X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=6e3024d7f0df99ad535d96128c74642e47beb042;hb=b28bddf12e2791a019fba9c233d46407deb65976;hp=34ccf9cafe663687b72b9c73d517464e9cad6da8;hpb=ead72caff9aef9b7103dbb15907aeae777200832;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 34ccf9c..6e3024d 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -768,7 +768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
-    showSeqFeatures.setSelected(av.showSequenceFeatures);
+    showSeqFeatures.setSelected(av.isShowSequenceFeatures());
     hiddenMarkers.setState(av.showHiddenMarkers);
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
@@ -1076,10 +1076,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 .lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
-      success = new Jalview2XML().SaveAlignment(this, file, shortName);
+      /*
+       * First save any linked Chimera session.
+       */
+      Desktop.instance.saveChimeraSessions(file);
+
+      success = new Jalview2XML().saveAlignment(this, file, shortName);
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.successfully_saved_to_file_in_format", new String[]
+              "label.successfully_saved_to_file_in_format", new Object[]
               { fileName, format }));
 
     }
@@ -1305,11 +1310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(alignPanel,
-            viewport.isShowAnnotation() ? viewport.getAlignment()
-                    .getAlignmentAnnotation() : null, viewport
-                    .getAlignment().getGroups(), ((Alignment) viewport
-                    .getAlignment()).alignmentProperties);
+    new AnnotationExporter().exportAnnotations(alignPanel);
   }
 
   @Override
@@ -1771,20 +1772,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Vector hiddenColumns = null;
+    ArrayList<int[]> hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new Vector();
+      hiddenColumns = new ArrayList<int[]>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
               .getSelectionGroup().getEndRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
-              .size(); i++)
+      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) viewport.getColumnSelection()
-                .getHiddenColumns().elementAt(i);
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
-          hiddenColumns.addElement(new int[]
+          hiddenColumns.add(new int[]
           { region[0] - hiddenOffset, region[1] - hiddenOffset });
         }
       }
@@ -2111,10 +2109,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (Desktop.jalviewClipboard != null
                 && Desktop.jalviewClipboard[2] != null)
         {
-          Vector hc = (Vector) Desktop.jalviewClipboard[2];
-          for (int i = 0; i < hc.size(); i++)
+          List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+          for (int[] region : hc)
           {
-            int[] region = (int[]) hc.elementAt(i);
             af.viewport.hideColumns(region[0], region[1]);
           }
         }
@@ -2171,10 +2168,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Desktop.jalviewClipboard != null
               && Desktop.jalviewClipboard[2] != null)
       {
-        Vector hc = (Vector) Desktop.jalviewClipboard[2];
-        for (int i = 0; i < hc.size(); i++)
+        List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+        for (int region[] : hc)
         {
-          int[] region = (int[]) hc.elementAt(i);
           af.viewport.hideColumns(region[0], region[1]);
         }
       }
@@ -3092,7 +3088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
             .isSelected());
-    if (viewport.getShowSequenceFeaturesHeight())
+    if (viewport.isShowSequenceFeaturesHeight())
     {
       // ensure we're actually displaying features
       viewport.setShowSequenceFeatures(true);
@@ -4888,7 +4884,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       featuresFile = new FeaturesFile(file, type).parse(viewport
               .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
-              .getFeatureRenderer().featureColours, false,
+              .getFeatureRenderer().getFeatureColours(), false,
               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
     {
@@ -4897,7 +4893,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (featuresFile)
     {
-      viewport.showSequenceFeatures = true;
+      viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
       if (alignPanel.getSeqPanel().seqCanvas.fr != null)
       {
@@ -5154,7 +5150,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // try to parse as annotation.
       boolean isAnnotation = (format == null || format
               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
-              .readAnnotationFile(viewport.getAlignment(), file, protocol)
+              .annotateAlignmentView(viewport, file, protocol)
               : false;
 
       if (!isAnnotation)
@@ -5759,6 +5755,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignPanel.paintAlignment(true);
     }
   }
+  public void clearAlignmentSeqRep()
+  {
+    // TODO refactor alignmentseqrep to controller
+    if (viewport.getAlignment().hasSeqrep()) {
+      viewport.getAlignment().setSeqrep(null);
+      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+      alignPanel.updateAnnotation();
+      alignPanel.paintAlignment(true);
+    }
+  }
 
   @Override
   protected void createGroup_actionPerformed(ActionEvent e)