Further adjustments to recent changes in LibrAlign.

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 057d71e18a17d17b12f19e05b94b7b284efb4b64..439f1c334e4e4e65654d343738c9aed7ed21c2d4 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
@@ -13,6 +13,7 @@ package eu.etaxonomy.taxeditor.editor.molecular;
 import info.bioinfweb.jphyloio.events.TokenSetType;
 import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
 import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
+import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter;
 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
 import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
 import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramAlignmentModel;
@@ -163,15 +164,15 @@ public class AlignmentEditor extends EditorPart {
     }
 
 
-    private AlignmentArea createIndexArea(MultipleAlignmentsContainer container) {
+  private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(false);
-               result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea()));
+               result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea(), labeledArea));
                return result;
-    }
+  }
 
 
-    private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
+  private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(allowVerticalScrolling);
 
@@ -180,6 +181,7 @@ public class AlignmentEditor extends EditorPart {
                AlignmentModel<NucleotideCompound> provider = new PackedAlignmentModel<NucleotideCompound>(tokenSet);
                result.setAlignmentModel(provider, false);
                provider.getChangeListeners().add(DIRTY_LISTENER);
+               result.getPaintSettings().getTokenPainterList().set(0, new NucleotideTokenPainter());
 
                return result;
        }
@@ -188,12 +190,12 @@ public class AlignmentEditor extends EditorPart {
     private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
                AlignmentArea labeledArea) {
 
-               AlignmentArea result = new AlignmentArea(container);
-               result.setAllowVerticalScrolling(false);
-               result.getDataAreas().getBottomAreas().add(
-                               new ConsensusSequenceArea(result.getContentArea(), labeledArea));
-               return result;
-    }
+               AlignmentArea result = new AlignmentArea(container);
+               result.setAllowVerticalScrolling(false);
+               result.getDataAreas().getBottomAreas().add(
+                               new ConsensusSequenceArea(result.getContentArea(), labeledArea));
+               return result;
+         }
 
 
     private MultipleAlignmentsContainer getAlignmentsContainer() {
@@ -201,8 +203,8 @@ public class AlignmentEditor extends EditorPart {
                alignmentsContainer = new MultipleAlignmentsContainer();
 
                AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
-               list.add(createIndexArea(alignmentsContainer));
                AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
+        list.add(createIndexArea(alignmentsContainer, readsArea));
                list.add(readsArea);  // Make sure READS_AREA_INDEX is correct.
                list.add(createEditableAlignmentArea(alignmentsContainer, false));  // Make sure COMSENSUS_AREA_INDEX is correct.
                list.add(createConsensusHintArea(alignmentsContainer, readsArea));
@@ -282,10 +284,10 @@ public class AlignmentEditor extends EditorPart {
 
 
        /* (non-Javadoc)
-     * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
-     */
-    @Override
-    public void createPartControl(Composite parent) {
+   * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
+   */
+  @Override
+  public void createPartControl(Composite parent) {
                getAlignmentsContainer().createSWTWidget(parent, SWT.NONE);
                updateStatusBar();
 
@@ -306,10 +308,10 @@ public class AlignmentEditor extends EditorPart {
                        throw new IllegalArgumentException("The editor input must have the type " +
                                        AlignmentEditorInput.class.getCanonicalName());  //TODO What should be done here?
                }
-    }
+       }
 
 
-    private void updateStatusBar() {
+  private void updateStatusBar() {
         IActionBars bars = getEditorSite().getActionBars();
         bars.getStatusLineManager().setMessage("Edit mode: " +
                        (getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + "  " +