Initial import of plugin files

[taxeditor.git] / .gitattributes

diff --git a/.gitattributes b/.gitattributes
index 01647faa59600c4eb278247122e9b1909a514654..ed822cf914b7f4960e71ee85645da2173d6805f6 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -376,8 +376,6 @@ eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-left-disabled-16x16.png -te
 eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-16x16.png -text
 eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-disabled-16x16.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
@@ -419,13 +417,19 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handle
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SpecimenPropertyTester.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/TaxonParameterConverter.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/AbstractAlignmentEditorHandler.java -text svneol=unset#text/plain
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/AbstractPherogramComponentHandler.java -text svneol=unset#text/plain
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ChangePherogramQualityOutputType.java -text svneol=unset#text/plain
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/CreateConsensusSequenceHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/CutPherogramLeftHandler.java -text svneol=unset#text/plain
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/CutPherogramRightHandler.java -text svneol=unset#text/plain
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ReverseComplementHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleInsertOverwriteHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleLeftRightInsertionHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleShowPherogramBaseCallLinesHandler.java -text svneol=unset#text/plain
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleShowPherogramProbabilitiesHandler.java -text svneol=unset#text/plain
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/UpdateConsensusSequenceHandler.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/package-info.java -text svneol=unset#text/plain
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewNameHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewPersonHandler.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewReferenceHandler.java -text
@@ -455,8 +459,6 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/po
 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/CDMAlignmentObjectPlaceholder.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/molecular/PherogramMouseListener.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java -text
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
@@ -650,6 +652,7 @@ eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/v
 eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorMessageMarkerField.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/AlignmentTestData/Test_qualityScore.scf -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
@@ -966,6 +969,44 @@ eu.etaxonomy.taxeditor.help/src/eu/etaxonomy/taxeditor/help/Activator.java -text
 eu.etaxonomy.taxeditor.help/toc.xml -text
 eu.etaxonomy.taxeditor.help/tocgettingstarted.xml -text
 eu.etaxonomy.taxeditor.help/tocnameparser.xml -text
+eu.etaxonomy.taxeditor.molecular/.classpath -text
+eu.etaxonomy.taxeditor.molecular/.project -text
+eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF -text
+eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin.properties -text
+eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_de.properties -text
+eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_en.properties -text
+eu.etaxonomy.taxeditor.molecular/build.properties -text
+eu.etaxonomy.taxeditor.molecular/icons/insert-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/overwrite-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-left-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-left-disabled-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-right-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-right-disabled-16x16.png -text
+eu.etaxonomy.taxeditor.molecular/plugin.xml -text
+eu.etaxonomy.taxeditor.molecular/pom.xml -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/TaxeditorMolecularPlugin.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditorInput.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/PherogramMouseListener.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/PherogramViewPart.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/AbstractAlignmentEditorHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/AbstractPherogramComponentHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ChangePherogramQualityOutputType.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CreateConsensusSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramLeftHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramRightHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/EditSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/HandlerTools.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/LoadPherogramHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ReverseComplementHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/SpecimenPropertyTester.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleInsertOverwriteHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleLeftRightInsertionHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramBaseCallLinesHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramProbabilitiesHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/UpdateConsensusSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/package-info.java -text
 eu.etaxonomy.taxeditor.navigation/.classpath -text
 eu.etaxonomy.taxeditor.navigation/.project -text
 eu.etaxonomy.taxeditor.navigation/META-INF/MANIFEST.MF -text
@@ -1009,7 +1050,6 @@ eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigatio
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonLinkHelper.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNavigator.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNavigatorDataChangeBehavior.java -text
-eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodeComparator.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodeContentProvider.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodeLabelProvider.java -text
 eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/navigator/TaxonNodePropertyTester.java -text
@@ -1225,6 +1265,7 @@ eu.etaxonomy.taxeditor.store/icons/specimen_scan_derivate_data-16x16-32.png -tex
 eu.etaxonomy.taxeditor.store/icons/step_done.gif -text
 eu.etaxonomy.taxeditor.store/icons/swap.gif -text
 eu.etaxonomy.taxeditor.store/icons/swap2.gif -text
+eu.etaxonomy.taxeditor.store/icons/switch_view_type-16x16-32.png -text
 eu.etaxonomy.taxeditor.store/icons/synced.gif -text
 eu.etaxonomy.taxeditor.store/icons/system-file-manager.png -text
 eu.etaxonomy.taxeditor.store/icons/system-users.png -text