X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=c7e94323cbb98b1b6c11913a1b0d58e15cc58148;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=dfc236e23e6dca7c0946ca30eb2e25c9f0413b51;hpb=3261dc1e0830659cf50d975f19177894af778ecd;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
old mode 100755
new mode 100644
index dfc236e..c7e9432
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -91,7 +91,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     seqCanvas.addMouseMotionListener(this);
     seqCanvas.addMouseListener(this);
-    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
     ssm.addStructureViewerListener(this);
 
     seqCanvas.repaint();
@@ -458,7 +458,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
     if (evt.getClickCount() > 1)
     {
-      if (av.getSelectionGroup().getSize() == 1
+      if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() == 1
               && av.getSelectionGroup().getEndRes()
                       - av.getSelectionGroup().getStartRes() < 2)
       {
@@ -641,9 +641,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (av.followHighlight)
     {
-      if (ap.scrollToPosition(results, false))
+      if (ap.scrollToPosition(results, true))
       {
-        // ap.invalidate();
+        ap.alignFrame.repaint();
       }
     }
     seqCanvas.highlightSearchResults(results);
@@ -1774,9 +1774,42 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     if (repaint)
     {
+      ap.scalePanelHolder.repaint();
       ap.repaint();
-      //ap.paintAlignment(false);
     }
   }
 
+  /**
+   * scroll to the given row/column - or nearest visible location
+   * @param row
+   * @param column
+   */
+  public void scrollTo(int row, int column)
+  {
+    
+    row = row<0 ? ap.av.startSeq : row;
+    column = column<0 ? ap.av.startRes : column;
+    ap.scrollTo(row, row, column, true, true);
+  }
+  /**
+   * scroll to the given row - or nearest visible location
+   * @param row
+   */
+  public void scrollToRow(int row)
+  {
+    
+    row = row<0 ? ap.av.startSeq : row;
+    ap.scrollTo(row, row, ap.av.startRes, true, true);
+  }
+  /**
+   * scroll to the given column - or nearest visible location
+   * @param column
+   */
+  public void scrollToColumn(int column)
+  {
+    
+    column = column<0 ? ap.av.startRes : column;
+    ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+  }
+
 }