X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=0c8c8a688b27ff4bb8f7d981f0529455f91ad3c9;hb=b55254252bf3878bb7cfd68f7a3dc4b064f3d9c8;hp=5b812c2aa54add75db8337146a9fe59bb340c3b2;hpb=5b0949ce83f4ae4f1327fe386340064c83d88178;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5b812c2..0c8c8a6 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1392,13 +1392,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void exportFeatures_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportFeatures(alignPanel);
+    new AnnotationExporter(alignPanel).exportFeatures();
   }
 
   @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(alignPanel);
+    new AnnotationExporter(alignPanel).exportAnnotations();
   }
 
   @Override
@@ -1828,7 +1828,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
-    System.gc();
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -1864,23 +1863,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
-      ArrayList<int[]> hiddenRegions = viewport.getAlignment()
-              .getHiddenColumns().getHiddenColumnsCopy();
-      for (int[] region : hiddenRegions)
-      {
-        if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
-        {
-          hiddenColumns
-                  .add(new int[]
-                  { region[0] - hiddenOffset, region[1] - hiddenOffset });
-        }
-      }
+
+      // create new HiddenColumns object with copy of hidden regions
+      // between startRes and endRes, offset by startRes
+      hiddenColumns = new HiddenColumns(
+              viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+              hiddenCutoff, hiddenOffset);
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs,
@@ -2209,11 +2202,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (Desktop.jalviewClipboard != null
                 && Desktop.jalviewClipboard[2] != null)
         {
-          List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
-          for (int[] region : hc)
-          {
-            af.viewport.hideColumns(region[0], region[1]);
-          }
+          HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+          af.viewport.setHiddenColumns(hc);
         }
 
         // >>>This is a fix for the moment, until a better solution is
@@ -2268,11 +2258,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Desktop.jalviewClipboard != null
               && Desktop.jalviewClipboard[2] != null)
       {
-        List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
-        for (int region[] : hc)
-        {
-          af.viewport.hideColumns(region[0], region[1]);
-        }
+        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+        af.viewport.setHiddenColumns(hc);
       }
 
       // >>>This is a fix for the moment, until a better solution is
@@ -3273,6 +3260,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 alignPanel.setOverviewPanel(null);
               };
             });
+    if (getKeyListeners().length > 0)
+    {
+      frame.addKeyListener(getKeyListeners()[0]);
+    }
 
     alignPanel.setOverviewPanel(overview);
   }
@@ -3337,6 +3328,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+            viewport,
             viewport.getAlignment(), viewport.getHiddenRepSequences());
     changeColour(cs);
   }
@@ -4473,17 +4465,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                      || JvOptionPane.showConfirmDialog(thisaf,
-                              MessageManager.formatMessage(
-                                      "label.automatically_associate_structure_files_with_sequences_same_name",
-                                      new Object[]
-                                      { Integer.valueOf(filesmatched.size())
-                                              .toString() }),
-                              MessageManager.getString(
-                                      "label.automatically_associate_structure_files_by_name"),
-                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
+              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              if (!autoAssociate)
+              {
+                String msg = MessageManager.formatMessage(
+                        "label.automatically_associate_structure_files_with_sequences_same_name",
+                        new Object[]
+                        { Integer.valueOf(filesmatched.size())
+                                .toString() });
+                String ttl = MessageManager.getString(
+                        "label.automatically_associate_structure_files_by_name");
+                int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+                        ttl, JvOptionPane.YES_NO_OPTION);
+                autoAssociate = choice == JvOptionPane.YES_OPTION;
+              }
+              if (autoAssociate)
               {
                 for (Object[] fm : filesmatched)
                 {
@@ -4509,6 +4505,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   alignPanel.paintAlignment(true, false);
                 }
               }
+              else
+              {
+                /*
+                 * add declined structures as sequences
+                 */
+                for (Object[] o : filesmatched)
+                {
+                  filesnotmatched.add((String) o[0]);
+                }
+              }
             }
             if (filesnotmatched.size() > 0)
             {
@@ -4641,11 +4647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             new JnetAnnotationMaker();
             JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
-            SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
-            viewport.getAlignment().setSeqrep(repseq);
-            HiddenColumns cs = new HiddenColumns();
-            cs.hideInsertionsFor(repseq);
-            viewport.getAlignment().setHiddenColumns(cs);
+            viewport.getAlignment().setupJPredAlignment();
             isAnnotation = true;
           }
           // else if (IdentifyFile.FeaturesFile.equals(format))
@@ -4867,14 +4869,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             MessageManager.getString("option.trim_retrieved_seqs"));
     trimrs.setToolTipText(
             MessageManager.getString("label.trim_retrieved_sequences"));
-    trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+    trimrs.setSelected(
+            Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
     trimrs.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         trimrs.setSelected(trimrs.isSelected());
-        Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+        Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
                 Boolean.valueOf(trimrs.isSelected()).toString());
       };
     });
@@ -5282,7 +5285,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true, true);
+      alignPanel.paintAlignment(true,
+              viewport.needToUpdateStructureViews());
     }
   }
 
@@ -5303,6 +5307,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.createGroup())
     {
+      if (applyAutoAnnotationSettings.isSelected())
+      {
+        alignPanel.updateAnnotation(true, false);
+      }
       alignPanel.alignmentChanged();
     }
   }
@@ -5603,7 +5611,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       String choice = chooser.getSelectedFile().getPath();
       Cache.setProperty("LAST_DIRECTORY", choice);
-      new VCFLoader(viewport.getAlignment()).loadVCF(choice, this);
+      SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+      new VCFLoader(choice).loadVCF(seqs, this);
     }
 
   }