Merge branch 'releases/Release_2_10_0_Branch'

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 1906829..3dd581e 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
  * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -99,7 +99,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
    * true, suppresses invoking the same method recursively.
    */
-  private boolean followingComplementScroll;
+  private boolean dontScrollComplement;
+
+  private PropertyChangeListener propertyChangeListener;
 
   /**
    * Creates a new AlignmentPanel object.
@@ -135,8 +137,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     vscroll.addAdjustmentListener(this);
 
     final AlignmentPanel ap = this;
-    av.addPropertyChangeListener(new PropertyChangeListener()
+    propertyChangeListener = new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         if (evt.getPropertyName().equals("alignment"))
@@ -145,7 +148,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
           alignmentChanged();
         }
       }
-    });
+    };
+    av.addPropertyChangeListener(propertyChangeListener);
     fontChanged();
     adjustAnnotationHeight();
     updateLayout();
@@ -509,6 +513,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * automatically adjust annotation panel height for new annotation whilst
    * ensuring the alignment is still visible.
    */
+  @Override
   public void adjustAnnotationHeight()
   {
     // TODO: display vertical annotation scrollbar if necessary
@@ -566,6 +571,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     annotationScroller.setPreferredSize(new Dimension(annotationScroller
             .getWidth(), annotationHeight));
 
+    Dimension e = idPanel.getSize();
+    alabels.setSize(new Dimension(e.width, annotationHeight));
+
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -729,7 +737,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       x = 0;
     }
 
+    /*
+     * each scroll adjustment triggers adjustmentValueChanged, which resets the
+     * 'do not scroll complement' flag; ensure it is the same for both
+     * operations
+     */
+    boolean flag = isDontScrollComplement();
     hscroll.setValues(x, hextent, 0, width);
+    setDontScrollComplement(flag);
     vscroll.setValues(y, vextent, 0, height);
   }
 
@@ -739,6 +754,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     int oldX = av.getStartRes();
@@ -772,6 +788,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // as preference setting
           SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
               setScrollValues(av.getStartRes(), av.getStartSeq());
@@ -828,9 +845,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * If there is one, scroll the (Protein/cDNA) complementary alignment to
      * match, unless we are ourselves doing that.
      */
-    if (isFollowingComplementScroll())
+    if (isDontScrollComplement())
     {
-      setFollowingComplementScroll(false);
+      setDontScrollComplement(false);
     }
     else
     {
@@ -842,6 +859,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Repaint the alignment including the annotations and overview panels (if
    * shown).
    */
+  @Override
   public void paintAlignment(boolean updateOverview)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
@@ -868,6 +886,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     invalidate();
@@ -877,6 +896,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
     validate();
 
+    /*
+     * set scroll bar positions; first suppress this being 'followed' in any
+     * complementary split pane
+     */
+    setDontScrollComplement(true);
+
     if (av.getWrapAlignment())
     {
       int maxwidth = av.getAlignment().getWidth();
@@ -920,6 +945,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @throws PrinterException
    *           DOCUMENT ME!
    */
+  @Override
   public int print(Graphics pg, PageFormat pf, int pi)
           throws PrinterException
   {
@@ -1246,14 +1272,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
   {
-    long progress = System.currentTimeMillis();
+    int boarderBottomOffset = 5;
+    long pSessionId = System.currentTimeMillis();
     headless = (System.getProperty("java.awt.headless") != null && System
             .getProperty("java.awt.headless").equals("true"));
     if (alignFrame != null && !headless)
     {
-      alignFrame.setProgressBar(MessageManager.formatMessage(
-              "status.saving_file", new Object[] { type.getLabel() }),
-              progress);
+      if (file != null)
+      {
+        alignFrame.setProgressBar(MessageManager.formatMessage(
+                "status.saving_file", new Object[] { type.getLabel() }),
+                pSessionId);
+      }
     }
     try
     {
@@ -1279,14 +1309,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
 
         im = new jalview.util.ImageMaker(this, type, imageAction,
-                aDimension.getWidth(), aDimension.getHeight(), file,
-                imageTitle);
+                aDimension.getWidth(), aDimension.getHeight()
+                        + boarderBottomOffset, file, imageTitle,
+                alignFrame, pSessionId, headless);
         if (av.getWrapAlignment())
         {
           if (im.getGraphics() != null)
           {
             printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
-                    aDimension.getHeight(), 0);
+                    aDimension.getHeight() + boarderBottomOffset, 0);
             im.writeImage();
           }
         }
@@ -1299,6 +1330,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
             im.writeImage();
           }
         }
+
       } catch (OutOfMemoryError err)
       {
         // Be noisy here.
@@ -1312,12 +1344,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     } finally
     {
-      if (alignFrame != null && !headless)
-      {
-        alignFrame.setProgressBar(
-                MessageManager.getString("status.export_complete"),
-                progress);
-      }
+
     }
   }
 
@@ -1571,8 +1598,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
+
+    /*
+     * try to ensure references are nulled
+     */
+    if (annotationPanel != null)
+    {
+      annotationPanel.dispose();
+    }
+
     if (av != null)
     {
+      av.removePropertyChangeListener(propertyChangeListener);
       jalview.structure.StructureSelectionManager ssm = av
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
@@ -1580,7 +1617,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       ssm.removeCommandListener(av);
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
-      av.setAlignment(null);
+      av.dispose();
       av = null;
     }
     else
@@ -1786,17 +1823,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+   * Set a flag to say do not scroll any (cDNA/protein) complement.
    * 
    * @param b
    */
-  protected void setFollowingComplementScroll(boolean b)
+  protected void setDontScrollComplement(boolean b)
   {
-    this.followingComplementScroll = b;
+    this.dontScrollComplement = b;
   }
 
-  protected boolean isFollowingComplementScroll()
+  protected boolean isDontScrollComplement()
   {
-    return this.followingComplementScroll;
+    return this.dontScrollComplement;
   }
 }