From: Patric Plitzner Date: Mon, 27 Oct 2014 13:45:51 +0000 (+0000) Subject: merge-update from trunk X-Git-Tag: 3.8.0^2~59^2~110 X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/commitdiff_plain/26254193b965dc0bb91a50b162b9e091c298e63f?hp=-c merge-update from trunk --- 26254193b965dc0bb91a50b162b9e091c298e63f diff --combined .gitattributes index 602aaca4f,7955a88cd..b784f78f8 --- a/.gitattributes +++ b/.gitattributes @@@ -358,11 -358,6 +358,11 @@@ eu.etaxonomy.taxeditor.editor/icons/edi eu.etaxonomy.taxeditor.editor/icons/emblem-photos.png -text eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text eu.etaxonomy.taxeditor.editor/icons/xper64.png -text +eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text +eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text +eu.etaxonomy.taxeditor.editor/lib/commons-lang3-3.1.jar -text +eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text +eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text eu.etaxonomy.taxeditor.editor/p2.inf -text eu.etaxonomy.taxeditor.editor/plugin.xml -text eu.etaxonomy.taxeditor.editor/pom.xml -text @@@ -386,10 -381,7 +386,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditor.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditorInput.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/handler/EditCdmAuthoritiesHandler.java -text +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/AddAHandler.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditNewTaxonHandler.java -text +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java -text +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenAlignmentEditor.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenChecklistEditorHandler.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenDerivateViewHandler.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenParentHandler.java -text @@@ -422,10 -414,6 +422,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/CreateNodeOperation.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/DeleteNodeOperation.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/RefreshNodeNumberingOperation.java -text +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CMDAlignmentObjectPlaceholder.java -text +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text @@@ -548,6 -536,8 +548,8 @@@ eu.etaxonomy.taxeditor.editor/src/main/ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/CreateDerivateContextMenu.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/DerivateViewContextMenu.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/contextMenu/SingleReadSequenceContextMenu.java -text + eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/handler/DeleteDerivateHandler.java -text + eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/derivate/operation/DeleteDerivateOperation.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementDragListener.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementDropAdapter.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/descriptive/DescriptionElementTransfer.java -text @@@ -595,10 -585,7 +597,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateTaxonUseOperation.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseRecordOperation.java -text eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseSummaryOperation.java -text +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text +eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/Application.java -text eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/ApplicationActionBarAdvisor.java -text @@@ -623,10 -610,12 +625,12 @@@ eu.etaxonomy.taxeditor.editor/src/test/ eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/MoveTaxonOperationTest.java -text eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/SwapSynonymAndAcceptedOperationTest.java -text eu.etaxonomy.taxeditor.feature.platform/.project -text + eu.etaxonomy.taxeditor.feature.platform/LICENSE.TXT -text eu.etaxonomy.taxeditor.feature.platform/build.properties -text eu.etaxonomy.taxeditor.feature.platform/feature.xml -text eu.etaxonomy.taxeditor.feature.platform/pom.xml -text eu.etaxonomy.taxeditor.feature/.project -text + eu.etaxonomy.taxeditor.feature/LICENSE.TXT -text eu.etaxonomy.taxeditor.feature/build.properties -text eu.etaxonomy.taxeditor.feature/feature.xml -text eu.etaxonomy.taxeditor.feature/pom.xml -text @@@ -1015,50 -1004,6 +1019,6 @@@ eu.etaxonomy.taxeditor.printpublisher/s eu.etaxonomy.taxeditor.printpublisher/src/main/java/eu/etaxonomy/taxeditor/printpublisher/wizard/SelectServiceWizardPage.java -text eu.etaxonomy.taxeditor.printpublisher/src/main/java/eu/etaxonomy/taxeditor/printpublisher/wizard/SelectStylesheetWizardPage.java -text eu.etaxonomy.taxeditor.printpublisher/src/main/java/eu/etaxonomy/taxeditor/printpublisher/wizard/SelectTaxaWizardPage.java -text - eu.etaxonomy.taxeditor.remoting/.classpath -text - eu.etaxonomy.taxeditor.remoting/.project -text - eu.etaxonomy.taxeditor.remoting/.settings/org.eclipse.jdt.core.prefs -text - eu.etaxonomy.taxeditor.remoting/.settings/org.eclipse.pde.core.prefs -text - eu.etaxonomy.taxeditor.remoting/META-INF/MANIFEST.MF -text - eu.etaxonomy.taxeditor.remoting/build.properties -text - eu.etaxonomy.taxeditor.remoting/pom.xml -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationRemoteConfiguration.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationRemoteController.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/api/cache/CdmServiceCacher.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmPersistentRemoteSource.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmRemoteSource.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmRemoteSourceBase.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/CdmRemoteSourceException.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/cdm/remote/ICdmRemoteSource.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/eu/etaxonomy/taxeditor/remoting/RemotingTestPluginActivator.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/org/hibernate/collection/internal/AbstractPersistentCollection.java -text - eu.etaxonomy.taxeditor.remoting/src/main/java/org/hibernate/proxy/AbstractLazyInitializer.java -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/etc/jetty/jetty-runner-9.2.3.v20140905.jar -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/etc/jetty/start-9.2.3.v20140905.jar -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/config.properties -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/httpInvokerServiceClients.xml -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/localApplicationContext.xml -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/remotingApplicationContext.xml -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/remoting_persistence_security.xml -text - eu.etaxonomy.taxeditor.remoting/src/main/resources/eu/etaxonomy/cdm/remoting_services_security.xml -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/exception/CDMServerException.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/BaseRemotingTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CDMServer.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CdmPersistentRemoteSourceTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CdmRemoteSourceTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/CdmServerTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/httpinvoker/HttpInvokerServicesTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/AbstractLazyInitializerTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/CdmServiceCacherTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/RemoteLazyLoadingTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/java/eu/etaxonomy/taxeditor/lazyloading/RemotePersistentCollectionTest.java -text - eu.etaxonomy.taxeditor.remoting/src/test/resources/datasources.xml -text - eu.etaxonomy.taxeditor.remoting/src/test/resources/eu/etaxonomy/cdm/cdm.datasources.xml -text - eu.etaxonomy.taxeditor.remoting/src/test/resources/eu/etaxonomy/cdm/testRemotingApplicationContext.xml -text - eu.etaxonomy.taxeditor.remoting/src/test/resources/eu/etaxonomy/taxeditor/lazyloading/AbstractLazyInitializerTest.xml -text - eu.etaxonomy.taxeditor.remoting/src/test/resources/h2/cdmTest.h2.db -text - eu.etaxonomy.taxeditor.remoting/src/test/resources/h2/cdmTest.trace.db -text - eu.etaxonomy.taxeditor.remoting/src/test/resources/unitils.properties -text eu.etaxonomy.taxeditor.store/.classpath -text eu.etaxonomy.taxeditor.store/.project -text eu.etaxonomy.taxeditor.store/META-INF/MANIFEST.MF -text @@@ -1099,6 -1044,7 +1059,7 @@@ eu.etaxonomy.taxeditor.store/icons/bina eu.etaxonomy.taxeditor.store/icons/bookmark.gif -text eu.etaxonomy.taxeditor.store/icons/category.gif -text eu.etaxonomy.taxeditor.store/icons/change.gif -text + eu.etaxonomy.taxeditor.store/icons/character_data_derivate-16x16-32.png -text eu.etaxonomy.taxeditor.store/icons/clear.gif -text eu.etaxonomy.taxeditor.store/icons/close.gif -text eu.etaxonomy.taxeditor.store/icons/close_view.gif -text @@@ -1492,6 -1438,7 +1453,7 @@@ eu.etaxonomy.taxeditor.store/src/main/j eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/MinMaxTextSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/MultilanguageTextElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/NumberWithLabelElement.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/OriginalLabelDataElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/PartialElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/PointElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/element/RootElement.java -text @@@ -1509,8 -1456,7 +1471,7 @@@ eu.etaxonomy.taxeditor.store/src/main/j eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/AbstractCdmComposite.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/DerivedUnitGeneralDetailElementMVC.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/GeographicPointElement.java -text - eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataController.java -text - eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataElement.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/OriginalLabelDataField.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/combo/EnumTermCombo.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/combo/EnumTermComboController.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/mvc/element/DateElement.java -text @@@ -1687,6 -1633,7 +1648,7 @@@ eu.etaxonomy.taxeditor.store/src/main/j eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/derivedUnit/PreservedSpecimenGeneralDetailElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/derivedUnit/PreservedSpecimenGeneralDetailSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/derivedUnit/PreservedSpecimenSourceCollectionDetailSection.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AbstractSampleDesignationDetailSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AbstractUnboundEntityCollectionSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationCloningDetailElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationCloningDetailSection.java -text @@@ -1696,11 -1643,16 +1658,16 @@@ eu.etaxonomy.taxeditor.store/src/main/j eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGeneralDetailSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationPrimerDetailElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationPrimerDetailSection.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/CurrentSampleDesignationDetailSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaQualityDetailSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/DnaSampleGeneralDetailSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/PrimerGeneralDetailElement.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationDetailElement.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationDetailSection.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationHistoryDetailSection.java -text + eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SampleDesignationTextDetailElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceContigFileCollectionDetailSection.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailElement.java -text eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceGeneralDetailSection.java -text diff --combined eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF index 15fa5be38,0718ed6fb..dc6052e58 --- a/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF +++ b/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF @@@ -2,7 -2,7 +2,7 @@@ Manifest-Version: 1. Bundle-ManifestVersion: 2 Bundle-Name: Editor Bundle Bundle-SymbolicName: eu.etaxonomy.taxeditor.editor;singleton:=true - Bundle-Version: 3.3.8.qualifier + Bundle-Version: 3.4.0.qualifier Bundle-Activator: eu.etaxonomy.taxeditor.editor.internal.TaxeditorEditorPlugin Bundle-Vendor: %Bundle-Vendor.0 Bundle-Localization: OSGI-INF/l10n/plugin @@@ -175,11 -175,4 +175,11 @@@ Bundle-ClassPath: . jdimodel.jar, pdebuild.jar, compatibility.jar, - junit.jar + junit.jar, + lib/biojava3-alignment-3.0.7.jar, + lib/biojava3-core-3.0.7.jar, + lib/core-1.8.5.jar, + lib/sequencing-1.8.5.jar, + lib/bioinfweb.commons/, + lib/LibrAlign/, + lib/commons-lang3-3.1.jar diff --combined eu.etaxonomy.taxeditor.editor/plugin.xml index 7f0394534,8788f3911..90254eae6 --- a/eu.etaxonomy.taxeditor.editor/plugin.xml +++ b/eu.etaxonomy.taxeditor.editor/plugin.xml @@@ -83,12 -83,6 +83,12 @@@ id="eu.etaxonomy.taxeditor.editor.view.checklist.ChecklistEditor" name="%editor.name.8"> + + @@@ -249,11 -243,6 +249,11 @@@ + + @@@ -755,8 -744,7 +755,7 @@@ commandId="taxeditor-editor.useExistingImage" label="%command.label.50" style="push"> - + @@@ -883,9 -871,6 +882,6 @@@ - - @@@ -929,31 -914,19 +925,43 @@@ + - + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + @@@ -1435,16 -1394,6 +1443,16 @@@ id="eu.etaxonomy.taxeditor.bindings.scheme.default" name="%scheme.name"> + + + + diff --combined eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java index ce1c9384d,000000000..ab3c65165 mode 100644,000000..100644 --- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java +++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java @@@ -1,218 -1,0 +1,218 @@@ +// $Id$ +/** +* Copyright (C) 2014 EDIT +* European Distributed Institute of Taxonomy +* http://www.e-taxonomy.eu +* +* The contents of this file are subject to the Mozilla Public License Version 1.1 +* See LICENSE.TXT at the top of this package for the full license terms. +*/ +package eu.etaxonomy.taxeditor.editor.molecular; + + +import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment; +import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment; +import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet; +import info.bioinfweb.libralign.AlignmentArea; +import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea; +import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea; +import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea; +import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider; +import info.bioinfweb.libralign.pherogram.PherogramProvider; +import info.bioinfweb.libralign.pherogram.ReverseComplementPherogramProvider; +import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider; +import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet; + +import java.io.File; + +import org.biojava.bio.chromatogram.ChromatogramFactory; +import org.biojava3.core.sequence.DNASequence; +import org.biojava3.core.sequence.compound.NucleotideCompound; +import org.eclipse.core.runtime.IProgressMonitor; +import org.eclipse.swt.SWT; +import org.eclipse.swt.widgets.Composite; +import org.eclipse.ui.IEditorInput; +import org.eclipse.ui.IEditorSite; +import org.eclipse.ui.PartInitException; +import org.eclipse.ui.part.EditorPart; + + + +/** + * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to + * a consensus sequence. + *

+ * The contained GUI components used to edit the alignment come from LibrAlign. + * + * @author pplitzner + * @author Ben Stöver + * @date 04.08.2014 + */ +public class AlignmentEditor extends EditorPart { + public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor"; + + private AlignmentArea alignmentArea; + + + private AlignmentArea createAlignmentArea() { + try { + //ResourcesPlugin.getWorkspace().getRoot().getFile("/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf"); + //System.out.println(AlignmentEditor.class.getResource("/")); + //System.out.println(AlignmentEditor.class.getResource("/../resources/TestPherogram_qualityScore.scf")); +// BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create( +// new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf"))); + //TODO Replace this absolute path with a path working with every workspace location. + + Alignment alignment = + new SimpleAlignment(); + alignment.add("Read 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCA-CCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA")); + alignment.add("Read 2", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA")); + //alignment.add("Consensus edit 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA")); + +// StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength()); +// for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) { +// seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase()); +// } +// alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) + +// seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49))); // One A is deleted for shift change specified below. + + BioJavaSequenceDataProvider sequenceProvider = + new BioJavaSequenceDataProvider( + new BioJavaTokenSet( + AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet(), true), + alignment); + + AlignmentArea result = new AlignmentArea(); + result.getContentArea().setSequenceProvider(sequenceProvider, false); + SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result.getContentArea()); + //sequenceIndexArea.setFirstIndex(5); + //sequenceIndexArea.setHeight(25); + result.getContentArea().getDataAreas().getTopAreas().add(sequenceIndexArea); + +// PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider); +// pherogramArea.setFirstSeqPos(34 + 5); +// pherogramArea.setLeftCutPosition(34); +// pherogramArea.setRightCutPosition(820); +// pherogramArea.getAlignmentModel().setShiftChange(38, -1); +// pherogramArea.getAlignmentModel().setShiftChange(49, 2); +// result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea); + + PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create( - new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\AlignmentTestData\\JR430_JR-P01.ab1"))); - PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider); - pherogramArea.setFirstSeqPos(1); - pherogramArea.setLeftCutPosition(13); - pherogramArea.setRightCutPosition(697); - pherogramArea.getAlignmentModel().setShiftChange(14, 1); - pherogramArea.getAlignmentModel().setShiftChange(35, 1); - result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea); - - pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create( - new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\AlignmentTestData\\JR444_JR-P05.ab1")))); ++ new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1"))); ++ PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider); ++ pherogramArea.setFirstSeqPos(1); ++ pherogramArea.setLeftCutPosition(13); ++ pherogramArea.setRightCutPosition(697); ++ pherogramArea.getAlignmentModel().setShiftChange(14, 1); ++ pherogramArea.getAlignmentModel().setShiftChange(35, 1); ++ result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea); ++ ++ pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create( ++ new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1")))); + pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider); + pherogramArea.setFirstSeqPos(1); + pherogramArea.setLeftCutPosition(267); + pherogramArea.getAlignmentModel().setShiftChange(273, -1); + pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale()); + result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea); + + + result.getContentArea().getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result.getContentArea())); + return result; + } + catch (Exception e) { + throw new RuntimeException(e); + } + +// Alignment alignment = +// new SimpleAlignment(); +// alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG")); +// alignment.add("Sequence 2", new DNASequence("AT-GTTG")); +// alignment.add("Sequence 3", new DNASequence("AT-GTAG")); +// +// BioJavaSequenceDataProvider sequenceProvider = +// new BioJavaSequenceDataProvider( +// new BioJavaTokenSet( +// AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()), +// alignment); +// +// AlignmentArea result = new AlignmentArea(); +// result.setSequenceProvider(sequenceProvider, false); +// SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result); +// //sequenceIndexArea.setFirstIndex(5); +// //sequenceIndexArea.setHeight(25); +// result.getDataAreas().getTopAreas().add(sequenceIndexArea); +// result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result)); +// return result; + } + + + /* (non-Javadoc) + * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite) + */ + @Override + public void createPartControl(Composite parent) { + alignmentArea = createAlignmentArea(); + Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE); + //getSite().setSelectionProvider(provider) + } + + + /* (non-Javadoc) + * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor) + */ + @Override + public void doSave(IProgressMonitor monitor) { + // TODO Auto-generated method stub + + } + + + /* (non-Javadoc) + * @see org.eclipse.ui.part.EditorPart#doSaveAs() + */ + @Override + public void doSaveAs() { + // TODO Auto-generated method stub + + } + + + /* (non-Javadoc) + * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput) + */ + @Override + public void init(IEditorSite site, IEditorInput input) throws PartInitException { + setSite(site); + setInput(input); + } + + + /* (non-Javadoc) + * @see org.eclipse.ui.part.EditorPart#isDirty() + */ + @Override + public boolean isDirty() { + // TODO Auto-generated method stub + return false; + } + + + /* (non-Javadoc) + * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed() + */ + @Override + public boolean isSaveAsAllowed() { + // TODO Auto-generated method stub + return false; + } + + + /* (non-Javadoc) + * @see org.eclipse.ui.part.WorkbenchPart#setFocus() + */ + @Override + public void setFocus() { + //alignmentArea.getToolkitComponent().redistributeHeight(); + } +}