X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f5634d247dab6a1cd6f340169d00c14605bf5e28;hb=4bb7ef2feb729af8a320e9c090e39aee12028375;hp=c8a0e1aae2da5076114e10be40bec8dce6121bdf;hpb=9b600c9d9f31e24560ca460bfe214e15bfe90408;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c8a0e1a..f5634d2 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -95,9 +95,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   private AnnotationLabels alabels;
 
-  // this value is set false when selection area being dragged
-  boolean fastPaint = true;
-
   private int hextent = 0;
 
   private int vextent = 0;
@@ -212,7 +209,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     alignFrame.updateEditMenuBar();
 
-    paintAlignment(true);
+    // no idea if we need to update structure
+    paintAlignment(true, true);
 
   }
 
@@ -241,11 +239,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
-    if (this.alignFrame.getSplitViewContainer() != null)
-    {
-      ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
-    }
-
     repaint();
   }
 
@@ -426,8 +419,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      start = hidden.findColumnPosition(start);
-      end = hidden.findColumnPosition(end);
+      start = hidden.absoluteToVisibleColumn(start);
+      end = hidden.absoluteToVisibleColumn(end);
       if (start == end)
       {
         if (!hidden.isVisible(r[0]))
@@ -485,7 +478,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       scrollNeeded = ranges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview);
+    paintAlignment(redrawOverview, false);
 
     return scrollNeeded;
   }
@@ -542,7 +535,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     validateAnnotationDimensions(true);
     addNotify();
-    paintAlignment(true);
+    // TODO: many places call this method and also paintAlignment with various
+    // different settings. this means multiple redraws are triggered...
+    paintAlignment(true, false);
   }
 
   /**
@@ -637,9 +632,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       else
       {
-        int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+        int widthInRes = (canvasWidth / av.getCharWidth());
         int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
-                / av.getCharHeight()) - 1;
+                / av.getCharHeight());
 
         ranges.setViewportWidth(widthInRes);
         ranges.setViewportHeight(heightInSeq);
@@ -683,7 +678,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         // reset the width to exclude hidden columns
         width = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(width);
+                .absoluteToVisibleColumn(width);
       }
 
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -775,10 +770,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       ranges.setViewportStartAndHeight(y, height);
     }
-    if (!fastPaint)
-    {
-      repaint();
-    }
+    repaint();
   }
 
   /**
@@ -846,12 +838,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     repaint();
   }
 
-  /**
-   * Repaint the alignment including the annotations and overview panels (if
-   * shown).
+  /* (non-Javadoc)
+   * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
    */
   @Override
-  public void paintAlignment(boolean updateOverview)
+  public void paintAlignment(boolean updateOverview,
+          boolean updateStructures)
   {
     final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
             av.isShowAutocalculatedAbove());
@@ -859,10 +851,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
             av.getSortAnnotationsBy());
     repaint();
 
-    if (updateOverview)
+    if (updateStructures)
     {
-      // TODO: determine if this paintAlignment changed structure colours
       av.getStructureSelectionManager().sequenceColoursChanged(this);
+    }
+    if (updateOverview)
+    {
 
       if (overviewPanel != null)
       {
@@ -880,15 +874,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void paintComponent(Graphics g)
   {
-    invalidate();
+    invalidate(); // needed so that the id width adjuster works correctly
 
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
     idPanelHolder.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
-    validate();
+
+    validate(); // needed so that the id width adjuster works correctly
 
     /*
-     * set scroll bar positions
+     * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+     * though I still think this call should be elsewhere.
      */
     ViewportRanges ranges = av.getRanges();
     setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
@@ -1180,7 +1176,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas
@@ -1372,7 +1368,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1590,7 +1586,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;
@@ -1616,6 +1612,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (annotationPanel != null)
     {
       annotationPanel.dispose();
+      annotationPanel = null;
     }
 
     if (av != null)
@@ -1645,9 +1642,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void closeChildFrames()
   {
+    if (overviewPanel != null)
+    {
+      overviewPanel.dispose();
+      overviewPanel = null;
+    }
     if (calculationDialog != null)
     {
       calculationDialog.closeFrame();
+      calculationDialog = null;
     }
   }
 
@@ -1812,35 +1815,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
-    /*
-     * To avoid jumpy vertical scrolling (if some sequences are gapped or not
-     * mapped), we can make the scroll-to location a sequence above the one
-     * actually mapped.
-     */
-    SequenceI mappedTo = sr.getResults().get(0).getSequence();
-    List<SequenceI> seqs = av.getAlignment().getSequences();
-
-    /*
-     * This is like AlignmentI.findIndex(seq) but here we are matching the
-     * dataset sequence not the aligned sequence
-     */
-    boolean matched = false;
-    for (SequenceI seq : seqs)
-    {
-      if (mappedTo == seq.getDatasetSequence())
-      {
-        matched = true;
-        break;
-      }
-    }
-    if (!matched)
-    {
-      return; // failsafe, shouldn't happen
-    }
-
-    /*
-     * Scroll to position but centring the target residue.
-     */
     scrollToPosition(sr, verticalOffset, true, true);
   }
 
@@ -1877,7 +1851,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (adjustHeight)
     {
       // sort, repaint, update overview
-      paintAlignment(true);
+      paintAlignment(true, false);
     }
     else
     {