService returns an error or is unavailable
@@ -72,7 +39,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>AttributePage</code>.
- *
+ *
* @param attributePages
* an array of <code>AttributePage</code>
* @param data
@@ -86,7 +53,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an <code>AttributePage</code>.
- *
+ *
* @param attributePage
* an <code>AttributePage</code>
* @param data
@@ -101,7 +68,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>AttributeGroup</code>.
- *
+ *
* @param attributeGroups
* an array of <code>AttributeGroup</code>
* @param data
@@ -115,7 +82,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an <code>AttributeGroup</code>.
- *
+ *
* @param attributeGroup
* an <code>AttributeGroup</code>
* @param data
@@ -130,7 +97,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>AttributeCollection</code>.
- *
+ *
* @param attributeCollections
* an array of <code>AttributeCollection</code>
* @param data
@@ -146,7 +113,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an
* <code>AttributeCollection</code>.
- *
+ *
* @param attributeCollection
* an <code>AttributeCollection</code>
* @param data
@@ -162,7 +129,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>AttributeDescription</code>.
- *
+ *
* @param attributeDescriptions
* an array of <code>AttributeDescription</code>
* @param data
@@ -178,7 +145,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an
* <code>AttributeDescription</code>.
- *
+ *
* @param attributeDescription
* an <code>AttributeDescription</code>
* @param data
@@ -194,7 +161,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>AttributeList</code>.
- *
+ *
* @param attributeLists
* an array of <code>AttributeList</code>
* @param data
@@ -210,7 +177,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an
* <code>AttributeList</code>.
- *
+ *
* @param attributeList
* an <code>AttributeList</code>
* @param data
@@ -226,7 +193,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>FilterPage</code>.
- *
+ *
* @param filterPages
* an array of <code>FilterPage</code>
* @param data
@@ -240,7 +207,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for a <code>FilterPage</code>.
- *
+ *
* @param filterPage
* a <code>FilterPage</code>
* @param data
@@ -255,7 +222,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>FilterGroup</code>.
- *
+ *
* @param filterGroups
* an array of <code>FilterGroup</code>
* @param data
@@ -269,7 +236,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for a <code>FilterGroup</code>.
- *
+ *
* @param filterGroup
* a <code>FilterGroup</code>
* @param data
@@ -284,7 +251,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>FilterCollection</code>.
- *
+ *
* @param filterCollections
* an array of <code>FilterCollection</code>
* @param data
@@ -299,7 +266,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for a <code>FilterCollection</code>.
- *
+ *
* @param filterCollection
* a <code>FilterCollection</code>
* @param data
@@ -314,7 +281,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for an array of
* <code>FilterDescription</code>.
- *
+ *
* @param filterDescriptions
* an array of <code>FilterDescription</code>
* @param data
@@ -329,7 +296,7 @@ public interface QueryConfigUIFactory {
/**
* Generates a <code>Component</code> for a <code>FilterDescription</code>.
- *
+ *
* @param filterDescription
* a <code>FilterDescription</code>
* @param data
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java
index 7ec9932..45dc0d4 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Attribute.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:43:40 $
- * by $Author: davidwithers $
- * Created on 26-Apr-2006
- *****************************************************************/
package org.biomart.martservice.query;
/**
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java
index 20ea68f..7e24117 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Dataset.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/03 15:57:30 $
- * by $Author: davidwithers $
- * Created on 21-Apr-2006
- *****************************************************************/
package org.biomart.martservice.query;
import java.util.ArrayList;
@@ -38,7 +5,7 @@ import java.util.List;
/**
* Class for creating dataset elements of mart queries.
- *
+ *
* @author David Withers
*/
public class Dataset {
@@ -53,7 +20,7 @@ public class Dataset {
/**
* Constructs an instance of a <code>Dataset</code> with the specified
* name.
- *
+ *
* @param name
* the name of the <code>Dataset</code>
*/
@@ -64,7 +31,7 @@ public class Dataset {
/**
* Constructs an instance of a <code>Dataset</code> which is a deep copy
* of another <code>Dataset</code>.
- *
+ *
* @param dataset
* the <code>Dataset</code> to copy
*/
@@ -80,7 +47,7 @@ public class Dataset {
/**
* Returns the name of the Dataset.
- *
+ *
* @return the name of the Dataset.
*/
public String getName() {
@@ -89,7 +56,7 @@ public class Dataset {
/**
* Set the name of the Dataset.
- *
+ *
* @param name
* the new name for this Dataset.
*/
@@ -99,7 +66,7 @@ public class Dataset {
/**
* Returns a List of the Attributes in this dataset.
- *
+ *
* @return a List of the Attributes in this dataset
*/
public List<Attribute> getAttributes() {
@@ -110,7 +77,7 @@ public class Dataset {
* Adds an Attribute to the dataset. The attribute's containing dataset will
* be set to this dataset. If this dataset is in a query an attribute added
* event will be fired.
- *
+ *
* @param attribute
* the Attribute to add
* @return true if the Attribute is not already in the dataset
@@ -130,7 +97,7 @@ public class Dataset {
/**
* Adds an array of Attributes to the dataset.
- *
+ *
* @param attributeArray
* the array of Attributes to add
*/
@@ -142,7 +109,7 @@ public class Dataset {
/**
* Returns true if attribute is in the dataset.
- *
+ *
* @param attribute
* @return true if attribute is in the dataset.
*/
@@ -152,7 +119,7 @@ public class Dataset {
/**
* Returns true if the dataset contains any Attributes.
- *
+ *
* @return true if the dataset contains any Attributes
*/
public boolean hasAttributes() {
@@ -160,13 +127,13 @@ public class Dataset {
}
/**
- * Removes an Attribute from the dataset.
- *
+ * Removes an Attribute from the dataset.
+ *
* If the attribute is contained in this dataset:
* <ul>
* <li>The attribute's containing dataset will be set to null.
* <li>If this dataset is in a query an attribute removed event will be fired.
- *
+ *
* @param attribute
* the attribute to remove
* @return true if the attribute is removed
@@ -194,7 +161,7 @@ public class Dataset {
/**
* Returns a List of the Filters in this dataset.
- *
+ *
* @return a List of the Filters in this dataset
*/
public List<Filter> getFilters() {
@@ -205,7 +172,7 @@ public class Dataset {
* Adds a Filter to the dataset. The filter's containing dataset will be set
* to this dataset. If this dataset is in a query a filter added event will
* be fired.
- *
+ *
* @param filter
* the Filter to add
* @return true if the Filter is not already in the dataset
@@ -225,7 +192,7 @@ public class Dataset {
/**
* Adds an array of Filters to the dataset.
- *
+ *
* @param filterArray
* the array of Filters to add
*/
@@ -237,7 +204,7 @@ public class Dataset {
/**
* Returns true if filter is in the dataset.
- *
+ *
* @param filter
* @return true if filter is in the dataset
*/
@@ -247,7 +214,7 @@ public class Dataset {
/**
* Returns true if the dataset contains any filters.
- *
+ *
* @return true if the dataset contains any filters
*/
public boolean hasFilters() {
@@ -256,12 +223,12 @@ public class Dataset {
/**
* Removes an Filter from the dataset.
- *
+ *
* If the filter is contained in this dataset:
* <ul>
* <li>The filter's containing dataset will be set to null.
* <li>If this dataset is in a query an attribute removed event will be fired.
- *
+ *
* @param filter
* the filter to remove
* @return true if the filter is removed
@@ -289,7 +256,7 @@ public class Dataset {
/**
* Returns the containingQuery.
- *
+ *
* @return the containingQuery.
*/
public Query getContainingQuery() {
@@ -298,7 +265,7 @@ public class Dataset {
/**
* Sets the containingQuery.
- *
+ *
* @param containingQuery
* the containingQuery to set.
*/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java
index 1c088d0..860e38f 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java
@@ -1,41 +1,8 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Filter.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:09 $
- * by $Author: davidwithers $
- * Created on 26-Apr-2006
- *****************************************************************/
package org.biomart.martservice.query;
/**
* Class for creating filter elements of mart queries.
- *
+ *
* @author David Withers
*/
public class Filter {
@@ -51,7 +18,7 @@ public class Filter {
/**
* Constructs an instance of a <code>Filter</code> with the specified name.
- *
+ *
* @param name
* the name of the <code>Filter</code>; must not be <code>null</code>
*/
@@ -62,7 +29,7 @@ public class Filter {
/**
* Constructs a instance of a <code>Filter</code> with the specified name
* and value.
- *
+ *
* @param name
* the name of the <code>Filter</code>; must not be <code>null</code>
* @param value
@@ -76,7 +43,7 @@ public class Filter {
* Constructs a instance of a <code>Filter</code> with the specified name
* and value, and sets a flag to indicate if this is a boolean
* <code>Filter</code>.
- *
+ *
* @param name
* the name of the <code>Filter</code>; must not be <code>null</code>
* @param value
@@ -95,7 +62,7 @@ public class Filter {
/**
* Constructs an instance of a <code>Filter</code> which is a copy of
* another <code>Filter</code>.
- *
+ *
* @param filter
* the <code>Filter</code> to copy; must not be <code>null</code>
*/
@@ -110,7 +77,7 @@ public class Filter {
/**
* Returns the name of the Filter.
- *
+ *
* @return the name of the Filter
*/
public String getName() {
@@ -119,7 +86,7 @@ public class Filter {
/**
* Sets the name of the Filter.
- *
+ *
* @param name
* the name of the Filter; must not be <code>null</code>
*/
@@ -132,11 +99,11 @@ public class Filter {
/**
* Returns the qualified name of this <code>Filter</code>.
- *
+ *
* The qualified name is <code>containingDatasetName.filterName</code> or
* just <code>attributeName</code> if the <code>Filter</code> is not in
* a <code>Dataset</code>.
- *
+ *
* @return the qualified name of this <code>Filter</code>.
*/
public String getQualifiedName() {
@@ -150,7 +117,7 @@ public class Filter {
/**
* Returns the <code>Dataset</code> containing this <code>Filter</code>
* or null if it is not in a <code>Dataset</code>.
- *
+ *
* @return the <code>Dataset</code> containing this <code>Filter</code>
* or null if it is not in a <code>Dataset</code>
*/
@@ -160,7 +127,7 @@ public class Filter {
/**
* Sets the containing <code>Dataset</code>.
- *
+ *
* @param dataset
* the containing <code>Dataset</code>
*/
@@ -170,7 +137,7 @@ public class Filter {
/**
* Returns the value.
- *
+ *
* @return the value.
*/
public String getValue() {
@@ -179,7 +146,7 @@ public class Filter {
/**
* Sets the value.
- *
+ *
* @param value
* the value to set.
*/
@@ -206,7 +173,7 @@ public class Filter {
/**
* Returns <code>true</code> if this is a boolean filter.
- *
+ *
* @return <code>true</code> if this is a boolean filter.
*/
public boolean isBoolean() {
@@ -215,7 +182,7 @@ public class Filter {
/**
* Sets the booleanFilter flag.
- *
+ *
* @param booleanFilter
*/
public void setBoolean(boolean booleanFilter) {
@@ -224,7 +191,7 @@ public class Filter {
/**
* Returns <code>true</code> if this is a list filter.
- *
+ *
* @return <code>true</code> if this is a list filter.
*/
public boolean isList() {
@@ -233,7 +200,7 @@ public class Filter {
/**
* Sets the listFilter flag.
- *
+ *
* @param listFilter
*/
public void setList(boolean listFilter) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java
index 721428c..834efa1 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java
@@ -1,41 +1,8 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Link.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:09 $
- * by $Author: davidwithers $
- * Created on 26-Apr-2006
- *****************************************************************/
package org.biomart.martservice.query;
/**
* Class for creating link elements of mart queries.
- *
+ *
* @author David Withers
*/
public class Link {
@@ -49,7 +16,7 @@ public class Link {
/**
* Constructs an instance of a <code>Link</code>.
- *
+ *
* @param source
* the source dataset of the <code>Link</code>
* @param target
@@ -66,7 +33,7 @@ public class Link {
/**
* Constructs an instance of a <code>Link</code> which is a copy of
* another <code>Link</code>.
- *
+ *
* @param filter
* the <code>Link</code> to copy
*/
@@ -78,7 +45,7 @@ public class Link {
/**
* Returns the defaultLink.
- *
+ *
* @return the defaultLink.
*/
public String getDefaultLink() {
@@ -95,7 +62,7 @@ public class Link {
/**
* Returns the source dataset.
- *
+ *
* @return the source dataset.
*/
public String getSource() {
@@ -104,7 +71,7 @@ public class Link {
/**
* Sets the source dataset.
- *
+ *
* @param source
* the source dataset to set.
*/
@@ -114,7 +81,7 @@ public class Link {
/**
* Returns the target dataset.
- *
+ *
* @return the target dataset.
*/
public String getTarget() {
@@ -123,7 +90,7 @@ public class Link {
/**
* Sets the target dataset.
- *
+ *
* @param target
* the target dataset to set.
*/
@@ -133,7 +100,7 @@ public class Link {
/**
* Returns the containingQuery.
- *
+ *
* @return the containingQuery.
*/
public Query getContainingQuery() {
@@ -142,7 +109,7 @@ public class Link {
/**
* Sets the containingQuery.
- *
+ *
* @param containingQuery
* the containingQuery to set.
*/
@@ -152,7 +119,7 @@ public class Link {
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#equals(java.lang.Object)
*/
public boolean equals(Object obj) {
@@ -171,7 +138,7 @@ public class Link {
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#hashCode()
*/
public int hashCode() {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java
index c7c9f20..5261bc4 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java
@@ -1,36 +1,3 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Query.java,v $
- * Revision $Revision: 1.4 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/03 15:57:30 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
package org.biomart.martservice.query;
import java.util.ArrayList;
@@ -44,7 +11,7 @@ import org.biomart.martservice.MartServiceException;
/**
* Class for creating mart queries.
- *
+ *
* @author David Withers
*/
public class Query {
@@ -55,7 +22,7 @@ public class Query {
private int uniqueRows;
private String softwareVersion;
-
+
private String formatter;
private String requestId;
@@ -73,7 +40,7 @@ public class Query {
/**
* Constructs an instance of a <code>Query</code> with the specified
* <code>virtualSchemaName</code> and a <code>count</code> of 0.
- *
+ *
* @param virtualSchemaName
*/
public Query(String virtualSchemaName) {
@@ -83,7 +50,7 @@ public class Query {
/**
* Constructs an instance of a <code>Query</code> with the specified
* <code>virtualSchemaName</code> and <code>count</code>.
- *
+ *
* @param virtualSchemaName
* @param count
*/
@@ -96,7 +63,7 @@ public class Query {
* Constructs an instance of a <code>Query</code> with the specified
* <code>virtualSchemaName</code>, <code>softwareVersion</code> and
* <code>requestId</code>.
- *
+ *
* @param virtualSchemaName
* @param softwareVersion
* @param requestId
@@ -110,7 +77,7 @@ public class Query {
* Constructs an instance of a <code>Query</code> with the specified
* <code>virtualSchemaName</code>, <code>count</code> and
* <code>softwareVersion</code>.
- *
+ *
* @param virtualSchemaName
* @param count
* @param softwareVersion
@@ -123,7 +90,7 @@ public class Query {
* Constructs an instance of a <code>Query</code> with the specified
* <code>virtualSchemaName</code>, <code>count</code>,
* <code>softwareVersion</code> and <code>requestId</code>.
- *
+ *
* @param virtualSchemaName
* @param count
* @param softwareVersion
@@ -140,7 +107,7 @@ public class Query {
/**
* Constructs an instance of a <code>Query</code> which is a deep copy of
* another <code>Query</code>.
- *
+ *
* @param query
* the <code>Query</code> to copy
* @throws MartServiceException
@@ -162,7 +129,7 @@ public class Query {
/**
* Returns the virtualSchema.
- *
+ *
* @return the virtualSchema.
*/
public String getVirtualSchemaName() {
@@ -171,7 +138,7 @@ public class Query {
/**
* Sets the virtualSchema.
- *
+ *
* @param virtualSchemaName
* the virtualSchema to set.
*/
@@ -181,7 +148,7 @@ public class Query {
/**
* Returns the count.
- *
+ *
* @return the count.
*/
public int getCount() {
@@ -190,7 +157,7 @@ public class Query {
/**
* Sets the count.
- *
+ *
* @param count
* the count to set.
*/
@@ -200,7 +167,7 @@ public class Query {
/**
* Returns the uniqueRows query attribute
- *
+ *
* @return the uniqueRows query attribute
*/
public int getUniqueRows() {
@@ -209,9 +176,9 @@ public class Query {
/**
* Sets the uniqueRows query attribute.
- *
+ *
* Valid values are 0 or 1.
- *
+ *
* @param uniqueRows value for the uniqueRows query attribute
*/
public void setUniqueRows(int uniqueRows) {
@@ -220,7 +187,7 @@ public class Query {
/**
* Returns the softwareVersion.
- *
+ *
* @return the softwareVersion
*/
public String getSoftwareVersion() {
@@ -229,7 +196,7 @@ public class Query {
/**
* Sets the softwareVersion.
- *
+ *
* @param softwareVersion
* the new softwareVersion
*/
@@ -239,7 +206,7 @@ public class Query {
/**
* Returns the formatter.
- *
+ *
* @return the formatter
*/
public String getFormatter() {
@@ -248,7 +215,7 @@ public class Query {
/**
* Sets the formatter.
- *
+ *
* @param formatter the new formatter
*/
public void setFormatter(String formatter) {
@@ -271,7 +238,7 @@ public class Query {
/**
* Returns the requestId.
- *
+ *
* @return the requestId
*/
public String getRequestId() {
@@ -280,7 +247,7 @@ public class Query {
/**
* Sets the requestId.
- *
+ *
* @param requestId
* the new requestId
*/
@@ -290,9 +257,9 @@ public class Query {
/**
* Adds a Dataset to the Query.
- *
+ *
* The Dataset is added at the end of the list of Datasets.
- *
+ *
* @param dataset
* the Dataset to add
*/
@@ -302,7 +269,7 @@ public class Query {
/**
* Adds a Dataset to the Query at the specified position.
- *
+ *
* @param index
* the position to add the Dataset
* @param dataset
@@ -319,7 +286,7 @@ public class Query {
/**
* Removes a Dataset from the Query.
- *
+ *
* @param dataset
* the Dataset to remove
*/
@@ -342,7 +309,7 @@ public class Query {
/**
* Returns the Datasets that this Query contains.
- *
+ *
* @return the Datasets that this Query contains.
*/
public List<Dataset> getDatasets() {
@@ -352,7 +319,7 @@ public class Query {
/**
* Returns a Dataset with the given datasetName. If the Query has no Dataset
* with the given datasetName null is returned.
- *
+ *
* @param datasetName
* @return a Dataset with the given datasetName
*/
@@ -363,7 +330,7 @@ public class Query {
/**
* Returns true if this Query contains a Dataset with the name
* <code>datasetName</code>.
- *
+ *
* @param datasetName
* @return true if this Query contains a Dataset with the name
* <code>datasetName</code>.
@@ -374,7 +341,7 @@ public class Query {
/**
* Adds a Link to the Query.
- *
+ *
* @param link
* the Link to add
*/
@@ -389,7 +356,7 @@ public class Query {
/**
* Removes a link from the Query
- *
+ *
* @param link
* the Link to remove
*/
@@ -401,7 +368,7 @@ public class Query {
/**
* Returns the Links that this Query contains.
- *
+ *
* @return the Links that this Query contains.
*/
public Set<Link> getLinks() {
@@ -411,7 +378,7 @@ public class Query {
/**
* Returns a Link with the given source. If the Query has no Link with the
* given source null is returned.
- *
+ *
* @param source
* the source of the link
* @return a Link with the given source
@@ -422,7 +389,7 @@ public class Query {
/**
* Returns true if this Query contains a Link with the same source.
- *
+ *
* @param source
* the source of the link
* @return true if this Query contains a Link with the same source.
@@ -434,7 +401,7 @@ public class Query {
/**
* Returns a List of Links with the given target. If the Query has no Link
* with the given target an empty List is returned.
- *
+ *
* @param target
* the target of the link
* @return a Link with the given target
@@ -452,7 +419,7 @@ public class Query {
/**
* Returns all the Attributes from all the Datasets in this Query.
- *
+ *
* @return all the Attributes from all the Datasets in this Query.
*/
public List<Attribute> getAttributes() {
@@ -465,7 +432,7 @@ public class Query {
/**
* Returns all the Filters from all the Datasets in this Query.
- *
+ *
* @return all the Filters from all the Datasets in this Query.
*/
public List<Filter> getFilters() {
@@ -480,7 +447,7 @@ public class Query {
* Adds the specified query listener to receive query events. If
* <code>listener</code> is null, no exception is thrown and no action is
* performed.
- *
+ *
* @param listener
* the query listener
*/
@@ -496,7 +463,7 @@ public class Query {
* if <code>listener</code> was not previously added to this component. If
* <code>listener</code> is null, no exception is thrown and no action is
* performed.
- *
+ *
* @param listener
* the query listener
*/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/33e003af/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java
index 9f10f45..1752823 100644
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java
+++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java
@@ -1,48 +1,15 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryListener.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/03 15:57:30 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
package org.biomart.martservice.query;
/**
* The listener interface for receiving Query events.
- *
+ *
* @author David Withers
*/
public interface QueryListener {
/**
* Invoked when an <code>Attribute</code> is added to a <code>Query</code>.
- *
+ *
* @param attribute
* the <code>Attribute</code> added.
*/
@@ -51,7 +18,7 @@ public interface QueryListener {
/**
* Invoked when an <code>Attribute</code> is removed from a
* <code>Query</code>.
- *
+ *
* @param attribute
* the <code>Attribute</code> removed.
*/
@@ -59,7 +26,7 @@ public interface QueryListener {
/**
* Invoked when a <code>Filter</code> is added to a <code>Query</code>.
- *
+ *
* @param filter
* the <code>Filter</code> added.
*/
@@ -67,7 +34,7 @@ public interface QueryListener {
/**
* Invoked when a <code>Filter</code> is removed from a <code>Query</code>.
- *
+ *
* @param filter
* the <code>Filter</code> removed.
*/
@@ -75,7 +42,7 @@ public interface QueryListener {
/**
* Invoked when the value of a <code>Filter</code> is changed.
- *
+ *
* @param filter
* the <code>Filter</code> whose value has changed.
*/
@@ -83,7 +50,7 @@ public interface QueryListener {
/**
* Invoked when a formatter is added to a <code>Query</code>.
- *
+ *
* @param formatter
* the formatter added.
*/
@@ -91,7 +58,7 @@ public interface QueryListener {
/**
* Invoked when a formatter is removed from a <code>Query</code>.
- *
+ *
* @param formatter
* the formatter removed.
*/
@@ -99,7 +66,7 @@ public interface QueryListener {
/**
* Invoked when the value of the formatter is changed.
- *
+ *
* @param filter
* the new value of the formatter.
*/