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Posted to commits@taverna.apache.org by st...@apache.org on 2016/09/07 12:14:17 UTC
[3/3] incubator-taverna-plugin-bioinformatics git commit: Removed (c)
Univ of Manchester LGPL license header
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
+}