You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2016/09/07 12:14:16 UTC
[2/3] incubator-taverna-plugin-bioinformatics git commit: Removed (c)
Univ of Manchester LGPL license header
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.
*/