JAL-2491 Resolved highlighting and initialisation problems

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 4cfa7d5..8619ad0 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -152,13 +152,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
         // reset the viewport ranges when the alignment panel is resized
         // in particular, this initialises the end residue value when Jalview
         // is initialised
-        
-        
         if (av.getWrapAlignment())
         {
           int widthInRes = getSeqPanel().seqCanvas
                   .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          vpRanges.setStartEndRes(vpRanges.getStartRes(), widthInRes);
+          vpRanges.setStartEndRes(vpRanges.getStartRes(),
+                  vpRanges.getStartRes() + widthInRes);
         }
         else
         {
@@ -166,11 +165,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
                   .getCharWidth()) - 1;
           int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()) - 1;
           
-          vpRanges.setStartEndRes(vpRanges.getStartRes(), widthInRes);
-          vpRanges.setStartEndSeq(vpRanges.getStartSeq(), heightInSeq);
+          vpRanges.setStartEndRes(vpRanges.getStartRes(),
+                  vpRanges.getStartRes() + widthInRes);
+          vpRanges.setStartEndSeq(vpRanges.getStartSeq(),
+                  vpRanges.getStartSeq() + heightInSeq);
         }
-
-        
       }
 
     });
@@ -488,7 +487,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
       else
       {
         vpRanges.scrollToWrappedVisible(start);
-        // scrollToWrappedVisible(start);
       }
     }
 
@@ -635,7 +633,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int widthInRes = getSeqPanel().seqCanvas
               .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-      vpRanges.setStartEndRes(vpRanges.getStartRes(), widthInRes);
+      vpRanges.setStartEndRes(vpRanges.getStartRes(),
+              vpRanges.getStartRes() + widthInRes - 1);
     }
     else
     {
@@ -760,7 +759,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         }
         else if (offy > -1)
         {
-          vpRanges.setStartEndRes(offy * rowSize, (offy + 1) * rowSize);
+          vpRanges.setStartEndRes(offy * rowSize, (offy + 1) * rowSize - 1);
         }
         else
         {

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index df953a2..d7f2679 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -511,7 +511,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     av.setWrappedWidth(cWidth);
 
-    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth - 1);
 
     int endx;
     int ypos = hgap;

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 82d98c0..c14854b 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -689,10 +689,16 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.isFollowHighlight())
     {
+      // don't allow highlight of protein/cDNA to also scroll a complementary
+      // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+      // over residue to change abruptly, causing highlighted residue in panel 2
+      // to change, causing a scroll in panel 1 etc)
+      ap.setDontScrollComplement(true);
       if (ap.scrollToPosition(results, false))
       {
         seqCanvas.revalidate();
       }
+      ap.setDontScrollComplement(false);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);