Added Apache header
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/47ca3660 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/47ca3660 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/47ca3660 Branch: refs/heads/master Commit: 47ca366073f0447a8ba2948ff9e9be0edf678bbd Parents: 02285a2 Author: Stian Soiland-Reyes <[email protected]> Authored: Wed Sep 7 14:42:07 2016 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Wed Sep 7 14:42:07 2016 +0100 ---------------------------------------------------------------------- .../actions/BiomartActivityConfigurationAction.java | 16 ++++++++++++++++ .../biomart/actions/BiomartConfigurationPanel.java | 16 ++++++++++++++++ .../menu/BiomartConfigurationMenuAction.java | 16 ++++++++++++++++ .../servicedescriptions/BiomartActivityIcon.java | 16 ++++++++++++++++ .../BiomartServiceDescription.java | 16 ++++++++++++++++ .../servicedescriptions/BiomartServiceProvider.java | 16 ++++++++++++++++ .../BiomartServiceProviderConfig.java | 16 ++++++++++++++++ .../views/BiomartActivityContextualView.java | 16 ++++++++++++++++ .../biomart/views/BiomartActivityViewFactory.java | 16 ++++++++++++++++ .../views/TestBiomartActivityContextualView.java | 16 ++++++++++++++++ .../t2/activities/biomart/BiomartActivity.java | 16 ++++++++++++++++ .../biomart/BiomartActivityConfigurationBean.java | 16 ++++++++++++++++ .../activities/biomart/BiomartActivityFactory.java | 16 ++++++++++++++++ .../biomart/BiomartActivityHealthChecker.java | 16 ++++++++++++++++ .../biomart/BiomartActivityFactoryTest.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/DatasetLink.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/MartDataset.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/MartQuery.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/MartRegistry.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/MartService.java | 16 ++++++++++++++++ .../biomart/martservice/MartServiceException.java | 16 ++++++++++++++++ .../org/biomart/martservice/MartServiceUtils.java | 16 ++++++++++++++++ .../biomart/martservice/MartServiceXMLHandler.java | 16 ++++++++++++++++ .../org/biomart/martservice/MartURLLocation.java | 16 ++++++++++++++++ .../org/biomart/martservice/ResultReceiver.java | 16 ++++++++++++++++ .../martservice/ResultReceiverException.java | 16 ++++++++++++++++ .../martservice/config/QueryConfigController.java | 16 ++++++++++++++++ .../martservice/config/QueryConfigUtils.java | 16 ++++++++++++++++ .../config/event/QueryComponentAdapter.java | 16 ++++++++++++++++ .../config/event/QueryComponentEvent.java | 16 ++++++++++++++++ .../config/event/QueryComponentListener.java | 16 ++++++++++++++++ .../martservice/config/ui/ConfigDisplayObject.java | 16 ++++++++++++++++ .../martservice/config/ui/ExpandableBox.java | 16 ++++++++++++++++ .../martservice/config/ui/MartServiceIcons.java | 16 ++++++++++++++++ .../config/ui/MartServiceQueryConfigUIFactory.java | 16 ++++++++++++++++ .../martservice/config/ui/MinimalLayout.java | 16 ++++++++++++++++ .../martservice/config/ui/QueryComponent.java | 16 ++++++++++++++++ .../martservice/config/ui/QueryConfigUIFactory.java | 16 ++++++++++++++++ .../org/biomart/martservice/query/Attribute.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/query/Dataset.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/query/Filter.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/query/Link.java | 16 ++++++++++++++++ .../java/org/biomart/martservice/query/Query.java | 16 ++++++++++++++++ .../biomart/martservice/query/QueryListener.java | 16 ++++++++++++++++ .../biomart/martservice/query/QueryXMLHandler.java | 16 ++++++++++++++++ .../org/biomart/martservice/MartDatasetTest.java | 16 ++++++++++++++++ .../org/biomart/martservice/MartRegistryTest.java | 16 ++++++++++++++++ .../biomart/martservice/MartServiceUtilsTest.java | 16 ++++++++++++++++ .../martservice/MartServiceXMLHandlerTest.java | 16 ++++++++++++++++ .../biomart/martservice/MartURLLocationTest.java | 16 ++++++++++++++++ .../config/event/QueryComponentEventTest.java | 16 ++++++++++++++++ .../martservice/config/ui/MartServiceIconsTest.java | 16 ++++++++++++++++ .../biomart/martservice/query/AttributeTest.java | 16 ++++++++++++++++ .../org/biomart/martservice/query/DatasetTest.java | 16 ++++++++++++++++ .../org/biomart/martservice/query/FilterTest.java | 16 ++++++++++++++++ .../org/biomart/martservice/query/QueryTest.java | 16 ++++++++++++++++ .../biomoby/actions/AddParserActionHelper.java | 16 ++++++++++++++++ .../actions/BioMobyObjectTreeCustomRenderer.java | 16 ++++++++++++++++ .../actions/BioMobyServiceTreeCustomRenderer.java | 16 ++++++++++++++++ .../biomoby/actions/BiomobyActionHelper.java | 16 ++++++++++++++++ .../actions/BiomobyActivityConfigurationAction.java | 16 ++++++++++++++++ .../biomoby/actions/BiomobyObjectActionHelper.java | 16 ++++++++++++++++ .../biomoby/actions/BiomobyScavengerDialog.java | 16 ++++++++++++++++ .../biomoby/actions/MobyObjectDetailsAction.java | 16 ++++++++++++++++ .../biomoby/actions/MobyObjectTreeNode.java | 16 ++++++++++++++++ .../t2/activities/biomoby/actions/MobyPanel.java | 16 ++++++++++++++++ .../biomoby/actions/MobyParserAction.java | 16 ++++++++++++++++ .../biomoby/actions/MobyServiceDetailsAction.java | 16 ++++++++++++++++ .../biomoby/actions/MobyServiceTreeNode.java | 16 ++++++++++++++++ .../t2/activities/biomoby/actions/PopupThread.java | 16 ++++++++++++++++ .../biomoby/actions/SimpleActionFrame.java | 16 ++++++++++++++++ .../BiomobyDatatypeDescription.java | 16 ++++++++++++++++ .../edits/AddBiomobyCollectionDataTypeEdit.java | 16 ++++++++++++++++ .../edits/AddBiomobyConsumingServiceEdit.java | 16 ++++++++++++++++ .../biomoby/edits/AddBiomobyDataTypeEdit.java | 16 ++++++++++++++++ .../biomoby/edits/AddMobyParseDatatypeEdit.java | 16 ++++++++++++++++ .../biomoby/edits/AddUpstreamObjectEdit.java | 16 ++++++++++++++++ .../menu/BiomobyActivityDetailsMenuAction.java | 16 ++++++++++++++++ .../menu/BiomobyActivityParserMenuAction.java | 16 ++++++++++++++++ .../biomoby/menu/ConfigureBiomobyMenuAction.java | 16 ++++++++++++++++ .../biomoby/query/BiomobyActivityIcon.java | 16 ++++++++++++++++ .../biomoby/query/BiomobyActivityItem.java | 16 ++++++++++++++++ .../biomoby/query/BiomobyObjectActivityIcon.java | 16 ++++++++++++++++ .../biomoby/query/BiomobyObjectActivityItem.java | 16 ++++++++++++++++ .../biomoby/query/BiomobyQueryHelper.java | 16 ++++++++++++++++ .../t2/activities/biomoby/query/CacheImpl.java | 16 ++++++++++++++++ .../BiomobyServiceDescription.java | 16 ++++++++++++++++ .../servicedescriptions/BiomobyServiceProvider.java | 16 ++++++++++++++++ .../BiomobyServiceProviderConfig.java | 16 ++++++++++++++++ .../activities/biomoby/ui/AddBiomobyDialogue.java | 16 ++++++++++++++++ .../t2/activities/biomoby/ui/BiomobyObjectTree.java | 16 ++++++++++++++++ .../t2/activities/biomoby/ui/DatatypeMenuItem.java | 16 ++++++++++++++++ .../biomoby/view/BiomobyActivityContextualView.java | 16 ++++++++++++++++ .../view/BiomobyActivityContextualViewFactory.java | 16 ++++++++++++++++ .../activities/biomoby/view/BiomobyConfigView.java | 16 ++++++++++++++++ .../view/BiomobyObjectActivityContextualView.java | 16 ++++++++++++++++ .../BiomobyObjectActivityContextualViewFactory.java | 16 ++++++++++++++++ .../view/MobyParseDatatypeContextualView.java | 16 ++++++++++++++++ .../MobyParseDatatypeContextualViewFactory.java | 16 ++++++++++++++++ .../view/BiomobyContextualViewFactoryTest.java | 16 ++++++++++++++++ .../actions/SoaplabActivityConfigurationAction.java | 16 ++++++++++++++++ .../soaplab/actions/SoaplabConfigurationPanel.java | 16 ++++++++++++++++ .../menu/ConfigureSoaplabActivityMenuAction.java | 16 ++++++++++++++++ .../MissingSoaplabException.java | 16 ++++++++++++++++ .../servicedescriptions/SoaplabActivityIcon.java | 16 ++++++++++++++++ .../servicedescriptions/SoaplabCategory.java | 16 ++++++++++++++++ .../servicedescriptions/SoaplabScavengerAgent.java | 16 ++++++++++++++++ .../SoaplabServiceDescription.java | 16 ++++++++++++++++ .../servicedescriptions/SoaplabServiceProvider.java | 16 ++++++++++++++++ .../SoaplabServiceProviderConfig.java | 16 ++++++++++++++++ .../views/SoaplabActivityContextualView.java | 16 ++++++++++++++++ .../soaplab/views/SoaplabActivityViewFactory.java | 16 ++++++++++++++++ .../views/TestSoaplabActivityContextualView.java | 16 ++++++++++++++++ .../net/sf/taverna/t2/activities/soaplab/Soap.java | 16 ++++++++++++++++ .../t2/activities/soaplab/SoaplabActivity.java | 16 ++++++++++++++++ .../soaplab/SoaplabActivityConfigurationBean.java | 16 ++++++++++++++++ .../activities/soaplab/SoaplabActivityFactory.java | 16 ++++++++++++++++ .../soaplab/SoaplabActivityHealthChecker.java | 16 ++++++++++++++++ .../SoaplabActivityConfigurationBeanTest.java | 16 ++++++++++++++++ .../t2/activities/soaplab/SoaplabActivityTest.java | 16 ++++++++++++++++ 120 files changed, 1920 insertions(+) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 10e74a3..3b355a7 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart.actions; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Frame; import java.awt.event.ActionEvent; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 86d1bb5..1dd940e 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart.actions; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Dimension; import java.io.File; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java index 775ce95..5f96b42 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart.menu; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.net.URI; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 2acd9f2..269a477 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart.servicedescriptions; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.net.URI; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 922e999..49d4e6e 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart.servicedescriptions; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.net.URI; import java.util.Arrays; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java index 712e8d8..3e21275 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java @@ -2,6 +2,22 @@ * */ package net.sf.taverna.t2.activities.biomart.servicedescriptions; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.net.URI; import java.util.ArrayList; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java index 9891fae..929c097 100644 --- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java +++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java @@ -2,6 +2,22 @@ * */ package net.sf.taverna.t2.activities.biomart.servicedescriptions; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import net.sf.taverna.t2.lang.beans.PropertyAnnotated; import net.sf.taverna.t2.lang.beans.PropertyAnnotation; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 a03e673..1c85aa4 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart.views; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Frame; import java.io.IOException; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 1cc34c1..c7bed24 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart.views; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.Arrays; import java.util.List; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 d8c81a8..ff1ae3c 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.biomart.views; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 2192090..06bc104 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.io.IOException; import java.io.StringReader; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 bfd13d6..16eda4e 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean; import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 786e1f1..af3fab6 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.io.IOException; import java.io.StringReader; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 4d0a792..f98b853 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.io.IOException; import java.io.StringReader; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 4fbc45e..2acf1c3 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 @@ -1,4 +1,20 @@ package net.sf.taverna.t2.activities.biomart; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 65330cf..a006ddb 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.Comparator; import java.util.HashSet; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 6090dcf..ffbb817 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.Comparator; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 fe4be71..caf4517 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.ArrayList; import java.util.HashMap; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 85df4ae..63950de 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.ArrayList; import java.util.List; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 c6f4de1..1157274 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.io.File; import java.io.FileInputStream; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 a6adb3b..d54c954 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * Thrown when a MartService is inaccessable or returns an error. http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 9319cee..eb5c3f2 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.io.BufferedReader; import java.io.IOException; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 c4d3982..3f19a8d 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.Iterator; import java.util.List; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 6a15aa1..bcf9842 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import org.ensembl.mart.lib.config.MartLocation; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 952899c..a3f0256 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * An interface for receiving results of a Query. http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 6386c9b..82b9b96 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 @@ -1,4 +1,20 @@ package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 bd44a7f..864af45 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.HashMap; import java.util.Iterator; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 8b93922..209b888 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Component; import java.awt.Font; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 c22d3ff..280b2f5 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.event; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * An abstract adapter class for receiving <code>QueryComponent</code> events. http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 8364233..cdfb741 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.event; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.EventObject; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 6542da8..c4a5b34 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.event; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.EventListener; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 0e5b1e1..fc5241f 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.ui; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Component; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 932ea9d..288df3b 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.ui; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Color; import java.awt.Component; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 33471fa..c538957 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.ui; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.HashMap; import java.util.Map; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 2655d7b..1ce34d0 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.ui; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.BorderLayout; import java.awt.Color; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 bf67bdb..0fee270 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.ui; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Component; import java.awt.Container; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 fdc92c7..27f646d 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.ui; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 20ca314..77edb6d 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.config.ui; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.awt.Component; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 a6bdcf7..82a909d 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.query; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * Class for creating attribute elements of mart queries. http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 7e24117..33d7fa0 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.query; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.ArrayList; import java.util.List; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 860e38f..c229b1a 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.query; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * Class for creating filter elements of mart queries. http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 834efa1..efcbdc9 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.query; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * Class for creating link elements of mart queries. http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 5261bc4..ad04856 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.query; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.ArrayList; import java.util.HashMap; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/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 1752823..192e147 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 @@ -1,4 +1,20 @@ package org.biomart.martservice.query; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ /** * The listener interface for receiving Query events. http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java index cacde0b..0f47ff1 100644 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java +++ b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java @@ -1,4 +1,20 @@ package org.biomart.martservice.query; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import java.util.List; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java index 37c8076..db63907 100644 --- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java +++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java @@ -1,5 +1,21 @@ /* package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import junit.framework.TestCase; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java index ec939b7..103a01c 100644 --- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java +++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java @@ -1,5 +1,21 @@ /* package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import junit.framework.TestCase; http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/47ca3660/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java index 0ec2009..5d0c981 100644 --- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java +++ b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java @@ -1,5 +1,21 @@ /* package org.biomart.martservice; +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ import static org.junit.Assert.*;
