Dependency refactoring
authorPatric Plitzner <p.plitzner@bgbm.org>
Wed, 15 Jul 2015 11:00:51 +0000 (11:00 +0000)
committerPatric Plitzner <p.plitzner@bgbm.org>
Wed, 15 Jul 2015 11:00:51 +0000 (11:00 +0000)
Arranged classes and classpath in accordance to other taxeditor projects.

28 files changed:
.gitattributes
eu.etaxonomy.taxeditor.molecular/.classpath
eu.etaxonomy.taxeditor.molecular/META-INF/MANIFEST.MF
eu.etaxonomy.taxeditor.molecular/build.properties
eu.etaxonomy.taxeditor.molecular/plugin.xml
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/TaxeditorMolecularPlugin.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/TaxeditorMolecularPlugin.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditorInput.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditorInput.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/PherogramMouseListener.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/PherogramMouseListener.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/PherogramViewPart.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/editor/PherogramViewPart.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractAlignmentEditorHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/AbstractAlignmentEditorHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractPherogramComponentHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/AbstractPherogramComponentHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ChangePherogramQualityOutputType.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ChangePherogramQualityOutputType.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CreateConsensusSequenceHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CreateConsensusSequenceHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramLeftHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramLeftHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramRightHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramRightHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/EditSequenceHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/EditSequenceHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/HandlerTools.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/HandlerTools.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/LoadPherogramHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/LoadPherogramHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ReverseComplementHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ReverseComplementHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/SpecimenPropertyTester.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/SpecimenPropertyTester.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleInsertOverwriteHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleInsertOverwriteHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleLeftRightInsertionHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleLeftRightInsertionHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramBaseCallLinesHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramBaseCallLinesHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramProbabilitiesHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramProbabilitiesHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/UpdateConsensusSequenceHandler.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/UpdateConsensusSequenceHandler.java with 100% similarity]
eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/package-info.java [moved from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/package-info.java with 73% similarity]

index a09fc596d25eed912f750a0f7a07d76c915984f7..0be4dd5af971964ec9d6b4d2d190691719b90f9f 100644 (file)
@@ -961,29 +961,29 @@ 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.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/TaxeditorMolecularPlugin.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditor.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/AlignmentEditorInput.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/PherogramMouseListener.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/editor/PherogramViewPart.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractAlignmentEditorHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AbstractPherogramComponentHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ChangePherogramQualityOutputType.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CreateConsensusSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramLeftHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/CutPherogramRightHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/EditSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/HandlerTools.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/LoadPherogramHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ReverseComplementHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ShowPherogramHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/SpecimenPropertyTester.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleInsertOverwriteHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleLeftRightInsertionHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramBaseCallLinesHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/ToggleShowPherogramProbabilitiesHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/UpdateConsensusSequenceHandler.java -text
+eu.etaxonomy.taxeditor.molecular/src/main/java/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
index fa2d0d0b9f1d616d9dfa19fb31549200a92ab5ed..547395172fc84295be21c3089108760e25a9f9ed 100644 (file)
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
+       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
+       <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+       <classpathentry including="**/*.java" kind="src" path="src/main/java"/>
        <classpathentry exported="true" kind="lib" path="lib/tic-swt-2-SNAPSHOT.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/core-1.9.2-SNAPSHOT.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2-SNAPSHOT.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/tic-core-2-SNAPSHOT.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/libralign-biojava1-0-SNAPSHOT.jar"/>
-       <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
-       <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
-       <classpathentry including="**/*.java" kind="src" path="src"/>
        <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-bio-2-SNAPSHOT.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-core-2-SNAPSHOT.jar"/>
        <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swing-2-SNAPSHOT.jar"/>
index 615af5b9eb89ebe16534a25878ba324f51cf48af..e6cae679e6a1cfb67b15259763780795d1dc338f 100644 (file)
@@ -7,14 +7,16 @@ Bundle-Activator: eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin
 Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,
  org.eclipse.core.expressions,
- eu.etaxonomy.taxeditor.cdmlib,
- eu.etaxonomy.taxeditor.store,
- eu.etaxonomy.taxeditor.editor,
- eu.etaxonomy.taxeditor.bulkeditor
+ org.eclipse.ui.ide,
+ eu.etaxonomy.taxeditor.bulkeditor;bundle-version="3.6.1",
+ eu.etaxonomy.taxeditor.cdmlib;bundle-version="3.6.1",
+ eu.etaxonomy.taxeditor.editor;bundle-version="3.6.1",
+ eu.etaxonomy.taxeditor.store;bundle-version="3.6.1"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.6
 Bundle-ActivationPolicy: lazy
 Bundle-Vendor: EDIT
-Bundle-ClassPath: lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
+Bundle-ClassPath: .,
+ lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
  lib/bioinfweb-commons-core-2-SNAPSHOT.jar,
  lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,
  lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,
@@ -27,4 +29,5 @@ Bundle-ClassPath: lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
  lib/tic-swt-2-SNAPSHOT.jar
 Export-Package: eu.etaxonomy.taxeditor.molecular,
  eu.etaxonomy.taxeditor.molecular.editor,
- eu.etaxonomy.taxeditor.molecular.handler
+ eu.etaxonomy.taxeditor.molecular.handler,
+ info.bioinfweb.commons
index 2884574bb34084b37b0a4ee9a9a151a5e10e06d1..76050db96f55f3206105c6228679eeb29edb587c 100644 (file)
@@ -1,5 +1,6 @@
-output.. = bin/
+source.. = src/main/java/
 bin.includes = META-INF/,\
+               .,\
                plugin.xml,\
                icons/,\
                OSGI-INF/,\
@@ -14,8 +15,3 @@ bin.includes = META-INF/,\
                lib/sequencing-1.9.2-SNAPSHOT.jar,\
                lib/tic-core-2-SNAPSHOT.jar,\
                lib/tic-swt-2-SNAPSHOT.jar
-src.includes = src/,\
-               plugin.xml,\
-               icons/,\
-               OSGI-INF/,\
-               META-INF/
index 4216fd92a51856b14de71af97999faa256986508..14d770ace9553dcadb1c3aa11755d864de7bbaf6 100644 (file)
                id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
                name="Change quality output">
          </command>
-         <command
-               defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.OpenAlignmentEditorHandler"
-               id="eu.etaxonomy.taxeditor.molecular.OpenAlignmentEditor"
-               name="Open Alignment Editor">
-         </command>
          <command
                id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
                name="Load Pherogram">
                      icon="icons/pherogram-insert-left-16x16.png"
                      style="push">
                   <visibleWhen
-                        checkEnabled="false">
+                        checkEnabled="true">
                      <with
                            variable="activePartId">
                         <equals
                      commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
                      style="push">
                </command>
-               <visibleWhen
+               <!--visibleWhen
                      checkEnabled="true">
                   <with
                         variable="activePartId">
                            value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
                      </equals>
                   </with>
-               </visibleWhen>
+               </visibleWhen-->
             </menu>
          </menuContribution>
          <menuContribution
similarity index 73%
rename from eu.etaxonomy.taxeditor.molecular/src/eu/etaxonomy/taxeditor/molecular/handler/package-info.java
rename to eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/package-info.java
index 8c761e387b5fbee4843572c90afc57dd81000e5a..b1e81d4caa541cf59e7504b5ddb734fad4675acf 100644 (file)
@@ -9,7 +9,7 @@
  */\r
 /**\r
  * Contains handlers that trigger actions in an active instance of\r
- * {@link eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor}. Handlers opening\r
+ * {@link main.java.eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor}. Handlers opening\r
  * an alignment editor or pherogram view are not contained in here.\r
  *\r
  * @author Ben Stöver\r