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Merge: 497958b 68dcaa7
[jalview.git] / src / jalview / gui / AlignFrame.java
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4b7f2f8..015b95b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -30,10 +30,12 @@ import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
 import jalview.commands.OrderCommand;
 import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
@@ -57,7 +59,7 @@ import jalview.io.BioJsHTMLOutput;
 import jalview.io.FeaturesFile;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
-import jalview.io.HTMLOutput;
+import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -115,6 +117,7 @@ import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
@@ -379,7 +382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
                 && Character.isDigit(evt.getKeyChar()))
         {
-          alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+          alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
         }
 
         switch (evt.getKeyCode())
@@ -397,7 +400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1);
           }
           break;
 
@@ -408,7 +411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1);
           }
 
           break;
@@ -416,11 +419,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+            slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
           }
           else
           {
-            alignPanel.seqPanel.moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0);
           }
 
           break;
@@ -428,18 +431,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+            slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
           }
           else
           {
-            alignPanel.seqPanel.moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0);
           }
           break;
 
         case KeyEvent.VK_SPACE:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+            alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
                     || evt.isShiftDown() || evt.isAltDown());
           }
           break;
@@ -463,7 +466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+            alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
                     || evt.isShiftDown() || evt.isAltDown());
           }
 
@@ -472,19 +475,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_S:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorRow();
+            alignPanel.getSeqPanel().setCursorRow();
           }
           break;
         case KeyEvent.VK_C:
           if (viewport.cursorMode && !evt.isControlDown())
           {
-            alignPanel.seqPanel.setCursorColumn();
+            alignPanel.getSeqPanel().setCursorColumn();
           }
           break;
         case KeyEvent.VK_P:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorPosition();
+            alignPanel.getSeqPanel().setCursorPosition();
           }
           break;
 
@@ -492,20 +495,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_COMMA:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorRowAndColumn();
+            alignPanel.getSeqPanel().setCursorRowAndColumn();
           }
           break;
 
         case KeyEvent.VK_Q:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+            alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
           }
           break;
         case KeyEvent.VK_M:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+            alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
           }
           break;
 
@@ -516,10 +519,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-            alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+            alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+            alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
           }
-          alignPanel.seqPanel.seqCanvas.repaint();
+          alignPanel.getSeqPanel().seqCanvas.repaint();
           break;
 
         case KeyEvent.VK_F1:
@@ -738,14 +741,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
     conservationMenuItem.setSelected(av.getConservationSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
-    idRightAlign.setSelected(av.rightAlignIds);
+    idRightAlign.setSelected(av.isRightAlignIds());
     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
     renderGapsMenuItem.setSelected(av.renderGaps);
     wrapMenuItem.setSelected(av.wrapAlignment);
     scaleAbove.setVisible(av.wrapAlignment);
     scaleLeft.setVisible(av.wrapAlignment);
     scaleRight.setVisible(av.wrapAlignment);
-    annotationPanelMenuItem.setState(av.showAnnotation);
+    annotationPanelMenuItem.setState(av.isShowAnnotation());
     /*
      * Show/hide annotations only enabled if annotation panel is shown
      */
@@ -896,7 +899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public FeatureRenderer getFeatureRenderer()
   {
-    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+    return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
   }
 
   @Override
@@ -1227,17 +1230,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HTMLOutput(alignPanel,
-            alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+    // new HTMLOutput(alignPanel,
+    // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
+    // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+    new HtmlSvgOutput(null, alignPanel);
   }
 
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     new BioJsHTMLOutput(alignPanel,
-            alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+            alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
   }
   public void createImageMap(File file, String image)
   {
@@ -1303,7 +1306,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(alignPanel,
-            viewport.showAnnotation ? viewport.getAlignment()
+            viewport.isShowAnnotation() ? viewport.getAlignment()
                     .getAlignmentAnnotation() : null, viewport
                     .getAlignment().getGroups(), ((Alignment) viewport
                     .getAlignment()).alignmentProperties);
@@ -1418,7 +1421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = (CommandI) viewport.historyList.peek();
+      CommandI command = viewport.historyList.peek();
       undoMenuItem.setText(MessageManager.formatMessage(
               "label.undo_command", new String[]
               { command.getDescription() }));
@@ -1433,7 +1436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       redoMenuItem.setEnabled(true);
 
-      CommandI command = (CommandI) viewport.redoList.peek();
+      CommandI command = viewport.redoList.peek();
       redoMenuItem.setText(MessageManager.formatMessage(
               "label.redo_command", new String[]
               { command.getDescription() }));
@@ -1497,7 +1500,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    CommandI command = (CommandI) viewport.historyList.pop();
+    CommandI command = viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand(getViewAlignments());
 
@@ -1536,7 +1539,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    CommandI command = (CommandI) viewport.redoList.pop();
+    CommandI command = viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand(getViewAlignments());
 
@@ -1629,7 +1632,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.cursorMode)
     {
       sg.add(viewport.getAlignment().getSequenceAt(
-              alignPanel.seqPanel.seqCanvas.cursorY));
+              alignPanel.getSeqPanel().seqCanvas.cursorY));
     }
     else if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() != viewport
@@ -1679,7 +1682,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.moveCursor(size, 0);
+        alignPanel.getSeqPanel().moveCursor(size, 0);
       }
       else
       {
@@ -1690,7 +1693,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.moveCursor(-size, 0);
+        alignPanel.getSeqPanel().moveCursor(-size, 0);
       }
       else
       {
@@ -1998,7 +2001,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // /////
         // ADD HISTORY ITEM
         //
-        addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
+        addHistoryItem(new EditCommand(
+                MessageManager.getString("label.add_sequences"),
+                Action.PASTE,
                 sequences, 0, alignment.getWidth(), alignment));
       }
       // Add any annotations attached to sequences
@@ -2116,9 +2121,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         // >>>This is a fix for the moment, until a better solution is
         // found!!<<<
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+        af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
                 .transferSettings(
-                        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                        alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
 
         // TODO: maintain provenance of an alignment, rather than just make the
         // title a concatenation of operations.
@@ -2176,9 +2181,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       // >>>This is a fix for the moment, until a better solution is
       // found!!<<<
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
               .transferSettings(
-                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                      alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
 
       // TODO: maintain provenance of an alignment, rather than just make the
       // title a concatenation of operations.
@@ -2269,8 +2274,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * //ADD HISTORY ITEM
      */
-    addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
-            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+    addHistoryItem(new EditCommand(
+            MessageManager.getString("label.cut_sequences"), Action.CUT,
+            cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
             viewport.getAlignment()));
 
     viewport.setSelectionGroup(null);
@@ -2341,14 +2347,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (viewport.cursorMode)
     {
-      alignPanel.seqPanel.keyboardNo1 = null;
-      alignPanel.seqPanel.keyboardNo2 = null;
+      alignPanel.getSeqPanel().keyboardNo1 = null;
+      alignPanel.getSeqPanel().keyboardNo2 = null;
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.idPanel.idCanvas.searchResults = null;
+    alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
+    alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
@@ -2749,7 +2755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
 
-    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+    alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
             .calculateIdWidth());
     alignPanel.paintAlignment(true);
   }
@@ -2757,7 +2763,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
-    viewport.rightAlignIds = idRightAlign.isSelected();
+    viewport.setRightAlignIds(idRightAlign.isSelected());
     alignPanel.paintAlignment(true);
   }
 
@@ -2779,7 +2785,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
     {
       alignPanel.scrollToPosition(
-              alignPanel.seqPanel.seqCanvas.searchResults, false);
+              alignPanel.getSeqPanel().seqCanvas.searchResults, false);
     }
   }
 
@@ -4188,16 +4194,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        */
       msa = viewport.getAlignmentView(true);
     }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() == 1)
+    {
+      int option = JOptionPane.showConfirmDialog(this,
+              MessageManager.getString("warn.oneseq_msainput_selection"),
+              MessageManager.getString("label.invalid_selection"),
+              JOptionPane.OK_CANCEL_OPTION);
+      if (option == JOptionPane.OK_OPTION)
+      {
+        msa = viewport.getAlignmentView(false);
+      }
+    }
     else
     {
-      /*
-       * Vector seqs = viewport.getAlignment().getSequences();
-       * 
-       * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       * 
-       * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
-       * seqs.elementAt(i); } }
-       */
       msa = viewport.getAlignmentView(false);
     }
     return msa;
@@ -4871,7 +4881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     try
     {
       featuresFile = new FeaturesFile(file, type).parse(viewport
-              .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
+              .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
               .getFeatureRenderer().getFeatureColours(), false,
               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
@@ -4883,10 +4893,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      if (alignPanel.seqPanel.seqCanvas.fr != null)
+      if (alignPanel.getSeqPanel().seqCanvas.fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+        alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
       }
       if (featureSettings != null)
       {
@@ -5805,7 +5815,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         aa.visible = visible;
       }
     }
-    this.alignPanel.paintAlignment(true);
+    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.alignmentChanged();
   }
 
   /**
@@ -5819,6 +5830,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
     alignPanel.paintAlignment(true);
   }
+
+  /**
+   * 
+   * @return alignment panels in this alignemnt frame
+   */
+  public List<AlignmentViewPanel> getAlignPanels()
+  {
+    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+  }
 }
 
 class PrintThread extends Thread