Merge branch 'releases/Release_2_10_4_Branch' into develop

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d843c7f..e08fce5 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -81,6 +81,7 @@ 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;
@@ -163,8 +164,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
-  ViewportRanges vpRanges;
-
   public AlignViewControllerI avc;
 
   List<AlignmentPanel> alignPanels = new ArrayList<>();
@@ -336,7 +335,6 @@ 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)
@@ -654,9 +652,10 @@ 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();
@@ -689,10 +688,10 @@ 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;
         }
       }
@@ -841,6 +840,7 @@ 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);
@@ -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
@@ -1711,7 +1711,7 @@ 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)
@@ -2141,7 +2141,7 @@ 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.
@@ -2259,11 +2259,8 @@ 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
@@ -2388,7 +2385,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -2414,7 +2411,7 @@ 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());
   }
 
@@ -2439,7 +2436,7 @@ 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());
     viewport.sendSelection();
   }
@@ -2470,7 +2467,7 @@ 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();
   }
@@ -2479,7 +2476,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void invertColSel_actionPerformed(ActionEvent e)
   {
     viewport.invertColumnSelection();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     viewport.sendSelection();
   }
 
@@ -2539,7 +2536,7 @@ 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
       {
@@ -2604,13 +2601,14 @@ 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());
 
@@ -2643,12 +2641,12 @@ 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());
@@ -2704,8 +2702,7 @@ 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)
     {
       /*
@@ -2859,21 +2856,21 @@ 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);
   }
 
   /*
@@ -2906,7 +2903,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -2935,7 +2932,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3039,7 +3036,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3055,7 +3052,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.showAllHiddenColumns();
     viewport.showAllHiddenSeqs();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3063,7 +3060,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
 
@@ -3084,7 +3081,8 @@ 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);
   }
 
   /**
@@ -3097,7 +3095,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3110,7 +3108,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3123,7 +3121,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -3136,7 +3134,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -3149,7 +3147,7 @@ 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;
@@ -3187,7 +3185,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -3344,7 +3342,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     viewport.setGlobalColourScheme(cs);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -3429,7 +3427,7 @@ 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);
   }
 
   /**
@@ -3445,7 +3443,7 @@ 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);
   }
 
   /**
@@ -3461,7 +3459,7 @@ 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);
   }
 
   /**
@@ -3478,7 +3476,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
             viewport.getAlignment()));
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -3635,7 +3633,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
                 viewport.getAlignment()));
 
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, false);
       }
     });
   }
@@ -3664,7 +3662,7 @@ 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);
       }
     });
   }
@@ -3779,7 +3777,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       addHistoryItem(new OrderCommand(undoname, oldOrder,
               viewport.getAlignment()));
     }
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     return true;
   }
 
@@ -4250,7 +4248,7 @@ 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();
   }
 
@@ -4494,7 +4492,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       assocfiles++;
                     }
                   }
-                  alignPanel.paintAlignment(true);
+                  // TODO: do we need to update overview ? only if features are
+                  // shown I guess
+                  alignPanel.paintAlignment(true, false);
                 }
               }
             }
@@ -4629,11 +4629,7 @@ 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))
@@ -4641,7 +4637,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             if (parseFeaturesFile(file, sourceType))
             {
-              alignPanel.paintAlignment(true);
+              alignPanel.paintAlignment(true, true);
             }
           }
           else
@@ -4656,7 +4652,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignPanel.adjustAnnotationHeight();
         viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, true);
       }
     } catch (Exception ex)
     {
@@ -4855,14 +4851,15 @@ 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());
       };
     });
@@ -5181,7 +5178,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /*
@@ -5270,7 +5267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -5282,7 +5279,7 @@ 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);
     }
   }
 
@@ -5372,7 +5369,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
     this.alignPanel.av
             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -5575,6 +5572,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       new CalculationChooser(AlignFrame.this);
     }
   }
+
+  @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