Context menu entry for exporting alignment files added.

ExportSingleReadAlignmentHandler renamed to ExportSequenceToFileHandler.

diff --git a/.gitattributes b/.gitattributes
index d993a4e0e57e6093c895c63dd41c4818ac931708..d3b0c2db22c41e97f051afaedbb4df220f7b04c6 100644 (file)
--- a/.gitattributes
+++ b/.gitattributes
@@ -1987,7 +1987,7 @@ src/site/site.xml -text
 **/feature.xml merge=ours
 eu.etaxonomy.taxeditor.cdmlib/.classpath merge=ours
 eu.etaxonomy.taxeditor.cdmlib/build.properties merge=ours
-eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSingleReadAlignmentHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java -text
 eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/CDMSequenceMatrixAdapter.java -text
 eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/ExportSingleReadAlignmentWizardPage.java -text
 eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/io/SequenceIDIterator.java -text

diff --git a/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle.properties b/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle.properties
index 06f7cf3213dc21d85dd4dd75ff3464be06fb1563..685f5ce7b010fff78f2fb936418a41134de3dab8 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle.properties
+++ b/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle.properties
@@ -3,6 +3,7 @@ editor.ALIGNMENT_EDITOR = Alignment Editor
 view.PHEROGRAM_VIEW = Pherogram View
 command.EDIT_SEQUENCE = Edit Sequence
 command.name.SHOW_PHEROGRAM = Show Pherogram
+command.name.EXPORT_SEQUENCE_TO_FILE = Export to alignment file
 command.name.CUT_PHEROGRAM_LEFT = Cut pherogram left
 command.name.CUT_PHEROGRAM_RIGHT = Cut pherogram right
 command.name.REVERSE_COMPLEMENT_SELECTED_ROWS = Reverse complement selected rows
@@ -18,4 +19,5 @@ command.TOGGLE_INSERT_OVERWRITE = Toggle insert/overwrite
 menu.ALIGNMENT_EDITOR = Alignment Editor
 menu.label.PHEROGRAM_VIEW = Pherogram View
 command.label.EDIT_SEQUENCE = Edit Sequence
+command.label.EXPORT_SEQUENCE_TO_FILE = Export to alignment file
 command.label.SHOW_PHEROGRAM = Show Pherogram
\ No newline at end of file

diff --git a/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle_de.properties b/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle_de.properties
index 59036928e0bf55b02f84a480b49a42a582881a3f..2fee24384be8a2864f0ab084b78bd0662a48f0ba 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle_de.properties
+++ b/eu.etaxonomy.taxeditor.molecular/OSGI-INF/l10n/bundle_de.properties
@@ -3,6 +3,7 @@ editor.ALIGNMENT_EDITOR = Alignment Editor
 view.PHEROGRAM_VIEW = PherogramView
 command.EDIT_SEQUENCE = Edit Sequence
 command.name.SHOW_PHEROGRAM = Show Pherogram
+command.name.EXPORT_SEQUENCE_TO_FILE = Alignmentdatei exportieren
 command.name.CUT_PHEROGRAM_LEFT = Cut pherogram left
 command.name.CUT_PHEROGRAM_RIGHT = Cut pherogram right
 command.name.REVERSE_COMPLEMENT_SELECTED_ROWS = Reverse complement selected rows
@@ -18,4 +19,5 @@ command.TOGGLE_INSERT_OVERWRITE = Toggle insert/overwrite
 menu.ALIGNMENT_EDITOR = Alignment Editor
 menu.label.PHEROGRAM_VIEW = Pherogram View
 command.label.EDIT_SEQUENCE = Edit Sequence
+command.label.EXPORT_SEQUENCE_TO_FILE = Alignmentdatei exportieren
 command.label.SHOW_PHEROGRAM = Show Pherogram
\ No newline at end of file

diff --git a/eu.etaxonomy.taxeditor.molecular/plugin.xml b/eu.etaxonomy.taxeditor.molecular/plugin.xml
index 78b734fd1ad72db0d93c26f003d3331af3159af4..7df2be1afbbc52fb9c3a097839186d5dbee532e1 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/plugin.xml
+++ b/eu.etaxonomy.taxeditor.molecular/plugin.xml
@@ -76,6 +76,11 @@
                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
                name="%command.name.TOGGLE_LEFT_RIGHT_INSERTION">
          </command>
+         <command
+               defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ExportSequenceToFileHandler"
+               id="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"
+               name="%command.name.EXPORT_SEQUENCE_TO_FILE">
+         </command>
       </extension>
       <extension
             point="org.eclipse.ui.menus">
@@ -197,6 +202,17 @@
                   </reference>
                </visibleWhen>
             </command>
+            <command
+                  commandId="eu.etaxonomy.taxeditor.molecular.exportSequenceToFile"
+                  label="%command.label.EXPORT_SEQUENCE_TO_FILE"
+                  style="push">
+               <visibleWhen
+                     checkEnabled="true">
+                  <reference
+                        definitionId="isSequence">
+                  </reference>
+               </visibleWhen>
+            </command>
             <command
                   commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
                   label="%command.label.SHOW_PHEROGRAM"

diff --git a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSingleReadAlignmentHandler.java b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java
similarity index 95%
rename from eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSingleReadAlignmentHandler.java
rename to eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java
index e99f9856fdf27a0301f92e62e0b025062ec2a00c..4ccb4d636ef60e12a7dcac2d8aa67d3c58c3ef07 100644 (file)
--- a/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSingleReadAlignmentHandler.java
+++ b/eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ExportSequenceToFileHandler.java
@@ -41,7 +41,7 @@ import eu.etaxonomy.taxeditor.molecular.io.CDMSequenceMatrixAdapter;
  * @author Ben Stöver\r
  * @date 24.04.2016\r
  */\r
-public class ExportSingleReadAlignmentHandler extends AbstractHandler {\r
+public class ExportSequenceToFileHandler extends AbstractHandler {\r
     private static final JPhyloIOReaderWriterFactory factory = new JPhyloIOReaderWriterFactory();\r
 \r
 \r