Merge branch 'develop' into features/mchmmer
[jalview.git] / src / jalview / gui / AlignFrame.java
index 9755729..834f4c8 100644 (file)
@@ -88,6 +88,7 @@ import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
 import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.io.vcf.VCFLoader;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
@@ -183,8 +184,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
-  ViewportRanges vpRanges;
-
   public AlignViewControllerI avc;
   /*
    * The selected HMM for this align frame
@@ -361,7 +360,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
-    vpRanges = viewport.getRanges();
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -679,9 +677,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+            ViewportRanges ranges = viewport.getRanges();
+            alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
                     .getStartRes();
-            alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+            alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
                     .getStartSeq();
           }
           alignPanel.getSeqPanel().seqCanvas.repaint();
@@ -714,10 +713,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          vpRanges.pageUp();
+          viewport.getRanges().pageUp();
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          vpRanges.pageDown();
+          viewport.getRanges().pageDown();
           break;
         }
       }
@@ -867,6 +866,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI al = getViewport().getAlignment();
     boolean nucleotide = al.isNucleotide();
 
+    loadVcf.setVisible(nucleotide);
     showTranslation.setVisible(nucleotide);
     showReverse.setVisible(nucleotide);
     showReverseComplement.setVisible(nucleotide);
@@ -1619,13 +1619,13 @@ 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
@@ -1939,7 +1939,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   synchronized void slideSequences(boolean right, int size)
@@ -2385,7 +2385,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        vpRanges.setEndSeq(alignment.getHeight());
+        viewport.getRanges().setEndSeq(alignment.getHeight());
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
@@ -2634,7 +2634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -2660,7 +2660,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
     // updating.
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -2681,12 +2681,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
     // updating.
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2717,7 +2716,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // alignPanel to decide if overview needs
     // updating.
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2726,7 +2725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void invertColSel_actionPerformed(ActionEvent e)
   {
     viewport.invertColumnSelection();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     viewport.sendSelection();
   }
 
@@ -2786,7 +2785,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
                 column, viewport.getAlignment());
-        vpRanges.setStartRes(0);
+        viewport.getRanges().setStartRes(0);
       }
       else
       {
@@ -2851,13 +2850,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    ViewportRanges ranges = viewport.getRanges();
+    int startRes = seq.findPosition(ranges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
 
@@ -2890,12 +2890,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(vpRanges.getStartRes());
+    int startRes = seq.findPosition(viewport.getRanges().getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
 
-    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
 
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
@@ -2951,8 +2951,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Create a new AlignmentPanel (with its own, new Viewport)
      */
-    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
-            true);
+    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
     if (!copyAnnotation)
     {
       /*
@@ -3106,21 +3105,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     alignPanel.getIdPanel().getIdCanvas()
             .setPreferredSize(alignPanel.calculateIdWidth());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   @Override
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
     viewport.setRightAlignIds(idRightAlign.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   @Override
   public void centreColumnLabels_actionPerformed(ActionEvent e)
   {
     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /*
@@ -3153,7 +3152,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -3182,7 +3181,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3286,7 +3285,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3302,7 +3301,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.showAllHiddenColumns();
     viewport.showAllHiddenSeqs();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3310,7 +3309,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3331,7 +3330,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    alignPanel.paintAlignment(true);
+    // TODO: do we actually need to update overview for scale above change ?
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3344,7 +3344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3357,7 +3357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3370,7 +3370,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -3383,7 +3383,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -3396,7 +3396,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   public FeatureSettings featureSettings;
@@ -3434,7 +3434,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -3591,7 +3591,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     viewport.setGlobalColourScheme(cs);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -3676,7 +3676,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             viewport.getAlignment().getSequenceAt(0));
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3692,7 +3692,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(
             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3708,7 +3708,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentSorter.sortByLength(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3725,7 +3725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
             viewport.getAlignment()));
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3882,7 +3882,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
                 viewport.getAlignment()));
 
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, false);
       }
     });
   }
@@ -3911,7 +3911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 viewport.getAlignment());// ,viewport.getSelectionGroup());
         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
                 viewport.getAlignment()));
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, false);
       }
     });
   }
@@ -4026,7 +4026,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       addHistoryItem(new OrderCommand(undoname, oldOrder,
               viewport.getAlignment()));
     }
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     return true;
   }
 
@@ -4497,7 +4497,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
-    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+    new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
             .start();
   }
 
@@ -4624,7 +4624,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // Java's Transferable for native dnd
     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    List<String> files = new ArrayList<>();
+    final AlignFrame thisaf = this;
+    final List<String> files = new ArrayList<>();
     List<DataSourceType> protocols = new ArrayList<>();
 
     try
@@ -4636,133 +4637,146 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     if (files != null)
     {
-      try
+      new Thread(new Runnable()
       {
-        // check to see if any of these files have names matching sequences in
-        // the alignment
-        SequenceIdMatcher idm = new SequenceIdMatcher(
-                viewport.getAlignment().getSequencesArray());
-        /**
-         * Object[] { String,SequenceI}
-         */
-        ArrayList<Object[]> filesmatched = new ArrayList<>();
-        ArrayList<String> filesnotmatched = new ArrayList<>();
-        for (int i = 0; i < files.size(); i++)
+        @Override
+        public void run()
         {
-          String file = files.get(i).toString();
-          String pdbfn = "";
-          DataSourceType protocol = FormatAdapter.checkProtocol(file);
-          if (protocol == DataSourceType.FILE)
-          {
-            File fl = new File(file);
-            pdbfn = fl.getName();
-          }
-          else if (protocol == DataSourceType.URL)
-          {
-            URL url = new URL(file);
-            pdbfn = url.getFile();
-          }
-          if (pdbfn.length() > 0)
+          try
           {
-            // attempt to find a match in the alignment
-            SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
-            int l = 0, c = pdbfn.indexOf(".");
-            while (mtch == null && c != -1)
+            // check to see if any of these files have names matching sequences
+            // in
+            // the alignment
+            SequenceIdMatcher idm = new SequenceIdMatcher(
+                    viewport.getAlignment().getSequencesArray());
+            /**
+             * Object[] { String,SequenceI}
+             */
+            ArrayList<Object[]> filesmatched = new ArrayList<>();
+            ArrayList<String> filesnotmatched = new ArrayList<>();
+            for (int i = 0; i < files.size(); i++)
             {
-              do
+              String file = files.get(i).toString();
+              String pdbfn = "";
+              DataSourceType protocol = FormatAdapter.checkProtocol(file);
+              if (protocol == DataSourceType.FILE)
               {
-                l = c;
-              } while ((c = pdbfn.indexOf(".", l)) > l);
-              if (l > -1)
-              {
-                pdbfn = pdbfn.substring(0, l);
+                File fl = new File(file);
+                pdbfn = fl.getName();
               }
-              mtch = idm.findAllIdMatches(pdbfn);
-            }
-            if (mtch != null)
-            {
-              FileFormatI type = null;
-              try
-              {
-                type = new IdentifyFile().identify(file, protocol);
-              } catch (Exception ex)
+              else if (protocol == DataSourceType.URL)
               {
-                type = null;
+                URL url = new URL(file);
+                pdbfn = url.getFile();
               }
-              if (type != null && type.isStructureFile())
+              if (pdbfn.length() > 0)
               {
-                filesmatched.add(new Object[] { file, protocol, mtch });
-                continue;
+                // attempt to find a match in the alignment
+                SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+                int l = 0, c = pdbfn.indexOf(".");
+                while (mtch == null && c != -1)
+                {
+                  do
+                  {
+                    l = c;
+                  } while ((c = pdbfn.indexOf(".", l)) > l);
+                  if (l > -1)
+                  {
+                    pdbfn = pdbfn.substring(0, l);
+                  }
+                  mtch = idm.findAllIdMatches(pdbfn);
+                }
+                if (mtch != null)
+                {
+                  FileFormatI type = null;
+                  try
+                  {
+                    type = new IdentifyFile().identify(file, protocol);
+                  } catch (Exception ex)
+                  {
+                    type = null;
+                  }
+                  if (type != null && type.isStructureFile())
+                  {
+                    filesmatched.add(new Object[] { file, protocol, mtch });
+                    continue;
+                  }
+                }
+                // File wasn't named like one of the sequences or wasn't a PDB
+                // file.
+                filesnotmatched.add(file);
               }
             }
-            // File wasn't named like one of the sequences or wasn't a PDB file.
-            filesnotmatched.add(file);
-          }
-        }
-        int assocfiles = 0;
-        if (filesmatched.size() > 0)
-        {
-          if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                  || JvOptionPane.showConfirmDialog(this,
-                          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)
-
-          {
-            for (Object[] fm : filesmatched)
+            int assocfiles = 0;
+            if (filesmatched.size() > 0)
             {
-              // try and associate
-              // TODO: may want to set a standard ID naming formalism for
-              // associating PDB files which have no IDs.
-              for (SequenceI toassoc : (SequenceI[]) fm[2])
+              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)
+
               {
-                PDBEntry pe = new AssociatePdbFileWithSeq()
-                        .associatePdbWithSeq((String) fm[0],
-                                (DataSourceType) fm[1], toassoc, false,
-                                Desktop.instance);
-                if (pe != null)
+                for (Object[] fm : filesmatched)
                 {
-                  System.err.println("Associated file : " + ((String) fm[0])
-                          + " with " + toassoc.getDisplayId(true));
-                  assocfiles++;
+                  // try and associate
+                  // TODO: may want to set a standard ID naming formalism for
+                  // associating PDB files which have no IDs.
+                  for (SequenceI toassoc : (SequenceI[]) fm[2])
+                  {
+                    PDBEntry pe = new AssociatePdbFileWithSeq()
+                            .associatePdbWithSeq((String) fm[0],
+                                    (DataSourceType) fm[1], toassoc, false,
+                                    Desktop.instance);
+                    if (pe != null)
+                    {
+                      System.err.println("Associated file : "
+                              + ((String) fm[0]) + " with "
+                              + toassoc.getDisplayId(true));
+                      assocfiles++;
+                    }
+                  }
+                  // TODO: do we need to update overview ? only if features are
+                  // shown I guess
+                  alignPanel.paintAlignment(true, false);
                 }
               }
-              alignPanel.paintAlignment(true);
             }
-          }
-        }
-        if (filesnotmatched.size() > 0)
-        {
-          if (assocfiles > 0 && (Cache.getDefault(
-                  "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
-                  || JvOptionPane.showConfirmDialog(this,
-                          "<html>" + MessageManager.formatMessage(
-                                  "label.ignore_unmatched_dropped_files_info",
-                                  new Object[]
-                                  { Integer.valueOf(filesnotmatched.size())
-                                          .toString() })
-                                  + "</html>",
-                          MessageManager.getString(
-                                  "label.ignore_unmatched_dropped_files"),
-                          JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
-          {
-            return;
-          }
-          for (String fn : filesnotmatched)
+            if (filesnotmatched.size() > 0)
+            {
+              if (assocfiles > 0 && (Cache.getDefault(
+                      "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
+                      || JvOptionPane.showConfirmDialog(thisaf,
+                              "<html>" + MessageManager.formatMessage(
+                                      "label.ignore_unmatched_dropped_files_info",
+                                      new Object[]
+                                      { Integer.valueOf(
+                                              filesnotmatched.size())
+                                              .toString() })
+                                      + "</html>",
+                              MessageManager.getString(
+                                      "label.ignore_unmatched_dropped_files"),
+                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
+              {
+                return;
+              }
+              for (String fn : filesnotmatched)
+              {
+                loadJalviewDataFile(fn, null, null, null);
+              }
+
+            }
+          } catch (Exception ex)
           {
-            loadJalviewDataFile(fn, null, null, null);
+            ex.printStackTrace();
           }
-
         }
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+      }).start();
     }
   }
 
@@ -4878,7 +4892,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             if (parseFeaturesFile(file, sourceType))
             {
-              alignPanel.paintAlignment(true);
+              alignPanel.paintAlignment(true, true);
             }
           }
           else
@@ -4892,7 +4906,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignPanel.adjustAnnotationHeight();
         viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, true);
       }
     } catch (Exception ex)
     {
@@ -5417,7 +5431,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /*
@@ -5530,7 +5544,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -5542,7 +5556,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.getAlignment().setSeqrep(null);
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -5632,7 +5646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
     this.alignPanel.av
             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -5898,6 +5912,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
+  protected void loadVcf_actionPerformed()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
+    chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+      new VCFLoader(choice).loadVCF(seqs, this);
+    }
+
+  }
 }
 
 class PrintThread extends Thread