JAL-2909 soft clip and handclap features (should use SO terms for ‘Clipped’)

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b48dec9..ef87671 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -343,7 +343,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     createAlignFrameWindow(embedded);
     validate();
     alignPanel.adjustAnnotationHeight();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   public AlignViewport getAlignViewport()
@@ -415,7 +415,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         viewport.featureSettings.refreshTable();
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       statusBar.setText(MessageManager
               .getString("label.successfully_added_features_alignment"));
     }
@@ -691,7 +691,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       break;
 
     }
-    alignPanel.paintAlignment(true);
+    // TODO: repaint flags set only if the keystroke warrants it
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -917,7 +918,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       applyAutoAnnotationSettings_actionPerformed();
     }
-    alignPanel.paintAlignment(true);
+    // TODO: repaint flags set only if warranted
+    alignPanel.paintAlignment(true, true);
   }
 
   /**
@@ -1094,7 +1096,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == invertColSel)
     {
       viewport.invertColumnSelection();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(false, false);
       viewport.sendSelection();
     }
     else if (source == remove2LeftMenuItem)
@@ -1128,34 +1130,34 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == showColumns)
     {
       viewport.showAllHiddenColumns();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == showSeqs)
     {
       viewport.showAllHiddenSeqs();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       // uncomment if we want to slave sequence selections in split frame
       // viewport.sendSelection();
     }
     else if (source == hideColumns)
     {
       viewport.hideSelectedColumns();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == hideSequences
             && viewport.getSelectionGroup() != null)
     {
       viewport.hideAllSelectedSeqs();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       // uncomment if we want to slave sequence selections in split frame
       // viewport.sendSelection();
     }
     else if (source == hideAllButSelection)
     {
       toggleHiddenRegions(false, false);
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == hideAllSelection)
@@ -1164,14 +1166,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.expandColSelection(sg, false);
       viewport.hideAllSelectedSeqs();
       viewport.hideSelectedColumns();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == showAllHidden)
     {
       viewport.showAllHiddenColumns();
       viewport.showAllHiddenSeqs();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
       viewport.sendSelection();
     }
     else if (source == showGroupConsensus)
@@ -1426,21 +1428,32 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return null;
   }
 
+  private List<String> getDisplayedFeatureGroups()
+  {
+    if (alignPanel.getFeatureRenderer() != null
+            && viewport.getFeaturesDisplayed() != null)
+    {
+      return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+    }
+    return null;
+  }
+
   public String outputFeatures(boolean displayTextbox, String format)
   {
     String features;
     FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = formatter.printJalviewFormat(
-              viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printJalviewFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
     else
     {
-      features = formatter.printGffFormat(
-              viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols());
+      features = formatter.printGffFormat(viewport.getAlignment()
+              .getSequencesArray(), getDisplayedFeatureCols(),
+              getDisplayedFeatureGroups(), true);
     }
 
     if (displayTextbox)
@@ -1590,10 +1603,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       System.exit(0);
     }
-    else
+
+    viewport = null;
+    if (alignPanel != null && alignPanel.overviewPanel != null)
     {
+      alignPanel.overviewPanel.dispose();
     }
-    viewport = null;
     alignPanel = null;
     this.dispose();
   }
@@ -1725,7 +1740,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       EditCommand editCommand = (EditCommand) command;
       al = editCommand.getAlignment();
-      Vector comps = (Vector) PaintRefresher.components
+      Vector comps = PaintRefresher.components
               .get(viewport.getSequenceSetId());
       for (int i = 0; i < comps.size(); i++)
       {
@@ -1770,7 +1785,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             up ? null : viewport.getHiddenRepSequences(), up);
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
 
     /*
      * Also move cDNA/protein complement sequences
@@ -1782,7 +1797,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               viewport, complement);
       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
               up ? null : complement.getHiddenRepSequences(), up);
-      getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
+      getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
+              false);
     }
   }
 
@@ -2215,7 +2231,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -2252,7 +2268,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // 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();
   }
@@ -2272,7 +2288,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // 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();
   }
@@ -2292,7 +2308,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void invertColSel_actionPerformed()
   {
     viewport.invertColumnSelection();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2485,7 +2501,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
             newaf.alignPanel.av.getSequenceSetId());
 
-    Vector comps = (Vector) PaintRefresher.components
+    Vector comps = PaintRefresher.components
             .get(viewport.getSequenceSetId());
     int viewSize = -1;
     for (int i = 0; i < comps.size(); i++)
@@ -2584,19 +2600,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     viewport.setShowJVSuffix(seqLimits.getState());
     alignPanel.fontChanged();
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   protected void colourTextMenuItem_actionPerformed()
   {
     viewport.setColourText(colourTextMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   protected void displayNonconservedMenuItem_actionPerformed()
   {
     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false, false);
   }
 
   protected void wrapMenuItem_actionPerformed()
@@ -2606,7 +2622,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     scaleAbove.setEnabled(wrapMenuItem.getState());
     scaleLeft.setEnabled(wrapMenuItem.getState());
     scaleRight.setEnabled(wrapMenuItem.getState());
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void overviewMenuItem_actionPerformed()
@@ -2649,7 +2665,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     viewport.setGlobalColourScheme(cs);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, true);
   }
 
   protected void modifyPID_actionPerformed()
@@ -2724,7 +2740,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void sortIDMenuItem_actionPerformed()
@@ -2733,7 +2749,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     AlignmentSorter.sortByID(viewport.getAlignment());
     addHistoryItem(
             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void sortLengthMenuItem_actionPerformed()
@@ -2742,7 +2758,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     AlignmentSorter.sortByLength(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   public void sortGroupMenuItem_actionPerformed()
@@ -2751,7 +2767,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
 
   }
 
@@ -2791,7 +2807,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           current.insertCharAt(Width - 1, viewport.getGapCharacter());
         }
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(false, false);
     }
 
     if ((viewport.getSelectionGroup() != null
@@ -2855,7 +2871,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           current.insertCharAt(Width - 1, viewport.getGapCharacter());
         }
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(false, false);
 
     }
 
@@ -2908,7 +2924,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     addHistoryItem(new OrderCommand(MessageManager
             .formatMessage("label.order_by_params", new String[]
             { title }), oldOrder, viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
   }
 
   /**
@@ -2966,7 +2982,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       addHistoryItem(new OrderCommand(undoname, oldOrder,
               viewport.getAlignment()));
     }
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
     return true;
   }
 
@@ -4133,7 +4149,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // register the association(s) and quit, don't create any windows.
       if (StructureSelectionManager.getStructureSelectionManager(applet)
-              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+              .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
       {
         System.err.println("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");