Revision 29b09b3a
Added by Patrick Plitzner almost 9 years ago
| .gitattributes | ||
|---|---|---|
| 969 | 969 |
eu.etaxonomy.taxeditor.help/toc.xml -text |
| 970 | 970 |
eu.etaxonomy.taxeditor.help/tocgettingstarted.xml -text |
| 971 | 971 |
eu.etaxonomy.taxeditor.help/tocnameparser.xml -text |
| 972 |
eu.etaxonomy.taxeditor.molecular/.classpath -text |
|
| 973 |
eu.etaxonomy.taxeditor.molecular/.project -text |
|
| 974 |
eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF -text |
|
| 975 |
eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin.properties -text |
|
| 976 |
eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_de.properties -text |
|
| 977 |
eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_en.properties -text |
|
| 978 |
eu.etaxonomy.taxeditor.molecular/build.properties -text |
|
| 979 |
eu.etaxonomy.taxeditor.molecular/icons/insert-16x16.png -text |
|
| 980 |
eu.etaxonomy.taxeditor.molecular/icons/overwrite-16x16.png -text |
|
| 981 |
eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-left-16x16.png -text |
|
| 982 |
eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-left-disabled-16x16.png -text |
|
| 983 |
eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-right-16x16.png -text |
|
| 984 |
eu.etaxonomy.taxeditor.molecular/icons/pherogram-insert-right-disabled-16x16.png -text |
|
| 985 |
eu.etaxonomy.taxeditor.molecular/plugin.xml -text |
|
| 986 |
eu.etaxonomy.taxeditor.molecular/pom.xml -text |
|
| 987 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/TaxeditorMolecularPlugin.java -text |
|
| 988 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java -text |
|
| 989 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditorInput.java -text |
|
| 990 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/PherogramMouseListener.java -text |
|
| 991 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/PherogramViewPart.java -text |
|
| 992 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/AbstractAlignmentEditorHandler.java -text |
|
| 993 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/AbstractPherogramComponentHandler.java -text |
|
| 994 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ChangePherogramQualityOutputType.java -text |
|
| 995 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CreateConsensusSequenceHandler.java -text |
|
| 996 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramLeftHandler.java -text |
|
| 997 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramRightHandler.java -text |
|
| 998 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/EditSequenceHandler.java -text |
|
| 999 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/HandlerTools.java -text |
|
| 1000 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/LoadPherogramHandler.java -text |
|
| 1001 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ReverseComplementHandler.java -text |
|
| 1002 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java -text |
|
| 1003 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/SpecimenPropertyTester.java -text |
|
| 1004 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleInsertOverwriteHandler.java -text |
|
| 1005 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleLeftRightInsertionHandler.java -text |
|
| 1006 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramBaseCallLinesHandler.java -text |
|
| 1007 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramProbabilitiesHandler.java -text |
|
| 1008 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/UpdateConsensusSequenceHandler.java -text |
|
| 1009 |
eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/package-info.java -text |
|
| 972 | 1010 |
eu.etaxonomy.taxeditor.navigation/.classpath -text |
| 973 | 1011 |
eu.etaxonomy.taxeditor.navigation/.project -text |
| 974 | 1012 |
eu.etaxonomy.taxeditor.navigation/META-INF/MANIFEST.MF -text |
| eu.etaxonomy.taxeditor.molecular/.classpath | ||
|---|---|---|
| 1 |
<?xml version="1.0" encoding="UTF-8"?> |
|
| 2 |
<classpath> |
|
| 3 |
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/> |
|
| 4 |
<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/> |
|
| 5 |
<classpathentry including="**/*.java" kind="src" path="src"/> |
|
| 6 |
<classpathentry kind="lib" path="commons-logging-1.1.1.jar" sourcepath="/home/pplitzner/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-sources.jar"> |
|
| 7 |
<attributes> |
|
| 8 |
<attribute name="javadoc_location" value="jar:file:/home/pplitzner/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-javadoc.jar!/"/> |
|
| 9 |
</attributes> |
|
| 10 |
</classpathentry> |
|
| 11 |
<classpathentry exported="true" kind="lib" path="bioinfweb-commons-bio-2-SNAPSHOT.jar"/> |
|
| 12 |
<classpathentry exported="true" kind="lib" path="bioinfweb-commons-core-2-SNAPSHOT.jar"/> |
|
| 13 |
<classpathentry exported="true" kind="lib" path="bioinfweb-commons-swing-2-SNAPSHOT.jar"/> |
|
| 14 |
<classpathentry exported="true" kind="lib" path="bioinfweb-commons-swt-2-SNAPSHOT.jar"/> |
|
| 15 |
<classpathentry exported="true" kind="lib" path="libralign-core-0-SNAPSHOT.jar"/> |
|
| 16 |
<classpathentry exported="true" kind="lib" path="libralign-swt-0-SNAPSHOT.jar"/> |
|
| 17 |
<classpathentry exported="true" kind="lib" path="tic-core-2-SNAPSHOT.jar"/> |
|
| 18 |
<classpathentry exported="true" kind="lib" path="tic-swt-2-SNAPSHOT.jar"/> |
|
| 19 |
<classpathentry kind="output" path="target/classes"/> |
|
| 20 |
</classpath> |
|
| eu.etaxonomy.taxeditor.molecular/.project | ||
|---|---|---|
| 1 |
<?xml version="1.0" encoding="UTF-8"?> |
|
| 2 |
<projectDescription> |
|
| 3 |
<name>eu.etaxonomy.taxeditor.molecular</name> |
|
| 4 |
<comment>Provides editors, views and operations for handling molecular data and alignments. NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment> |
|
| 5 |
<projects> |
|
| 6 |
</projects> |
|
| 7 |
<buildSpec> |
|
| 8 |
<buildCommand> |
|
| 9 |
<name>org.eclipse.jdt.core.javabuilder</name> |
|
| 10 |
<arguments> |
|
| 11 |
</arguments> |
|
| 12 |
</buildCommand> |
|
| 13 |
<buildCommand> |
|
| 14 |
<name>org.eclipse.pde.ManifestBuilder</name> |
|
| 15 |
<arguments> |
|
| 16 |
</arguments> |
|
| 17 |
</buildCommand> |
|
| 18 |
<buildCommand> |
|
| 19 |
<name>org.eclipse.pde.SchemaBuilder</name> |
|
| 20 |
<arguments> |
|
| 21 |
</arguments> |
|
| 22 |
</buildCommand> |
|
| 23 |
</buildSpec> |
|
| 24 |
<natures> |
|
| 25 |
<nature>org.eclipse.jdt.core.javanature</nature> |
|
| 26 |
<nature>org.eclipse.pde.PluginNature</nature> |
|
| 27 |
</natures> |
|
| 28 |
<linkedResources> |
|
| 29 |
<link> |
|
| 30 |
<name>bioinfweb-commons-bio-2-SNAPSHOT.jar</name> |
|
| 31 |
<type>1</type> |
|
| 32 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-bio/2-SNAPSHOT/bioinfweb-commons-bio-2-SNAPSHOT.jar</location> |
|
| 33 |
</link> |
|
| 34 |
<link> |
|
| 35 |
<name>bioinfweb-commons-core-2-SNAPSHOT.jar</name> |
|
| 36 |
<type>1</type> |
|
| 37 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-core/2-SNAPSHOT/bioinfweb-commons-core-2-SNAPSHOT.jar</location> |
|
| 38 |
</link> |
|
| 39 |
<link> |
|
| 40 |
<name>bioinfweb-commons-swing-2-SNAPSHOT.jar</name> |
|
| 41 |
<type>1</type> |
|
| 42 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-swing/2-SNAPSHOT/bioinfweb-commons-swing-2-SNAPSHOT.jar</location> |
|
| 43 |
</link> |
|
| 44 |
<link> |
|
| 45 |
<name>bioinfweb-commons-swt-2-SNAPSHOT.jar</name> |
|
| 46 |
<type>1</type> |
|
| 47 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/commons/java/bioinfweb-commons-swt/2-SNAPSHOT/bioinfweb-commons-swt-2-SNAPSHOT.jar</location> |
|
| 48 |
</link> |
|
| 49 |
<link> |
|
| 50 |
<name>commons-logging-1.1.1.jar</name> |
|
| 51 |
<type>1</type> |
|
| 52 |
<location>/home/pplitzner/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar</location> |
|
| 53 |
</link> |
|
| 54 |
<link> |
|
| 55 |
<name>libralign-core-0-SNAPSHOT.jar</name> |
|
| 56 |
<type>1</type> |
|
| 57 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/libralign/libralign-core/0-SNAPSHOT/libralign-core-0-SNAPSHOT.jar</location> |
|
| 58 |
</link> |
|
| 59 |
<link> |
|
| 60 |
<name>libralign-swt-0-SNAPSHOT.jar</name> |
|
| 61 |
<type>1</type> |
|
| 62 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/libralign/libralign-swt/0-SNAPSHOT/libralign-swt-0-SNAPSHOT.jar</location> |
|
| 63 |
</link> |
|
| 64 |
<link> |
|
| 65 |
<name>tic-core-2-SNAPSHOT.jar</name> |
|
| 66 |
<type>1</type> |
|
| 67 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/tic/tic-core/2-SNAPSHOT/tic-core-2-SNAPSHOT.jar</location> |
|
| 68 |
</link> |
|
| 69 |
<link> |
|
| 70 |
<name>tic-swt-2-SNAPSHOT.jar</name> |
|
| 71 |
<type>1</type> |
|
| 72 |
<location>/home/pplitzner/.m2/repository/info/bioinfweb/tic/tic-swt/2-SNAPSHOT/tic-swt-2-SNAPSHOT.jar</location> |
|
| 73 |
</link> |
|
| 74 |
</linkedResources> |
|
| 75 |
</projectDescription> |
|
| eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF | ||
|---|---|---|
| 1 |
Manifest-Version: 1.0 |
|
| 2 |
Bundle-ManifestVersion: 2 |
|
| 3 |
Bundle-Name: Molecular Bundle |
|
| 4 |
Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular;singleton:=true |
|
| 5 |
Bundle-Version: 3.6.1.SNAPSHOT |
|
| 6 |
Bundle-Activator: eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin |
|
| 7 |
Require-Bundle: org.eclipse.ui, |
|
| 8 |
org.eclipse.core.runtime, |
|
| 9 |
org.eclipse.core.expressions, |
|
| 10 |
eu.etaxonomy.taxeditor.store, |
|
| 11 |
eu.etaxonomy.taxeditor.cdmlib, |
|
| 12 |
eu.etaxonomy.taxeditor.editor |
|
| 13 |
Bundle-RequiredExecutionEnvironment: JavaSE-1.7 |
|
| 14 |
Bundle-ActivationPolicy: lazy |
|
| 15 |
Bundle-Vendor: EDIT |
|
| 16 |
Bundle-ClassPath: ., |
|
| 17 |
commons-logging-1.1.1.jar, |
|
| 18 |
bioinfweb-commons-bio-2-SNAPSHOT.jar, |
|
| 19 |
bioinfweb-commons-core-2-SNAPSHOT.jar, |
|
| 20 |
bioinfweb-commons-swing-2-SNAPSHOT.jar, |
|
| 21 |
bioinfweb-commons-swt-2-SNAPSHOT.jar, |
|
| 22 |
libralign-core-0-SNAPSHOT.jar, |
|
| 23 |
libralign-swt-0-SNAPSHOT.jar, |
|
| 24 |
tic-core-2-SNAPSHOT.jar, |
|
| 25 |
tic-swt-2-SNAPSHOT.jar |
|
| 26 |
Import-Package: eu.etaxonomy.cdm.model.molecular |
|
| eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin.properties | ||
|---|---|---|
| 1 |
#Properties file for taxeditor-editor |
|
| 2 |
Bundle-Vendor.0 = EDIT |
|
| 3 |
Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle |
|
| 4 |
command.name.17 = Set Basionym |
|
| 5 |
command.name.18 = Remove Basionym |
|
| 6 |
editor.name = Multipage Taxon Editor |
|
| 7 |
editor.name.0 = Taxon Name Editor |
|
| 8 |
editor.name.1 = Key |
|
| 9 |
editor.name.2 = Polytomous Key Graph Editor |
|
| 10 |
editor.name.3 = Polytomous Key List Editor |
|
| 11 |
editor.name.4 = Cdm Authority Editor |
|
| 12 |
editor.name.5 = Derivative View |
|
| 13 |
view.name = Factual Data |
|
| 14 |
view.name.0 = Uses |
|
| 15 |
view.name.1 = Media |
|
| 16 |
view.name.2 = Concept Relations |
|
| 17 |
view.name.3 = Concept Graph |
|
| 18 |
category.name = Taxonomic Editor |
|
| 19 |
command.label = Reference |
|
| 20 |
command.label.0 = Name |
|
| 21 |
command.label.1 = Team |
|
| 22 |
command.label.2 = Person |
|
| 23 |
command.label.3 = Specimen |
|
| 24 |
command.label.4 = Factual Data |
|
| 25 |
command.label.5 = Media |
|
| 26 |
command.label.6 = Concept |
|
| 27 |
command.label.7 = Concept Graph |
|
| 28 |
command.label.8 = Open Parent |
|
| 29 |
menu.label = New |
|
| 30 |
command.label.9 = Heterotypic Synonym |
|
| 31 |
command.label.10 = Homotypic Synonym |
|
| 32 |
command.label.11 = Synonym In Homotypical Group |
|
| 33 |
menu.label.0 = Change To |
|
| 34 |
command.label.12 = Accepted Taxon |
|
| 35 |
command.label.13 = Synonym |
|
| 36 |
command.label.14 = Misapplication |
|
| 37 |
command.label.15 = Delete |
|
| 38 |
command.label.16 = Delete All Empty Names |
|
| 39 |
command.label.17 = Swap Synonym With Accepted |
|
| 40 |
command.label.18 = Show Details |
|
| 41 |
command.label.19 = Save |
|
| 42 |
command.label.20 = New Node |
|
| 43 |
command.label.21 = Delete |
|
| 44 |
command.label.22 = Apply Layout |
|
| 45 |
command.label.23 = New Key Number |
|
| 46 |
command.label.24 = New Alternative |
|
| 47 |
command.label.25 = Refresh Nodes |
|
| 48 |
command.label.26 = Delete |
|
| 49 |
command.label.27 = New Factual Data |
|
| 50 |
menu.label.1 = New |
|
| 51 |
command.label.28 = Move Description to Taxon |
|
| 52 |
command.label.29 = Move Elements to Taxon |
|
| 53 |
command.label.30 = Delete |
|
| 54 |
command.label.31 = Save |
|
| 55 |
menu.label.2 = New Derivative |
|
| 56 |
command.label.32 = New Use |
|
| 57 |
command.label.33 = New Use Summary |
|
| 58 |
command.label.34 = New Use Record |
|
| 59 |
command.label.35 = Delete |
|
| 60 |
command.label.36 = Save |
|
| 61 |
command.label.37 = New Image Gallery |
|
| 62 |
command.label.38 = New Image |
|
| 63 |
command.label.39 = Move Image Up In List |
|
| 64 |
command.label.40 = Move Image Down In List |
|
| 65 |
command.label.41 = Delete |
|
| 66 |
command.label.42 = Save |
|
| 67 |
menu.label.3 = New |
|
| 68 |
command.label.43 = Open Related Concept |
|
| 69 |
command.label.44 = Delete |
|
| 70 |
command.label.45 = Edit Authorities |
|
| 71 |
extension.name = Name Commands |
|
| 72 |
category.name.0 = -- Name Editor |
|
| 73 |
command.name = Open Parent |
|
| 74 |
command.name.0 = Create Homotypic Synonym |
|
| 75 |
command.name.1 = Create Heterotypic Synonym |
|
| 76 |
command.name.2 = Create Synonym In Homotypical Group |
|
| 77 |
command.name.3 = Change To Synonym |
|
| 78 |
command.name.4 = Change To Accepted Taxon |
|
| 79 |
command.name.5 = Change To Misapplication |
|
| 80 |
command.name.6 = Swap Synonym With Accepted |
|
| 81 |
|
|
| 82 |
command.name.7 = Set Basionym / Original Combination |
|
| 83 |
command.name.8 = Remove Basionym / Original Combination |
|
| 84 |
command.name.9 = Delete All Empty Names |
|
| 85 |
category.name.1 = -- Factual |
|
| 86 |
command.name.10 = Create Description Element |
|
| 87 |
command.name.11 = New Description |
|
| 88 |
command.name.12 = Move Description Elements to Taxon |
|
| 89 |
command.name.13 = Move Description to Taxon |
|
| 90 |
category.name.2 = -- New Uses |
|
| 91 |
command.name.14 = New Use |
|
| 92 |
command.name.15 = New Use Summary |
|
| 93 |
command.name.16 = New Use Record |
|
| 94 |
category.name.3 = -- Media |
|
| 95 |
command.name.19 = Move Image Down In List |
|
| 96 |
command.name.20 = New Image Gallery |
|
| 97 |
command.name.21 = New Image |
|
| 98 |
command.name.22 = Move Image Up In List |
|
| 99 |
category.name.4 = -- New Entity |
|
| 100 |
command.name.23 = New Reference |
|
| 101 |
command.name.24 = New Name |
|
| 102 |
command.name.25 = New Team |
|
| 103 |
command.name.26 = New Person |
|
| 104 |
command.name.27 = New Specimen |
|
| 105 |
category.name.5 = -- Polytomous Keys |
|
| 106 |
command.name.28 = New Child Node |
|
| 107 |
command.name.29 = New Sibling Node |
|
| 108 |
command.name.30 = Refresh Node Numbering |
|
| 109 |
command.name.31 = Apply Layout |
|
| 110 |
category.name.6 = -- Concept Relations |
|
| 111 |
command.name.32 = Create Concept Relation |
|
| 112 |
command.name.33 = Open Related Concept |
|
| 113 |
category.name.7 = -- Group |
|
| 114 |
command.name.34 = Edit CDM Authorities |
|
| 115 |
command.name.35 = Open Derivative View |
|
| 116 |
scheme.description = The default key binding scheme for the Taxonomic Editor |
|
| 117 |
scheme.name = Taxonomic Editor Default Key Bindings |
|
| 118 |
editor.name.6 = Specimen Import Editor |
|
| 119 |
editor.name.7 = Gbif Import Editor |
|
| 120 |
editor.name.8 = Checklist Editor |
|
| 121 |
view.name.4 = Specimen Import |
|
| 122 |
view.name.5 = GBIF Specimen Import |
|
| 123 |
command.label.46 = Name |
|
| 124 |
command.label.47 = Reference |
|
| 125 |
command.label.48 = Datasource |
|
| 126 |
command.label.49 = Misapplication |
|
| 127 |
command.label.50 = Use Existing Image |
|
| 128 |
command.name.36 = Create Misapplication |
|
| 129 |
command.name.37 = Use Existing Image |
|
| 130 |
command.name.38 = Open Checklist Editor |
|
| 131 |
command.name.39 = New Datasource |
|
| 132 |
wizard.name = Specimen Search/Import |
|
| 133 |
wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100. |
|
| 134 |
command.name.40 = Validation |
|
| 135 |
view.name.6 = Validation |
|
| 136 |
marker.field.0 = Object Type |
|
| 137 |
marker.field.1 = Object |
|
| 138 |
marker.field.2 = Attribute |
|
| 139 |
marker.field.3 = Problematic Value |
|
| 140 |
marker.field.4 = Problem description |
|
| 141 |
marker.field.5 = Validator |
|
| 142 |
marker.field.6 = Entity Class |
|
| 143 |
marker.field.7 = Entity Id |
|
| 144 |
extension.name.0 = Validation Error |
|
| 145 |
command.label.51 = Open in Specimen Editor |
|
| 146 |
command.label.52 = Delete |
|
| 147 |
command.label.53 = Create Field Unit |
|
| 148 |
command.label.54 = Delete (with children) |
|
| 149 |
command.tooltip = Show Only Individuals Associations |
|
| 150 |
command.label.55 = Open Associated Specimens |
|
| 151 |
command.name.41 = Show Only Individual Associations |
|
| 152 |
command.name.42 = Open Taxon Editor |
|
| 153 |
command.name.43 = Create Field Unit |
|
| 154 |
command.name.44 = Deep Delete |
|
| 155 |
command.name.46 = Move Synonym (Homotypical Group) to another Accepted Taxon |
|
| 156 |
command.label.56 = Move Synonym (Homotypical Group) to another Accepted Taxon |
|
| 157 |
markerContentGenerator.name = Validation Problems Marker Generator |
|
| 158 |
command.name.45 = Delete |
|
| 159 |
command.name.47 = Delete |
|
| 160 |
commandParameter.name = taxonUUID |
|
| 161 |
Bundle-Name = Editor Bundle |
|
| 162 |
command.name.48 = delete |
|
| 163 |
command.name.49 = delete |
|
| 164 |
command.name.50 = delete |
|
| eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_de.properties | ||
|---|---|---|
| 1 |
# Properties file for taxeditor-editor |
|
| 2 |
Bundle-Vendor.0 = EDIT |
|
| 3 |
Bundle-Name.0 = EDIT Taxonomischer Editor - Editor Bundle |
|
| 4 |
command.name.17 = Setze Basionym |
|
| 5 |
command.name.18 = Entferne Basionym |
|
| 6 |
editor.name = Multipage Taxon Editor |
|
| 7 |
editor.name.0 = Editor Taxonname |
|
| 8 |
editor.name.1 = Bestimmungsschl\u00fcssel |
|
| 9 |
editor.name.2 = Polytomer Bestimmungsschl\u00fcssel Graph Editor |
|
| 10 |
editor.name.3 = Polytomer Bestimmungsschl\u00fcssel List Editor |
|
| 11 |
editor.name.4 = CDM Rechtemanagement |
|
| 12 |
editor.name.5 = Ansicht Derivate |
|
| 13 |
view.name = Faktendaten |
|
| 14 |
view.name.0 = Nutzung |
|
| 15 |
view.name.1 = Medien |
|
| 16 |
view.name.2 = Konzeptrelationen |
|
| 17 |
view.name.3 = Konzeptgraph |
|
| 18 |
category.name = Taxonomischer Editor |
|
| 19 |
command.label = Referenz |
|
| 20 |
command.label.0 = Name |
|
| 21 |
command.label.1 = Team |
|
| 22 |
command.label.2 = Person |
|
| 23 |
command.label.3 = Beleg |
|
| 24 |
command.label.4 = Faktendaten |
|
| 25 |
command.label.5 = Medien |
|
| 26 |
command.label.6 = Konzeptrelationen |
|
| 27 |
command.label.7 = Konzeptgraph |
|
| 28 |
command.label.8 = \u00d6ffne Parent |
|
| 29 |
menu.label = Neue |
|
| 30 |
command.label.9 = Heterotypisches Synonym |
|
| 31 |
command.label.10 = Homotypisches Synonym |
|
| 32 |
command.label.11 = Synonym in Homotypischer Gruppe |
|
| 33 |
menu.label.0 = \u00c4ndere zu |
|
| 34 |
command.label.12 = Akzeptiertes Taxon |
|
| 35 |
command.label.13 = Synonym |
|
| 36 |
command.label.14 = Misapplication |
|
| 37 |
command.label.15 = L\u00f6schen |
|
| 38 |
command.label.16 = L\u00f6sche alle leeren Namen |
|
| 39 |
command.label.17 = Tausche Synonym mit akzeptiertem Namen |
|
| 40 |
command.label.18 = Zeige Details |
|
| 41 |
command.label.19 = Speichern |
|
| 42 |
command.label.20 = Neue Knoten |
|
| 43 |
command.label.21 = L\u00f6schen |
|
| 44 |
command.label.22 = Wende Layout an |
|
| 45 |
command.label.23 = Neue Bestimmungsschl\u00fcsselnummer |
|
| 46 |
command.label.24 = Neue Alternative |
|
| 47 |
command.label.25 = Erneuere Knoten |
|
| 48 |
command.label.26 = L\u00f6schen |
|
| 49 |
command.label.27 = Neue Faktendaten |
|
| 50 |
menu.label.1 = Neue |
|
| 51 |
command.label.28 = Verschiebe Eigenschaften zu Taxon |
|
| 52 |
command.label.29 = Verschiebe Elemente zu Taxon |
|
| 53 |
command.label.30 = L\u00f6schen |
|
| 54 |
command.label.31 = Speichern |
|
| 55 |
menu.label.2 = Neue Derivate |
|
| 56 |
command.label.32 = Neue Nutzung |
|
| 57 |
command.label.33 = Neue Zusammenfassung |
|
| 58 |
command.label.34 = Neuer Nutzungsdatensatz |
|
| 59 |
command.label.35 = L\u00f6schen |
|
| 60 |
command.label.36 = Speichern |
|
| 61 |
command.label.37 = Neue Bildergalerie |
|
| 62 |
command.label.38 = Neues Bild |
|
| 63 |
command.label.39 = Bild nach oben |
|
| 64 |
command.label.40 = Bild nach unten |
|
| 65 |
command.label.41 = L\u00f6schen |
|
| 66 |
command.label.42 = Speichern |
|
| 67 |
menu.label.3 = Neue |
|
| 68 |
command.label.43 = \u00d6ffne verbundenes Konzept |
|
| 69 |
command.label.44 = L\u00f6schen |
|
| 70 |
command.label.45 = Bearbeite Rechte |
|
| 71 |
extension.name = Namensbefehle |
|
| 72 |
category.name.0 = -- Namenseditor |
|
| 73 |
command.name = \u00d6ffne Elter |
|
| 74 |
command.name.0 = Erstelle homotypisches Synonym |
|
| 75 |
command.name.1 = Erstelle heterotypisches Synonym |
|
| 76 |
command.name.2 = Erstelle Synonym in homotypischer Gruppe |
|
| 77 |
command.name.3 = \u00c4ndere zu Synonym |
|
| 78 |
command.name.4 = \u00c4ndere zu akzeptiertem Taxon |
|
| 79 |
command.name.5 = \u00c4ndere zu Misapplication |
|
| 80 |
command.name.6 = Tausche Synonym mit akzeptiertem Namen |
|
| 81 |
|
|
| 82 |
command.name.7 = Setze Basionym / Originalkombination |
|
| 83 |
command.name.8 = Entferne Basionym / Originalkombination |
|
| 84 |
command.name.9 = L\u00f6sche alle leeren Namen |
|
| 85 |
category.name.1 = -- Fakten |
|
| 86 |
command.name.10 = Erstelle Beschreibungselement |
|
| 87 |
command.name.11 = Neue Beschreibung |
|
| 88 |
command.name.12 = Bewege Beschreibungselement zu Taxon |
|
| 89 |
command.name.13 = Bewege Beschreibung zu Taxon |
|
| 90 |
category.name.2 = -- Neue Nutzung |
|
| 91 |
command.name.14 = Neue Nutzung |
|
| 92 |
command.name.15 = Neue Zusammenfassung |
|
| 93 |
command.name.16 = Neuer Nutzungsdatensatz |
|
| 94 |
category.name.3 = -- Media |
|
| 95 |
command.name.19 = Bewege Bild nach unten |
|
| 96 |
command.name.20 = Neue Bildergalerie |
|
| 97 |
command.name.21 = Neues Bild |
|
| 98 |
command.name.22 = Bewege Bild nach oben |
|
| 99 |
category.name.4 = -- Neue Entit\u00e4t |
|
| 100 |
command.name.23 = Neue Referenz |
|
| 101 |
command.name.24 = Neuer Name |
|
| 102 |
command.name.25 = Neues Team |
|
| 103 |
command.name.26 = Neue Person |
|
| 104 |
command.name.27 = Neuer Beleg |
|
| 105 |
category.name.5 = -- Polytomer Bestimmungsschl\u00fcssel |
|
| 106 |
command.name.28 = Neue Kinderknoten |
|
| 107 |
command.name.29 = Neuer Geschwisterknoten |
|
| 108 |
command.name.30 = Knotennummerierung aktualisieren |
|
| 109 |
command.name.31 = Layout anwenden |
|
| 110 |
category.name.6 = -- Konzeptbeziehungen |
|
| 111 |
command.name.32 = Erstelle Konzeptrelationen |
|
| 112 |
command.name.33 = \u00d6ffne verbundenes Konzept |
|
| 113 |
category.name.7 = -- Gruppe |
|
| 114 |
command.name.34 = Bearbeite CDM Rechte |
|
| 115 |
command.name.35 = \u00d6ffne Derivate Ansicht |
|
| 116 |
scheme.description = Die Standard Tastenkombinationsschema f\u00fcr den Taxonomischen Editor |
|
| 117 |
scheme.name = Taxonomic Editor Standard Tastenkombinationen |
|
| 118 |
editor.name.6 = Specimen Import Editor |
|
| 119 |
editor.name.7 = GBIF Import Editor |
|
| 120 |
editor.name.8 = Checklist Editor |
|
| 121 |
view.name.4 = Specimen Import |
|
| 122 |
view.name.5 = GBIF Specimen Import |
|
| 123 |
command.label.46 = Name |
|
| 124 |
command.label.47 = Referenz |
|
| 125 |
command.label.48 = Datenquelle |
|
| 126 |
command.label.49 = Misapplication |
|
| 127 |
command.label.50 = Benutze vorhandenes Bild |
|
| 128 |
command.name.36 = Erstelle Misapplication |
|
| 129 |
command.name.37 = Benutze vorhandenes Bild |
|
| 130 |
command.name.38 = \u00d6ffne Checklist Editor |
|
| 131 |
command.name.39 = Neue Datenquelle |
|
| 132 |
wizard.name = Specimen Suche/Import |
|
| 133 |
wizard.description = Sendet eine Anfrage mit den eingegebenen Parametern an den Datenprovider.\nHinweis: Die Anzahl der Anfrageergebnisse sind auf 100 begrenzt. |
|
| 134 |
command.name.40 = Validierung |
|
| 135 |
view.name.6 = Validierung |
|
| 136 |
marker.field.0 = Objekttyp |
|
| 137 |
marker.field.1 = Objekt |
|
| 138 |
marker.field.2 = Attribut |
|
| 139 |
marker.field.3 = Problematischer Wert |
|
| 140 |
marker.field.4 = Problembeschreibung |
|
| 141 |
marker.field.5 = Validierer |
|
| 142 |
marker.field.6 = Entit�tsklasse |
|
| 143 |
marker.field.7 = Entit�ts ID |
|
| 144 |
extension.name.0 = Validierungs-Fehler |
|
| 145 |
command.label.51 = \u00d6ffne Specimen-Editor |
|
| 146 |
command.label.52 = L\u00f6schen |
|
| 147 |
command.label.53 = Neue Field Unit |
|
| 148 |
command.label.54 = L\u00f6schen (mit Kindern) |
|
| 149 |
command.tooltip = Nur Individuals Associations anzeigen |
|
| 150 |
command.label.55 = \u00d6ffne zugeh\u00f6rige Specimens |
|
| 151 |
command.name.41 = Nur Individuals Associations anzeigen |
|
| 152 |
command.name.42 = \u00d6ffne Taxon Editor |
|
| 153 |
command.name.43 = Neue Field Unit |
|
| 154 |
command.name.44 = L\u00f6schen (mit Kindern) |
|
| 155 |
command.name.46 = Verschiebe Synonym(Homotypische Gruppe) zu neuem Akzeptierten Taxon |
|
| 156 |
command.label.56 = Verschiebe Synonym(Homotypische Gruppe) zu neuem Akzeptierten Taxon |
|
| eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/plugin_en.properties | ||
|---|---|---|
| 1 |
#Properties file for taxeditor-editor |
|
| 2 |
Bundle-Vendor.0 = EDIT |
|
| 3 |
Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle |
|
| 4 |
command.name.17 = Set Basionym |
|
| 5 |
command.name.18 = Remove Basionym |
|
| 6 |
editor.name = Multipage Taxon Editor |
|
| 7 |
editor.name.0 = Taxon Name Editor |
|
| 8 |
editor.name.1 = Key |
|
| 9 |
editor.name.2 = Polytomous Key Graph Editor |
|
| 10 |
editor.name.3 = Polytomous Key List Editor |
|
| 11 |
editor.name.4 = Cdm Authority Editor |
|
| 12 |
editor.name.5 = Derivate View |
|
| 13 |
view.name = Factual Data |
|
| 14 |
view.name.0 = Uses |
|
| 15 |
view.name.1 = Media |
|
| 16 |
view.name.2 = Concept Relations |
|
| 17 |
view.name.3 = Concept Graph |
|
| 18 |
category.name = Taxonomic Editor |
|
| 19 |
command.label = Reference |
|
| 20 |
command.label.0 = Name |
|
| 21 |
command.label.1 = Team |
|
| 22 |
command.label.2 = Person |
|
| 23 |
command.label.3 = Specimen |
|
| 24 |
command.label.4 = Factual Data |
|
| 25 |
command.label.5 = Media |
|
| 26 |
command.label.6 = Concept |
|
| 27 |
command.label.7 = Concept Graph |
|
| 28 |
command.label.8 = Open Parent |
|
| 29 |
menu.label = New |
|
| 30 |
command.label.9 = Heterotypic Synonym |
|
| 31 |
command.label.10 = Homotypic Synonym |
|
| 32 |
command.label.11 = Synonym In Homotypical Group |
|
| 33 |
menu.label.0 = Change To |
|
| 34 |
command.label.12 = Accepted Taxon |
|
| 35 |
command.label.13 = Synonym |
|
| 36 |
command.label.14 = Misapplication |
|
| 37 |
command.label.15 = Delete |
|
| 38 |
command.label.16 = Delete All Empty Names |
|
| 39 |
command.label.17 = Swap Synonym With Accepted |
|
| 40 |
command.label.18 = Show Details |
|
| 41 |
command.label.19 = Save |
|
| 42 |
command.label.20 = New Node |
|
| 43 |
command.label.21 = Delete |
|
| 44 |
command.label.22 = Apply Layout |
|
| 45 |
command.label.23 = New Key Number |
|
| 46 |
command.label.24 = New Alternative |
|
| 47 |
command.label.25 = Refresh Nodes |
|
| 48 |
command.label.26 = Delete |
|
| 49 |
command.label.27 = New Factual Data |
|
| 50 |
menu.label.1 = New |
|
| 51 |
command.label.28 = Move Description to Taxon |
|
| 52 |
command.label.29 = Move Elements to Taxon |
|
| 53 |
command.label.30 = Delete |
|
| 54 |
command.label.31 = Save |
|
| 55 |
menu.label.2 = New Derivate |
|
| 56 |
command.label.32 = New Use |
|
| 57 |
command.label.33 = New Use Summary |
|
| 58 |
command.label.34 = New Use Record |
|
| 59 |
command.label.35 = Delete |
|
| 60 |
command.label.36 = Save |
|
| 61 |
command.label.37 = New Image Gallery |
|
| 62 |
command.label.38 = New Image |
|
| 63 |
command.label.39 = Move Image Up In List |
|
| 64 |
command.label.40 = Move Image Down In List |
|
| 65 |
command.label.41 = Delete |
|
| 66 |
command.label.42 = Save |
|
| 67 |
menu.label.3 = New |
|
| 68 |
command.label.43 = Open Related Concept |
|
| 69 |
command.label.44 = Delete |
|
| 70 |
command.label.45 = Edit Authorities |
|
| 71 |
extension.name = Name Commands |
|
| 72 |
category.name.0 = -- Name Editor |
|
| 73 |
command.name = Open Parent |
|
| 74 |
command.name.0 = Create Homotypic Synonym |
|
| 75 |
command.name.1 = Create Heterotypic Synonym |
|
| 76 |
command.name.2 = Create Synonym In Homotypical Group |
|
| 77 |
command.name.3 = Change To Synonym |
|
| 78 |
command.name.4 = Change To Accepted Taxon |
|
| 79 |
command.name.5 = Change To Misapplication |
|
| 80 |
command.name.6 = Swap Synonym With Accepted |
|
| 81 |
command.name.7 = Set Basionym / Original Combination |
|
| 82 |
command.name.8 = Remove Basionym / Original Combination |
|
| 83 |
command.name.9 = Delete All Empty Names |
|
| 84 |
category.name.1 = -- Factual |
|
| 85 |
command.name.10 = Create Description Element |
|
| 86 |
command.name.11 = New Description |
|
| 87 |
command.name.12 = Move Description Elements to Taxon |
|
| 88 |
command.name.13 = Move Description to Taxon |
|
| 89 |
category.name.2 = -- New Uses |
|
| 90 |
command.name.14 = New Use |
|
| 91 |
command.name.15 = New Use Summary |
|
| 92 |
command.name.16 = New Use Record |
|
| 93 |
category.name.3 = -- Media |
|
| 94 |
command.name.19 = Move Image Down In List |
|
| 95 |
command.name.20 = New Image Gallery |
|
| 96 |
command.name.21 = New Image |
|
| 97 |
command.name.22 = Move Image Up In List |
|
| 98 |
category.name.4 = -- New Entity |
|
| 99 |
command.name.23 = New Reference |
|
| 100 |
command.name.24 = New Name |
|
| 101 |
command.name.25 = New Team |
|
| 102 |
command.name.26 = New Person |
|
| 103 |
command.name.27 = New Specimen |
|
| 104 |
category.name.5 = -- Polytomous Keys |
|
| 105 |
command.name.28 = New Child Node |
|
| 106 |
command.name.29 = New Sibling Node |
|
| 107 |
command.name.30 = Refresh Node Numbering |
|
| 108 |
command.name.31 = Apply Layout |
|
| 109 |
category.name.6 = -- Concept Relations |
|
| 110 |
command.name.32 = Create Concept Relation |
|
| 111 |
command.name.33 = Open Related Concept |
|
| 112 |
category.name.7 = -- Group |
|
| 113 |
command.name.34 = Edit CDM Authorities |
|
| 114 |
command.name.35 = Open Derivate View |
|
| 115 |
scheme.description = The default key binding scheme for the Taxonomic Editor |
|
| 116 |
scheme.name = Taxonomic Editor Default Key Bindingseditor.name.6 = Specimen Import Editor |
|
| 117 |
editor.name.7 = Gbif Import Editor |
|
| 118 |
editor.name.8 = Checklist Editor |
|
| 119 |
view.name.4 = Specimen Import |
|
| 120 |
view.name.5 = GBIF Specimen Import |
|
| 121 |
command.label.46 = Name |
|
| 122 |
command.label.47 = Reference |
|
| 123 |
command.label.48 = Datasource |
|
| 124 |
command.label.49 = Misapplication |
|
| 125 |
command.label.50 = Use Existing Image |
|
| 126 |
command.name.36 = Create Misapplication |
|
| 127 |
command.name.37 = Use Existing Image |
|
| 128 |
command.name.38 = Open Checklist Editor |
|
| 129 |
command.name.39 = New Datasource |
|
| 130 |
wizard.name = Specimen Search/Import |
|
| 131 |
wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100. |
|
| 132 |
command.name.40 = Validation |
|
| 133 |
view.name.6 = Validation |
|
| 134 |
marker.field.0 = Object Type |
|
| 135 |
marker.field.1 = Object |
|
| 136 |
marker.field.2 = Attribute |
|
| 137 |
marker.field.3 = Problematic Value |
|
| 138 |
marker.field.4 = Problem description |
|
| 139 |
marker.field.5 = Validator |
|
| 140 |
marker.field.6 = Entity Class |
|
| 141 |
marker.field.7 = Entity Id |
|
| eu.etaxonomy.taxeditor.molecular/build.properties | ||
|---|---|---|
| 1 |
source.. = src/ |
|
| 2 |
output.. = bin/ |
|
| 3 |
bin.includes = META-INF/,\ |
|
| 4 |
plugin.xml,\ |
|
| 5 |
lib/libralign-core-0-20150713.112743-1.jar,\ |
|
| 6 |
lib/libralign-swt-0-20150713.113034-1.jar,\ |
|
| 7 |
icons/,\ |
|
| 8 |
OSGI-INF/ |
|
| 9 |
source.. = src/ |
|
| 10 |
src.includes = src/,\ |
|
| 11 |
plugin.xml,\ |
|
| 12 |
icons/,\ |
|
| 13 |
OSGI-INF/,\ |
|
| 14 |
META-INF/ |
|
| eu.etaxonomy.taxeditor.molecular/plugin.xml | ||
|---|---|---|
| 1 |
<?xml version="1.0" encoding="UTF-8"?> |
|
| 2 |
<?eclipse version="3.4"?> |
|
| 3 |
<plugin> |
|
| 4 |
<extension |
|
| 5 |
point="org.eclipse.ui.editors"> |
|
| 6 |
<editor |
|
| 7 |
class="eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor" |
|
| 8 |
default="false" |
|
| 9 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor" |
|
| 10 |
name="Alignment Editor"> |
|
| 11 |
</editor> |
|
| 12 |
</extension> |
|
| 13 |
<extension |
|
| 14 |
point="org.eclipse.ui.views"> |
|
| 15 |
<view |
|
| 16 |
allowMultiple="true" |
|
| 17 |
class="eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart" |
|
| 18 |
id="eu.etaxonomy.taxeditor.molecular.PherogramView" |
|
| 19 |
name="PherogramView" |
|
| 20 |
restorable="true"> |
|
| 21 |
</view> |
|
| 22 |
</extension> |
|
| 23 |
<extension |
|
| 24 |
point="org.eclipse.ui.commands"> |
|
| 25 |
<command |
|
| 26 |
defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler" |
|
| 27 |
id="eu.etaxonomy.taxeditor.molecular.editSequence" |
|
| 28 |
name="Edit Sequence"> |
|
| 29 |
</command> |
|
| 30 |
<command |
|
| 31 |
defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler" |
|
| 32 |
id="eu.etaxonomy.taxeditor.molecular.showPherogram" |
|
| 33 |
name="Show Pherogram"> |
|
| 34 |
</command> |
|
| 35 |
<command |
|
| 36 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" |
|
| 37 |
name="Cut pherogram left"> |
|
| 38 |
</command> |
|
| 39 |
<command |
|
| 40 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight" |
|
| 41 |
name="Cut pherogram right"> |
|
| 42 |
</command> |
|
| 43 |
<command |
|
| 44 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows" |
|
| 45 |
name="Reverse complement selected rows"> |
|
| 46 |
</command> |
|
| 47 |
<command |
|
| 48 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus" |
|
| 49 |
name="(Re)create consensus sequence"> |
|
| 50 |
</command> |
|
| 51 |
<command |
|
| 52 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus" |
|
| 53 |
name="Update consensus sequence"> |
|
| 54 |
</command> |
|
| 55 |
<command |
|
| 56 |
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities" |
|
| 57 |
name="Toggle show probability values"> |
|
| 58 |
</command> |
|
| 59 |
<command |
|
| 60 |
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines" |
|
| 61 |
name="Toggle show base call lines"> |
|
| 62 |
</command> |
|
| 63 |
<command |
|
| 64 |
id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput" |
|
| 65 |
name="Change quality output"> |
|
| 66 |
</command> |
|
| 67 |
<command |
|
| 68 |
defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.OpenAlignmentEditorHandler" |
|
| 69 |
id="eu.etaxonomy.taxeditor.molecular.OpenAlignmentEditor" |
|
| 70 |
name="Open Alignment Editor"> |
|
| 71 |
</command> |
|
| 72 |
<command |
|
| 73 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram" |
|
| 74 |
name="Load Pherogram"> |
|
| 75 |
</command> |
|
| 76 |
<command |
|
| 77 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite" |
|
| 78 |
name="Toggle insert/overwrite"> |
|
| 79 |
</command> |
|
| 80 |
<command |
|
| 81 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion" |
|
| 82 |
name="Toggle left/right insertion in base call sequence"> |
|
| 83 |
</command> |
|
| 84 |
</extension> |
|
| 85 |
<extension |
|
| 86 |
point="org.eclipse.ui.menus"> |
|
| 87 |
<menuContribution |
|
| 88 |
locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar"> |
|
| 89 |
<toolbar |
|
| 90 |
id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar"> |
|
| 91 |
<command |
|
| 92 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite" |
|
| 93 |
label="Toggle insert/overwrite" |
|
| 94 |
style="push"> |
|
| 95 |
<visibleWhen |
|
| 96 |
checkEnabled="true"> |
|
| 97 |
<with |
|
| 98 |
variable="activePartId"> |
|
| 99 |
<equals |
|
| 100 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
| 101 |
</equals> |
|
| 102 |
</with> |
|
| 103 |
</visibleWhen> |
|
| 104 |
</command> |
|
| 105 |
<command |
|
| 106 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion" |
|
| 107 |
icon="icons/pherogram-insert-left-16x16.png" |
|
| 108 |
style="push"> |
|
| 109 |
<visibleWhen |
|
| 110 |
checkEnabled="false"> |
|
| 111 |
<with |
|
| 112 |
variable="activePartId"> |
|
| 113 |
<equals |
|
| 114 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
| 115 |
</equals> |
|
| 116 |
</with> |
|
| 117 |
</visibleWhen> |
|
| 118 |
</command> |
|
| 119 |
</toolbar> |
|
| 120 |
</menuContribution> |
|
| 121 |
<menuContribution |
|
| 122 |
allPopups="false" |
|
| 123 |
locationURI="menu:org.eclipse.ui.main.menu"> |
|
| 124 |
<menu |
|
| 125 |
label="View"> |
|
| 126 |
<menu |
|
| 127 |
label="Pherogram"> |
|
| 128 |
<command |
|
| 129 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput" |
|
| 130 |
style="push"> |
|
| 131 |
</command> |
|
| 132 |
<command |
|
| 133 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities" |
|
| 134 |
style="push"> |
|
| 135 |
</command> |
|
| 136 |
<command |
|
| 137 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines" |
|
| 138 |
style="push"> |
|
| 139 |
</command> |
|
| 140 |
<visibleWhen |
|
| 141 |
checkEnabled="true"> |
|
| 142 |
<with |
|
| 143 |
variable="activePartId"> |
|
| 144 |
<or> |
|
| 145 |
<equals |
|
| 146 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
| 147 |
</equals> |
|
| 148 |
<equals |
|
| 149 |
value="eu.etaxonomy.taxeditor.molecular.PherogramView"> |
|
| 150 |
</equals> |
|
| 151 |
</or> |
|
| 152 |
</with> |
|
| 153 |
</visibleWhen> |
|
| 154 |
</menu> |
|
| 155 |
</menu> |
|
| 156 |
<menu |
|
| 157 |
label="Alignment Editor"> |
|
| 158 |
<command |
|
| 159 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram" |
|
| 160 |
style="push"> |
|
| 161 |
</command> |
|
| 162 |
<command |
|
| 163 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" |
|
| 164 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft" |
|
| 165 |
name="Cut pherogram left"> |
|
| 166 |
</command> |
|
| 167 |
<command |
|
| 168 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight" |
|
| 169 |
id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight" |
|
| 170 |
style="push"> |
|
| 171 |
</command> |
|
| 172 |
<command |
|
| 173 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows" |
|
| 174 |
mnemonic="r" |
|
| 175 |
style="push"> |
|
| 176 |
</command> |
|
| 177 |
<command |
|
| 178 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus" |
|
| 179 |
style="push"> |
|
| 180 |
</command> |
|
| 181 |
<command |
|
| 182 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus" |
|
| 183 |
style="push"> |
|
| 184 |
</command> |
|
| 185 |
<visibleWhen |
|
| 186 |
checkEnabled="true"> |
|
| 187 |
<with |
|
| 188 |
variable="activePartId"> |
|
| 189 |
<equals |
|
| 190 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
| 191 |
</equals> |
|
| 192 |
</with> |
|
| 193 |
</visibleWhen> |
|
| 194 |
</menu> |
|
| 195 |
</menuContribution> |
|
| 196 |
<menuContribution |
|
| 197 |
locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView"> |
|
| 198 |
<command |
|
| 199 |
commandId="eu.etaxonomy.taxeditor.molecular.editSequence" |
|
| 200 |
label="Edit Sequence" |
|
| 201 |
style="push"> |
|
| 202 |
<visibleWhen |
|
| 203 |
checkEnabled="true"> |
|
| 204 |
<reference |
|
| 205 |
definitionId="isSequence"> |
|
| 206 |
</reference> |
|
| 207 |
</visibleWhen> |
|
| 208 |
</command> |
|
| 209 |
<command |
|
| 210 |
commandId="eu.etaxonomy.taxeditor.molecular.showPherogram" |
|
| 211 |
label="Show Pherogram" |
|
| 212 |
style="push"> |
|
| 213 |
<visibleWhen |
|
| 214 |
checkEnabled="true"> |
|
| 215 |
<reference |
|
| 216 |
definitionId="isSingleRead"> |
|
| 217 |
</reference> |
|
| 218 |
</visibleWhen> |
|
| 219 |
</command> |
|
| 220 |
</menuContribution> |
|
| 221 |
</extension> |
|
| 222 |
<extension |
|
| 223 |
point="org.eclipse.ui.handlers"> |
|
| 224 |
<handler |
|
| 225 |
class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler" |
|
| 226 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"> |
|
| 227 |
<activeWhen> |
|
| 228 |
<with |
|
| 229 |
variable="activePartId"> |
|
| 230 |
<equals |
|
| 231 |
value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"> |
|
| 232 |
</equals> |
|
| 233 |
</with> |
|
| 234 |
</activeWhen> |
|
| 235 |
</handler> |
|
| 236 |
<handler |
|
| 237 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler" |
|
| 238 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"> |
|
| 239 |
</handler> |
|
| 240 |
<handler |
|
| 241 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler" |
|
| 242 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"> |
|
| 243 |
</handler> |
|
| 244 |
<handler |
|
| 245 |
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler" |
|
| 246 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"> |
|
| 247 |
</handler> |
|
| 248 |
<handler |
|
| 249 |
class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler" |
|
| 250 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"> |
|
| 251 |
</handler> |
|
| 252 |
<handler |
|
| 253 |
class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler" |
|
| 254 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"> |
|
| 255 |
</handler> |
|
| 256 |
<handler |
|
| 257 |
class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler" |
|
| 258 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"> |
|
| 259 |
</handler> |
|
| 260 |
<handler |
|
| 261 |
class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler" |
|
| 262 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"> |
|
| 263 |
</handler> |
|
| 264 |
<handler |
|
| 265 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler" |
|
| 266 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"> |
|
| 267 |
</handler> |
|
| 268 |
<handler |
|
| 269 |
class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler" |
|
| 270 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"> |
|
| 271 |
</handler> |
|
| 272 |
<handler |
|
| 273 |
class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType" |
|
| 274 |
commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"> |
|
| 275 |
</handler> |
|
| 276 |
</extension> |
|
| 277 |
<extension |
|
| 278 |
point="org.eclipse.core.expressions.definitions"> |
|
| 279 |
<definition |
|
| 280 |
id="isSequence"> |
|
| 281 |
<with |
|
| 282 |
variable="selection"> |
|
| 283 |
<test |
|
| 284 |
property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence"> |
|
| 285 |
</test> |
|
| 286 |
</with> |
|
| 287 |
</definition> |
|
| 288 |
<definition |
|
| 289 |
id="isSingleRead"> |
|
| 290 |
<with |
|
| 291 |
variable="selection"> |
|
| 292 |
<test |
|
| 293 |
property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead"> |
|
| 294 |
</test> |
|
| 295 |
</with> |
|
| 296 |
</definition> |
|
| 297 |
</extension> |
|
| 298 |
<extension |
|
| 299 |
point="org.eclipse.core.expressions.propertyTesters"> |
|
| 300 |
<propertyTester |
|
| 301 |
class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester" |
|
| 302 |
id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester" |
|
| 303 |
namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester" |
|
| 304 |
properties="isSequence,isSingleRead" |
|
| 305 |
type="org.eclipse.jface.viewers.IStructuredSelection"> |
|
| 306 |
</propertyTester> |
|
| 307 |
</extension> |
|
| 308 |
<extension |
|
| 309 |
point="org.eclipse.ui.bindings"> |
|
| 310 |
<scheme |
|
| 311 |
description="%scheme.description" |
|
| 312 |
id="eu.etaxonomy.taxeditor.bindings.scheme.default" |
|
| 313 |
name="%scheme.name"> |
|
| 314 |
</scheme> |
|
| 315 |
<key |
|
| 316 |
commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram" |
|
| 317 |
schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default" |
|
| 318 |
sequence="M1+O"> |
|
| 319 |
</key> |
|
| 320 |
</extension> |
|
| 321 |
|
|
| 322 |
</plugin> |
|
| eu.etaxonomy.taxeditor.molecular/pom.xml | ||
|---|---|---|
| 1 |
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" |
|
| 2 |
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> |
|
| 3 |
|
|
| 4 |
<parent> |
|
| 5 |
<groupId>eu.etaxonomy</groupId> |
|
| 6 |
<artifactId>taxeditor-parent</artifactId> |
|
| 7 |
<version>3.6.1-SNAPSHOT</version> |
|
| 8 |
</parent> |
|
| 9 |
|
|
| 10 |
<modelVersion>4.0.0</modelVersion> |
|
| 11 |
<artifactId>eu.etaxonomy.taxeditor.molecular</artifactId> |
|
| 12 |
<packaging>eclipse-plugin</packaging> |
|
| 13 |
|
|
| 14 |
<name>Molecular Bundle</name> |
|
| 15 |
<description>Provides editors, views and operations for handling molecular data and alignments</description> |
|
| 16 |
|
|
| 17 |
<!-- <build> --> |
|
| 18 |
<!-- <plugins> --> |
|
| 19 |
<!-- <plugin> --> |
|
| 20 |
<!-- <groupId>org.apache.maven.plugins</groupId> --> |
|
| 21 |
<!-- <artifactId>maven-dependency-plugin</artifactId> --> |
|
| 22 |
<!-- <version>2.4</version> --> |
|
| 23 |
<!-- <executions> --> |
|
| 24 |
<!-- <execution> --> |
|
| 25 |
<!-- <id>copy-dependencies</id> --> |
|
| 26 |
<!-- <phase>validate</phase> --> |
|
| 27 |
<!-- <goals> --> |
|
| 28 |
<!-- <goal>copy-dependencies</goal> --> |
|
| 29 |
<!-- </goals> --> |
|
| 30 |
<!-- <configuration> --> |
|
| 31 |
<!-- <includeGroupIds>info.bioinfweb.libralign, info.bioinfweb.commons.java</includeGroupIds> --> |
|
| 32 |
<!-- <includeArtifactIds>libralign-swt, libralign-core</includeArtifactIds> --> |
|
| 33 |
<!-- <outputDirectory>lib</outputDirectory> --> |
|
| 34 |
<!-- <overWriteReleases>true</overWriteReleases> --> |
|
| 35 |
<!-- <overWriteSnapshots>true</overWriteSnapshots> --> |
|
| 36 |
<!-- <excludeTransitive>true</excludeTransitive> --> |
|
| 37 |
<!-- </configuration> --> |
|
| 38 |
<!-- </execution> --> |
|
| 39 |
<!-- <execution> --> |
|
| 40 |
<!-- <id>copy-dependencies-sources</id> --> |
|
| 41 |
<!-- <phase>validate</phase> --> |
|
| 42 |
<!-- <goals> --> |
|
| 43 |
<!-- <goal>copy-dependencies</goal> --> |
|
| 44 |
<!-- </goals> --> |
|
| 45 |
<!-- <configuration> --> |
|
| 46 |
<!-- <classifier>sources</classifier> --> |
|
| 47 |
<!-- <includeArtifactIds>cdmlib-commons,cdmlib-model,cdmlib-persistence,cdmlib-remote,cdmlib-print,cdmlib-services,cdmlib-ext,cdmlib-io</includeArtifactIds> --> |
|
| 48 |
<!-- <outputDirectory>lib</outputDirectory> --> |
|
| 49 |
<!-- <overWriteReleases>true</overWriteReleases> --> |
|
| 50 |
<!-- <overWriteSnapshots>true</overWriteSnapshots> --> |
|
| 51 |
<!-- <excludeTransitive>true</excludeTransitive> --> |
|
| 52 |
<!-- <failOnMissingClassifierArtifact>false</failOnMissingClassifierArtifact> --> |
|
| 53 |
<!-- </configuration> --> |
|
| 54 |
<!-- </execution> --> |
|
| 55 |
<!-- </executions> --> |
|
| 56 |
<!-- </plugin> --> |
|
| 57 |
<!-- </plugins> --> |
|
| 58 |
<!-- </build> --> |
|
| 59 |
|
|
| 60 |
<dependencies> |
|
| 61 |
<dependency> |
|
| 62 |
<groupId>info.bioinfweb.libralign</groupId> |
|
| 63 |
<artifactId>libralign-core</artifactId> |
|
| 64 |
<version>0-SNAPSHOT</version> |
|
| 65 |
</dependency> |
|
| 66 |
<dependency> |
|
| 67 |
<groupId>info.bioinfweb.libralign</groupId> |
|
| 68 |
<artifactId>libralign-swt</artifactId> |
|
| 69 |
<version>0-SNAPSHOT</version> |
|
| 70 |
</dependency> |
|
| 71 |
<dependency> |
|
| 72 |
<groupId>info.bioinfweb.commons.java</groupId> |
|
| 73 |
<artifactId>bioinfweb-commons-swt</artifactId> |
|
| 74 |
<version>2-SNAPSHOT</version> |
|
| 75 |
</dependency> |
|
| 76 |
<dependency> |
|
| 77 |
<groupId>info.bioinfweb.commons.java</groupId> |
|
| 78 |
<artifactId>bioinfweb-commons-core</artifactId> |
|
| 79 |
<version>2-SNAPSHOT</version> |
|
| 80 |
</dependency> |
|
| 81 |
<dependency> |
|
| 82 |
<groupId>info.bioinfweb.commons.java</groupId> |
|
| 83 |
<artifactId>bioinfweb-commons-bio</artifactId> |
|
| 84 |
<version>2-SNAPSHOT</version> |
|
| 85 |
</dependency> |
|
| 86 |
<dependency> |
|
| 87 |
<groupId>info.bioinfweb.commons.java</groupId> |
|
| 88 |
<artifactId>bioinfweb-commons-swing</artifactId> |
|
| 89 |
<version>2-SNAPSHOT</version> |
|
| 90 |
</dependency> |
|
| 91 |
<dependency> |
|
| 92 |
<groupId>info.bioinfweb.tic</groupId> |
|
| 93 |
<artifactId>tic-core</artifactId> |
|
| 94 |
<version>2-SNAPSHOT</version> |
|
| 95 |
</dependency> |
|
| 96 |
</dependencies> |
|
| 97 |
|
|
| 98 |
<repositories> |
|
| 99 |
<repository> |
|
| 100 |
<id>bioinfweb-maven-repo</id> |
|
| 101 |
<name>bioinfweb repository</name> |
|
| 102 |
<url>http://bioinfweb.info/MavenRepository/</url> |
|
| 103 |
</repository> |
|
| 104 |
</repositories> |
|
| 105 |
|
|
| 106 |
</project> |
|
| eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/TaxeditorMolecularPlugin.java | ||
|---|---|---|
| 1 |
package eu.etaxonomy.taxeditor.molecular; |
|
| 2 |
|
|
| 3 |
import org.eclipse.ui.plugin.AbstractUIPlugin; |
|
| 4 |
import org.osgi.framework.BundleContext; |
|
| 5 |
|
|
| 6 |
/** |
|
| 7 |
* The activator class controls the plug-in life cycle |
|
| 8 |
*/ |
|
| 9 |
public class TaxeditorMolecularPlugin extends AbstractUIPlugin {
|
|
| 10 |
|
|
| 11 |
// The plug-in ID |
|
| 12 |
public static final String PLUGIN_ID = "eu.etaxonomy.taxeditor.molecular"; //$NON-NLS-1$ |
|
| 13 |
|
|
| 14 |
// The shared instance |
|
| 15 |
private static TaxeditorMolecularPlugin plugin; |
|
| 16 |
|
|
| 17 |
/** |
|
| 18 |
* The constructor |
|
| 19 |
*/ |
|
| 20 |
public TaxeditorMolecularPlugin() {
|
|
| 21 |
} |
|
| 22 |
|
|
| 23 |
@Override |
|
| 24 |
public void start(BundleContext context) throws Exception {
|
|
| 25 |
super.start(context); |
|
| 26 |
plugin = this; |
|
| 27 |
} |
|
| 28 |
|
|
| 29 |
@Override |
|
| 30 |
public void stop(BundleContext context) throws Exception {
|
|
| 31 |
plugin = null; |
|
| 32 |
super.stop(context); |
|
| 33 |
} |
|
| 34 |
|
|
| 35 |
/** |
|
| 36 |
* Returns the shared instance |
|
| 37 |
* |
|
| 38 |
* @return the shared instance |
|
| 39 |
*/ |
|
| 40 |
public static TaxeditorMolecularPlugin getDefault() {
|
|
| 41 |
return plugin; |
|
| 42 |
} |
|
| 43 |
|
|
| 44 |
} |
|
| eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2014 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
package eu.etaxonomy.taxeditor.molecular.editor; |
|
| 11 |
|
|
| 12 |
|
|
| 13 |
import info.bioinfweb.libralign.alignmentarea.AlignmentArea; |
|
| 14 |
import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel; |
|
| 15 |
import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter; |
|
| 16 |
import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea; |
|
| 17 |
import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea; |
|
| 18 |
import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea; |
|
| 19 |
import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent; |
|
| 20 |
import info.bioinfweb.libralign.editsettings.EditSettingsListener; |
|
| 21 |
import info.bioinfweb.libralign.model.AlignmentModel; |
|
| 22 |
import info.bioinfweb.libralign.model.AlignmentModelChangeListener; |
|
| 23 |
import info.bioinfweb.libralign.model.AlignmentModelUtils; |
|
| 24 |
import info.bioinfweb.libralign.model.adapters.StringAdapter; |
|
| 25 |
import info.bioinfweb.libralign.model.events.SequenceChangeEvent; |
|
| 26 |
import info.bioinfweb.libralign.model.events.SequenceRenamedEvent; |
|
| 27 |
import info.bioinfweb.libralign.model.events.TokenChangeEvent; |
|
| 28 |
import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel; |
|
| 29 |
import info.bioinfweb.libralign.model.tokenset.CharacterTokenSet; |
|
| 30 |
import info.bioinfweb.libralign.model.tokenset.TokenSet; |
|
| 31 |
import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList; |
|
| 32 |
import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer; |
|
| 33 |
import info.bioinfweb.libralign.pherogram.model.PherogramAreaModel; |
|
| 34 |
import info.bioinfweb.libralign.pherogram.model.ShiftChange; |
|
| 35 |
import info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider; |
|
| 36 |
import info.bioinfweb.libralign.pherogram.provider.PherogramProvider; |
|
| 37 |
import info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider; |
|
| 38 |
import info.bioinfweb.tic.SWTComponentFactory; |
|
| 39 |
|
|
| 40 |
import java.io.File; |
|
| 41 |
import java.io.IOException; |
|
| 42 |
import java.io.InputStream; |
|
| 43 |
import java.net.URI; |
|
| 44 |
import java.util.ArrayList; |
|
| 45 |
import java.util.Collection; |
|
| 46 |
import java.util.Collections; |
|
| 47 |
import java.util.Iterator; |
|
| 48 |
import java.util.List; |
|
| 49 |
import java.util.Map; |
|
| 50 |
import java.util.TreeMap; |
|
| 51 |
|
|
| 52 |
import org.biojava.bio.chromatogram.ChromatogramFactory; |
|
| 53 |
import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException; |
|
| 54 |
import org.eclipse.core.runtime.IProgressMonitor; |
|
| 55 |
import org.eclipse.swt.SWT; |
|
| 56 |
import org.eclipse.swt.widgets.Composite; |
|
| 57 |
import org.eclipse.ui.IActionBars; |
|
| 58 |
import org.eclipse.ui.IEditorInput; |
|
| 59 |
import org.eclipse.ui.IEditorPart; |
|
| 60 |
import org.eclipse.ui.IEditorSite; |
|
| 61 |
import org.eclipse.ui.PartInitException; |
|
| 62 |
import org.eclipse.ui.PlatformUI; |
|
| 63 |
import org.eclipse.ui.commands.ICommandService; |
|
| 64 |
import org.eclipse.ui.part.EditorPart; |
|
| 65 |
|
|
| 66 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
|
| 67 |
import eu.etaxonomy.cdm.api.service.molecular.ISequenceService; |
|
| 68 |
import eu.etaxonomy.cdm.model.media.MediaUtils; |
|
| 69 |
import eu.etaxonomy.cdm.model.molecular.Sequence; |
|
| 70 |
import eu.etaxonomy.cdm.model.molecular.SequenceString; |
|
| 71 |
import eu.etaxonomy.cdm.model.molecular.SingleRead; |
|
| 72 |
import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment; |
|
| 73 |
import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift; |
|
| 74 |
import eu.etaxonomy.taxeditor.model.MessagingUtils; |
|
| 75 |
import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin; |
|
| 76 |
import eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler; |
|
| 77 |
import eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler; |
|
| 78 |
import eu.etaxonomy.taxeditor.store.CdmStore; |
|
| 79 |
import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider; |
|
| 80 |
|
|
| 81 |
|
|
| 82 |
|
|
| 83 |
/** |
|
| 84 |
* Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to |
|
| 85 |
* a consensus sequence. |
|
| 86 |
* <p> |
|
| 87 |
* The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>. |
|
| 88 |
* |
|
| 89 |
* @author Ben Stöver |
|
| 90 |
* @author pplitzner |
|
| 91 |
* @date 04.08.2014 |
|
| 92 |
*/ |
|
| 93 |
public class AlignmentEditor extends EditorPart {
|
|
| 94 |
public static final String ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor"; |
|
| 95 |
|
|
| 96 |
public static final int READS_AREA_INDEX = 1; |
|
| 97 |
public static final int EDITABLE_CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1; |
|
| 98 |
public static final int CONSENSUS_HINT_AREA_INDEX = EDITABLE_CONSENSUS_AREA_INDEX + 1; |
|
| 99 |
public static final int PHEROGRAM_AREA_INDEX = 0; |
|
| 100 |
public static final int CONSENSUS_DATA_AREA_INDEX = 0; |
|
| 101 |
public static final String DEFAULT_READ_NAME_PREFIX = "Read "; |
|
| 102 |
public static final String CONSENSUS_NAME = "Consensus"; |
|
| 103 |
|
|
| 104 |
|
|
| 105 |
private final ConversationHolder conversationHolder; |
|
| 106 |
|
|
| 107 |
private final AlignmentModelChangeListener DIRTY_LISTENER = new AlignmentModelChangeListener() {
|
|
| 108 |
@Override |
|
| 109 |
public <T> void afterTokenChange(TokenChangeEvent<T> e) {
|
|
| 110 |
setDirty(); |
|
| 111 |
} |
|
| 112 |
|
|
| 113 |
@Override |
|
| 114 |
public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e) {
|
|
| 115 |
setDirty(); |
|
| 116 |
} |
|
| 117 |
|
|
| 118 |
@Override |
|
| 119 |
public <T> void afterSequenceChange(SequenceChangeEvent<T> e) {
|
|
| 120 |
setDirty(); |
|
| 121 |
} |
|
| 122 |
|
|
| 123 |
@Override |
|
| 124 |
public <T, U> void afterProviderChanged(AlignmentModel<T> oldProvider, |
|
| 125 |
AlignmentModel<U> newProvider) { // Not expected.
|
|
| 126 |
|
|
| 127 |
setDirty(); |
|
| 128 |
} |
|
| 129 |
}; |
|
| 130 |
|
|
| 131 |
private MultipleAlignmentsContainer alignmentsContainer = null; |
|
| 132 |
private final Map<Integer, SingleReadAlignment> cdmMap = new TreeMap<Integer, SingleReadAlignment>(); //TODO Move this to ContigSequenceDataProvider |
|
| 133 |
private boolean dirty = false; |
|
| 134 |
|
|
| 135 |
|
|
| 136 |
public AlignmentEditor() {
|
|
| 137 |
super(); |
|
| 138 |
conversationHolder = CdmStore.createConversation(); |
|
| 139 |
//conversationHolder = null; |
|
| 140 |
} |
|
| 141 |
|
|
| 142 |
|
|
| 143 |
private void refreshToolbarElement(String id) {
|
|
| 144 |
ICommandService commandService = |
|
| 145 |
(ICommandService)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class); |
|
| 146 |
if (commandService != null) {
|
|
| 147 |
commandService.refreshElements(id, Collections.EMPTY_MAP); |
|
| 148 |
} |
|
| 149 |
} |
|
| 150 |
|
|
| 151 |
|
|
| 152 |
private void registerEditSettingListener(MultipleAlignmentsContainer container) {
|
|
| 153 |
container.getEditSettings().addListener(new EditSettingsListener() {
|
|
| 154 |
@Override |
|
| 155 |
public void workingModeChanged(EditSettingsChangeEvent e) {} // Currently nothing to do
|
|
| 156 |
|
|
| 157 |
@Override |
|
| 158 |
public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
|
|
| 159 |
updateStatusBar(); |
|
| 160 |
refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID); |
|
| 161 |
} |
|
| 162 |
|
|
| 163 |
@Override |
|
| 164 |
public void insertChanged(EditSettingsChangeEvent e) {
|
|
| 165 |
updateStatusBar(); |
|
| 166 |
refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID); |
|
| 167 |
} |
|
| 168 |
}); |
|
| 169 |
} |
|
| 170 |
|
|
| 171 |
|
|
| 172 |
private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {
|
|
| 173 |
AlignmentArea result = new AlignmentArea(container); |
|
| 174 |
result.setAllowVerticalScrolling(false); |
|
| 175 |
result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea(), labeledArea)); |
|
| 176 |
return result; |
|
| 177 |
} |
|
| 178 |
|
|
| 179 |
|
|
| 180 |
private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
|
|
| 181 |
AlignmentArea result = new AlignmentArea(container); |
|
| 182 |
result.setAllowVerticalScrolling(allowVerticalScrolling); |
|
| 183 |
|
|
| 184 |
CharacterTokenSet tokenSet = CharacterTokenSet.newDNAInstance(); //TODO Should NUCLEOTIDE be used instead? |
|
| 185 |
AlignmentModel<Character> provider = new PackedAlignmentModel<Character>(tokenSet); |
|
| 186 |
result.setAlignmentModel(provider, false); |
|
| 187 |
provider.getChangeListeners().add(DIRTY_LISTENER); |
|
| 188 |
result.getPaintSettings().getTokenPainterList().set(0, new NucleotideTokenPainter()); |
|
| 189 |
|
|
| 190 |
return result; |
|
| 191 |
} |
|
| 192 |
|
|
| 193 |
|
|
| 194 |
private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container, |
|
| 195 |
AlignmentArea labeledArea) {
|
|
| 196 |
|
|
| 197 |
AlignmentArea result = new AlignmentArea(container); |
|
| 198 |
result.setAllowVerticalScrolling(false); |
|
| 199 |
result.getDataAreas().getBottomAreas().add( |
|
| 200 |
new ConsensusSequenceArea(result.getContentArea(), labeledArea)); |
|
| 201 |
return result; |
|
| 202 |
} |
|
| 203 |
|
|
| 204 |
|
|
| 205 |
private MultipleAlignmentsContainer getAlignmentsContainer() {
|
|
| 206 |
if (alignmentsContainer == null) {
|
|
| 207 |
alignmentsContainer = new MultipleAlignmentsContainer(); |
|
| 208 |
|
|
| 209 |
AlignmentAreaList list = alignmentsContainer.getAlignmentAreas(); |
|
| 210 |
AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true); |
|
| 211 |
list.add(createIndexArea(alignmentsContainer, readsArea)); |
|
| 212 |
list.add(readsArea); // Make sure READS_AREA_INDEX is correct. |
|
| 213 |
list.add(createEditableAlignmentArea(alignmentsContainer, false)); // Make sure COMSENSUS_AREA_INDEX is correct. |
|
| 214 |
list.add(createConsensusHintArea(alignmentsContainer, readsArea)); |
|
| 215 |
|
|
| 216 |
registerEditSettingListener(alignmentsContainer); |
|
| 217 |
} |
|
| 218 |
return alignmentsContainer; |
|
| 219 |
} |
|
| 220 |
|
|
| 221 |
|
|
| 222 |
public AlignmentArea getReadsArea() {
|
|
| 223 |
return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX); |
|
| 224 |
} |
|
| 225 |
|
|
| 226 |
|
|
| 227 |
private AlignmentArea getEditableConsensusArea() {
|
|
| 228 |
return getAlignmentsContainer().getAlignmentAreas().get(EDITABLE_CONSENSUS_AREA_INDEX); |
|
| 229 |
} |
|
| 230 |
|
|
| 231 |
|
|
| 232 |
public boolean hasPherogram(int sequenceID) {
|
|
| 233 |
return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX; |
|
| 234 |
} |
|
| 235 |
|
|
| 236 |
|
|
| 237 |
public PherogramArea getPherogramArea(int sequenceID) {
|
|
| 238 |
if (hasPherogram(sequenceID)) {
|
|
| 239 |
return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX); |
|
| 240 |
} |
|
| 241 |
else {
|
|
| 242 |
return null; |
|
| 243 |
} |
|
| 244 |
} |
|
| 245 |
|
|
| 246 |
|
|
| 247 |
private ConsensusSequenceArea getConsensusHintDataArea() {
|
|
| 248 |
return (ConsensusSequenceArea)getAlignmentsContainer().getAlignmentAreas(). |
|
| 249 |
get(CONSENSUS_HINT_AREA_INDEX).getDataAreas().getBottomAreas(). |
|
| 250 |
get(CONSENSUS_DATA_AREA_INDEX); |
|
| 251 |
} |
|
| 252 |
|
|
| 253 |
|
|
| 254 |
@Deprecated //TODO Remove as soon as testing period is over |
|
| 255 |
private void createTestContents() {
|
|
| 256 |
// Just for testing: |
|
| 257 |
try {
|
|
| 258 |
addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1").toURI(), false);
|
|
| 259 |
//addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI(), false);
|
|
| 260 |
addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/Test_qualityScore.scf").toURI(), false);
|
|
| 261 |
|
|
| 262 |
// Add test consensus sequence: |
|
| 263 |
AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel(); |
|
| 264 |
int id = consensusModel.addSequence(CONSENSUS_NAME); |
|
| 265 |
Collection<Object> tokens = new ArrayList<Object>(); // First save tokens in a collection to avoid GUI updated for each token. |
|
| 266 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("A"));
|
|
| 267 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C"));
|
|
| 268 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G"));
|
|
| 269 |
tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T"));
|
|
| 270 |
consensusModel.insertTokensAt(id, 0, tokens); |
|
| 271 |
} |
|
| 272 |
catch (Exception e) {
|
|
| 273 |
throw new RuntimeException(e); |
|
| 274 |
} |
|
| 275 |
} |
|
| 276 |
|
|
| 277 |
|
|
| 278 |
private void readCDMData(Sequence sequenceNode) {
|
|
| 279 |
//TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated). |
|
| 280 |
|
|
| 281 |
// Add reads: |
|
| 282 |
for (SingleReadAlignment singleReadAlignment : sequenceNode.getSingleReadAlignments()) {
|
|
| 283 |
try {
|
|
| 284 |
SingleRead pherogramInfo = singleReadAlignment.getSingleRead(); |
|
| 285 |
URI uri = null; |
|
Also available in: Unified diff
Initial import of plugin files