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JAL-1605 merge commit
[jalview.git] / src / jalview / gui / AlignFrame.java
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9f5b8f0..be8af7b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -59,7 +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;
@@ -382,7 +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())
@@ -400,7 +400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1);
           }
           break;
 
@@ -411,7 +411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1);
           }
 
           break;
@@ -419,11 +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;
@@ -431,18 +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;
@@ -466,7 +466,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+            alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
                     || evt.isShiftDown() || evt.isAltDown());
           }
 
@@ -475,19 +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;
 
@@ -495,20 +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;
 
@@ -519,10 +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:
@@ -741,14 +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
      */
@@ -899,7 +899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public FeatureRenderer getFeatureRenderer()
   {
-    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+    return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
   }
 
   @Override
@@ -1230,16 +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(alignPanel);
   }
 
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
     new BioJsHTMLOutput(alignPanel,
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+            alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
   }
   public void createImageMap(File file, String image)
   {
@@ -1305,7 +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);
@@ -1631,7 +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
@@ -1681,7 +1682,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.moveCursor(size, 0);
+        alignPanel.getSeqPanel().moveCursor(size, 0);
       }
       else
       {
@@ -1692,7 +1693,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.moveCursor(-size, 0);
+        alignPanel.getSeqPanel().moveCursor(-size, 0);
       }
       else
       {
@@ -2120,9 +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.
@@ -2180,9 +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.
@@ -2346,14 +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();
@@ -2754,7 +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);
   }
@@ -2762,7 +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);
   }
 
@@ -2784,7 +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);
     }
   }
 
@@ -4880,7 +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().featureColours, false,
               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
@@ -4892,10 +4893,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       viewport.showSequenceFeatures = 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)
       {