X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=a4d924073bbc11d04364c081b3d5e5b8f00135c6;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=4135cb0152ff39b0df12ae5a5e3aca9543e6fd85;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4135cb0..a4d9240 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -147,7 +147,6 @@ public class SeqPanel extends JPanel implements MouseListener,
 
    int findSeq(MouseEvent evt)
    {
-
      int seq = 0;
      int y = evt.getY();
 
@@ -162,11 +161,13 @@ public class SeqPanel extends JPanel implements MouseListener,
 
          y -= hgap;
 
-       seq = ( (y % cHeight) / av.getCharHeight());
+       seq = Math.min( (y % cHeight) / av.getCharHeight(),
+                       av.alignment.getHeight() -1);
      }
      else
      {
-       seq = (y / av.getCharHeight()) + av.getStartSeq();
+       seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                       av.alignment.getHeight() -1);
      }
 
      return seq;
@@ -820,12 +821,10 @@ public class SeqPanel extends JPanel implements MouseListener,
             {
               if(startres>=y2)
               {
-                System.out.println("left of line");
                 fixedLeft = y2;
               }
               else
-             {
-               System.out.println("right of line");
+              {
                fixedRight = y2 - 1;
              }
             }
@@ -876,12 +875,26 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (!blank)
             {
-              if(sg.getSize(false) == av.alignment.getHeight())
+              if(sg.getSize(false) == av.alignment.getHeight()  )
               {
+                if((av.hasHiddenColumns
+                    && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
+                {
+                  endEditing();
+                  return;
+                }
+
+                int alWidth = av.alignment.getWidth();
+                if(av.hasHiddenRows)
+                {
+                  int hwidth = av.alignment.getHiddenSequences().getWidth();
+                  if(hwidth>alWidth)
+                    alWidth = hwidth;
+                }
                 //We can still insert gaps if the selectionGroup
                 //contains all the sequences
                 sg.setEndRes(sg.getEndRes()+startres-lastres);
-                fixedRight = av.alignment.getWidth()+startres-lastres;
+                fixedRight = alWidth+startres-lastres;
               }
               else
               {
@@ -964,19 +977,6 @@ public class SeqPanel extends JPanel implements MouseListener,
             {
               if (fixedColumns && fixedRight != -1)
               {
-                /*if (sg!=null &&
-                    sg.getStartRes() == 0
-                    && sg.getEndRes()  == fixedRight
-                    && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
-                {
-                  System.out.println("still here");
-                  //Single sequence edit, whole sequence selected,
-                  //extend the selection group
-                  sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
-                  fixedColumns = false;
-                  insertChar(j, seq);
-                }
-                else*/
                   insertChar(j, seq, fixedRight);
               }
               else
@@ -1033,6 +1033,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       if (blankColumn <= j)
       {
+        blankColumn = fixedColumn;
         endEditing();
         return;
       }
@@ -1242,14 +1243,6 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         }
 
-        if (av.cursorMode)
-        {
-          seqCanvas.cursorX = findRes(evt);
-          seqCanvas.cursorY = findSeq(evt);
-          seqCanvas.repaint();
-          return;
-        }
-
 
         if (javax.swing.SwingUtilities.isRightMouseButton(evt))
         {
@@ -1270,9 +1263,18 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
             pop.show(this, evt.getX(), evt.getY());
+            return;
+        }
 
+        if (av.cursorMode)
+        {
+          seqCanvas.cursorX = findRes(evt);
+          seqCanvas.cursorY = findSeq(evt);
+          seqCanvas.repaint();
+          return;
         }
-        else if (stretchGroup == null)
+
+        if (stretchGroup == null)
         {
           //Only if left mouse button do we want to change group sizes
 
@@ -1371,11 +1373,6 @@ public class SeqPanel extends JPanel implements MouseListener,
             return;
        }
 
-
-        if(y > av.alignment.getHeight())
-        {
-          y = av.alignment.getHeight() -1;
-        }
         if(res> av.alignment.getWidth())
         {
           res = av.alignment.getWidth()-1;