X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=cc89098b499749361bd5b61f2a49a5a3797c33cc;hb=476d13d644d3bf2886519b13bc7f02d1ae9729f9;hp=0e9a0d8ff14cdda2fafbe0cdeb899a020e849e9a;hpb=59183747dbffe3ab6b141c5440d2f70799ae360b;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 0e9a0d8..cc89098 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -185,54 +185,59 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
   }
 
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
 
-    // do we need to scroll the panel?
+   // do we need to scroll the panel?
     if (results != null)
     {
-      SequenceI seq = av.alignment.getSequenceAt(results[0]);
-      int start = seq.findIndex(results[1]) - 1;
-      int end = seq.findIndex(results[2]) - 1;
+      SequenceI seq = results.getResultSequence(0);
+      int seqIndex = av.alignment.findIndex(seq);
+      int start = seq.findIndex(results.getResultStart(0)) - 1;
+      int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
-      if(!av.wrapAlignment)
-      {
-        if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
-            ( (av.getStartSeq() > results[0]) ||
-             (av.getEndSeq() < results[0])))
+        if(!av.wrapAlignment)
         {
-          int newy = results[0];
-          if(start > av.alignment.getWidth() - hextent)
-          {
-            start = av.alignment.getWidth() - hextent;
-            if(start<0)
-              start = 0;
-          }
-          if(newy > av.alignment.getHeight() - vextent)
+          if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+             ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
           {
-            newy = av.alignment.getHeight() - vextent;
-            if(newy<0)
-              newy = 0;
+            if (start > av.alignment.getWidth() - hextent)
+            {
+              start = av.alignment.getWidth() - hextent;
+              if (start < 0)
+                start = 0;
+            }
+            if (seqIndex > av.alignment.getHeight() - vextent)
+            {
+              seqIndex = av.alignment.getHeight() - vextent;
+              if (seqIndex < 0)
+                seqIndex = 0;
+            }
+            setScrollValues(start, seqIndex);
           }
-          setScrollValues(start, newy);
         }
-      }
-      else
-      {
-        int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        if( start<av.getStartRes() || start>(av.getStartRes()+cwidth) )
+        else
         {
-
-          vscroll.setValue(start / cwidth);
-          av.startRes = vscroll.getValue() * cwidth;
+          scrollToWrappedVisible(start);
         }
-      }
     }
 
     repaint();
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
+        getWidth());
+    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
+
   public OverviewPanel getOverviewPanel()
   {
     return overviewPanel;
@@ -297,8 +302,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() - 1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue()-1);
     }
     else
     {
@@ -306,24 +310,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      fastPaint = false;
-      vscroll.setValue(vscroll.getValue() + 1);
+      setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
     }
-    fastPaint = true;
+
+    repaint();
     return true;
   }
 
   public boolean scrollRight(boolean right)
   {
-
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
         return false;
       }
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() - 1);
+      setScrollValues(hscroll.getValue()-1, vscroll.getValue());
     }
     else
     {
@@ -331,16 +333,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       {
         return false;
       }
-      fastPaint = false;
-      hscroll.setValue(hscroll.getValue() + 1);
+      setScrollValues(hscroll.getValue()+1, vscroll.getValue());
     }
-    fastPaint = true;
+
+    repaint();
     return true;
   }
 
   public void setScrollValues(int x, int y)
   {
-
     av.setStartRes(x);
     av.setStartSeq(y);
     av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
@@ -387,6 +388,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
     vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
 
+    if(overviewPanel!=null)
+          overviewPanel.setBoxPosition();
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -394,6 +397,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
+
     if (evt==null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
@@ -402,6 +406,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
                    1);
     }
 
+
     if (evt==null || evt.getSource() == vscroll)
     {
       int offy = vscroll.getValue();
@@ -432,12 +437,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     {
       repaint();
     }
-    else if(!seqPanel.seqCanvas.fastPaint)
+    else
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
       if(scrollX>av.endRes-av.startRes)
-        scrollX = av.endRes-av.startRes;
+      {
+        scrollX = av.endRes - av.startRes;
+      }
       else if(scrollX<av.startRes-av.endRes)
         scrollX = av.startRes - av.endRes;
 
@@ -461,6 +468,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
   public void paint(Graphics g)
   {
+    invalidate();
     Dimension d = idPanel.idCanvas.getSize();
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,