PherogramViewPart that is started from within AlignmentEditor now uses a shared...

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java
index 149e5ceb8b82885fda4a912f642bc7e2332f2167..8d7d2b242617a4e868ad3ab37e3b2b888374c9b6 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java
@@ -1,18 +1,20 @@
 package eu.etaxonomy.taxeditor.editor.handler;\r
 \r
 \r
-import java.net.URI;\r
+import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;\r
 \r
 import org.eclipse.core.commands.AbstractHandler;\r
 import org.eclipse.core.commands.ExecutionEvent;\r
 import org.eclipse.core.commands.ExecutionException;\r
 import org.eclipse.jface.viewers.ISelection;\r
 import org.eclipse.jface.viewers.TreeNode;\r
+import org.eclipse.ui.PartInitException;\r
 import org.eclipse.ui.handlers.HandlerUtil;\r
 \r
 import eu.etaxonomy.cdm.model.media.MediaUtils;\r
 import eu.etaxonomy.cdm.model.molecular.SingleRead;\r
 import eu.etaxonomy.taxeditor.editor.EditorUtil;\r
+import eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor;\r
 import eu.etaxonomy.taxeditor.editor.molecular.PherogramViewPart;\r
 import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
 \r
@@ -20,29 +22,33 @@ import eu.etaxonomy.taxeditor.model.MessagingUtils;
 \r
 /**\r
  * Displays an undistorted pherogram with {@link PherogramViewPart}.\r
- * \r
+ *\r
  * @author Ben Stöver\r
  *\r
  */\r
 public class ShowPherogramHandler extends AbstractHandler {\r
-       public static void showPherogram(URI uri) {\r
-               try {\r
-                       PherogramViewPart.createView(uri);\r
-               }\r
-               catch (Exception e) {\r
-                       MessagingUtils.errorDialog("Error", null, e.getLocalizedMessage(), "eu.etaxonomy.taxeditor.editor",  //TODO Is null a valid value here? \r
-                                       e, false);  //TODO set pluginID\r
-               }                       \r
+       public static void showPherogram(PherogramComponentModel model) throws PartInitException {\r
+               PherogramViewPart.createView(model);\r
        }\r
-       \r
-       \r
+\r
+\r
        @Override\r
        public Object execute(ExecutionEvent event) throws ExecutionException {\r
                ISelection currentSelection = HandlerUtil.getCurrentSelection(event);\r
                TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);\r
                if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof SingleRead) {\r
-                       showPherogram(MediaUtils.getFirstMediaRepresentationPart(\r
-                                       ((SingleRead)treeNodeOfSelection.getValue()).getPherogram()).getUri());\r
+//                 SingleRead singleRead = (SingleRead)treeNodeOfSelection.getValue();\r
+//                 singleRead.get\r
+                   //TODO Can the parent node (containing the cut positions) be extracted from SingleRead?\r
+\r
+                       try {\r
+                           showPherogram(new PherogramComponentModel(AlignmentEditor.readPherogram(MediaUtils.getFirstMediaRepresentationPart(\r
+                           ((SingleRead)treeNodeOfSelection.getValue()).getPherogram()).getUri())));\r
+                       }\r
+               catch (Exception e) {\r
+                   MessagingUtils.errorDialog("Error", null, e.getLocalizedMessage(), "eu.etaxonomy.taxeditor.editor",  //TODO Is null a valid value here?\r
+                           e, false);  //TODO set pluginID\r
+               }\r
         }\r
         return null;\r
     }\r

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
index 8d44ea247014a2be6f7e85e9f7bb17c8177f000d..48b7c7f8d5b1773260742f418049e5f61a90ef35 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
@@ -686,7 +686,7 @@ public class AlignmentEditor extends EditorPart {
                }
 
                // Add pherogram area to GUI:
-               pherogramArea.addMouseListener(new PherogramMouseListener(pherogramURI));
+               pherogramArea.addMouseListener(new PherogramMouseListener(pherogramArea));
                getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
 
                // Save source URI:

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java
index 26191e10fcebede2a87aa300407af82ce28d29bd..fd95c09cef7fbbf11acc662097df59e1bcd0e7ce 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java
@@ -11,10 +11,12 @@ package eu.etaxonomy.taxeditor.editor.molecular;
 \r
 import info.bioinfweb.commons.tic.input.TICMouseAdapter;\r
 import info.bioinfweb.commons.tic.input.TICMouseEvent;\r
+import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;\r
 \r
-import java.net.URI;\r
+import org.eclipse.ui.PartInitException;\r
 \r
 import eu.etaxonomy.taxeditor.editor.handler.ShowPherogramHandler;\r
+import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
 \r
 \r
 \r
@@ -25,19 +27,25 @@ import eu.etaxonomy.taxeditor.editor.handler.ShowPherogramHandler;
  * @date 25.11.2014\r
  */\r
 public class PherogramMouseListener extends TICMouseAdapter {\r
-       private final URI uri;\r
+       private final PherogramArea area;\r
 \r
 \r
-       public PherogramMouseListener(URI uri) {\r
+       public PherogramMouseListener(PherogramArea area) {\r
                super();\r
-               this.uri = uri;\r
+               this.area = area;\r
        }\r
 \r
 \r
        @Override\r
        public void mousePressed(TICMouseEvent event) {\r
                if (event.getClickCount() == 2) {  // Double click\r
-                       ShowPherogramHandler.showPherogram(uri);\r
+                       try {\r
+                           ShowPherogramHandler.showPherogram(area.getModel());\r
+                       }\r
+                       catch (PartInitException e) {\r
+                MessagingUtils.errorDialog("Unable to create pherogram view", null, e.getLocalizedMessage(),\r
+                        "eu.etaxonomy.taxeditor.editor",  e, false);  //TODO set pluginID\r
+                       }\r
                }\r
        }\r
 }\r

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java
index 1d43dd7150246139c5810c51425465d33766d963..752ef9e1d379734f563d19c9e989ba35da0a9c91 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java
@@ -10,16 +10,9 @@ package eu.etaxonomy.taxeditor.editor.molecular;
 \r
 \r
 import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;\r
-import info.bioinfweb.libralign.pherogram.model.PherogramAreaModel;\r
 import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;\r
-import info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView;\r
 import info.bioinfweb.libralign.pherogram.view.PherogramView;\r
 \r
-import java.io.IOException;\r
-import java.net.MalformedURLException;\r
-import java.net.URI;\r
-\r
-import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;\r
 import org.eclipse.swt.SWT;\r
 import org.eclipse.swt.widgets.Composite;\r
 import org.eclipse.ui.PartInitException;\r
@@ -38,16 +31,14 @@ import org.eclipse.ui.part.ViewPart;
 public class PherogramViewPart extends ViewPart {\r
     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.PherogramView";\r
 \r
-    private URI uri = null;\r
     private PherogramView pherogramView = null;\r
 \r
 \r
-    public static PherogramViewPart createView(URI uri) throws PartInitException, MalformedURLException,\r
-               UnsupportedChromatogramFormatException, IOException {\r
-\r
-       PherogramViewPart view = (PherogramViewPart)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().showView(ID);\r
-       view.setURI(uri);\r
-       return view;\r
+    public static PherogramViewPart createView(PherogramComponentModel model) throws PartInitException {\r
+        PherogramViewPart view = (PherogramViewPart)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().showView(ID);\r
+        view.getPherogramView().getTraceCurveView().setModel(model);\r
+        view.getPherogramView().assignSize();\r
+        return view;\r
     }\r
 \r
 \r
@@ -64,25 +55,6 @@ public class PherogramViewPart extends ViewPart {
        }\r
 \r
 \r
-       public URI getURI() {\r
-               return uri;\r
-       }\r
-\r
-\r
-       protected void setURI(URI uri) throws MalformedURLException, IOException, UnsupportedChromatogramFormatException {\r
-               this.uri = uri;\r
-               PherogramTraceCurveView view = getPherogramView().getTraceCurveView();\r
-               if ((view.getModel() == null) || (view.getModel() instanceof PherogramAreaModel)) {  // Avoid changing the provider of a model that is used elsewhere\r
-                   view.setModel(new PherogramComponentModel(AlignmentEditor.readPherogram(uri)));\r
-               }\r
-               else {\r
-                   getPherogramView().getTraceCurveView().getModel().setProvider(AlignmentEditor.readPherogram(uri));\r
-               }\r
-               //TODO Refactor to use model from PherogramArea, if present, to have cut positions.\r
-               getPherogramView().assignSize();\r
-       }\r
-\r
-\r
        @Override\r
        public void createPartControl(Composite parent) {\r
                getPherogramView().createSWTWidget(parent, SWT.NONE);\r