X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=6f9d84bfa54ce17b5e7189a6129a7a1a7235b905;hb=c9c74c082bdd9323850a864144dc8a9b36399157;hp=c00f29f89af693c12fc0ac27d405490797dfc30a;hpb=6a04c7bd4d21f8facf77a43f3bee6376f1c96c9d;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c00f29f..6f9d84b 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -113,8 +113,7 @@ public class AlignmentPanel extends GAlignmentPanel
         switch (evt.getKeyCode())
         {
           case 27: // escape key
-            av.setSelectionGroup(null);
-            repaint();
+            alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);
 
             break;
 
@@ -162,7 +161,6 @@ public class AlignmentPanel extends GAlignmentPanel
             if(!av.cursorMode)
             {
               alignFrame.cut_actionPerformed(null);
-              seqPanel.seqCanvas.repaint();
             }
             else
               seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
@@ -176,7 +174,7 @@ public class AlignmentPanel extends GAlignmentPanel
             }
             break;
           case KeyEvent.VK_C:
-            if(av.cursorMode)
+            if(av.cursorMode && !evt.isControlDown())
             {
               seqPanel.setCursorColumn();
             }
@@ -698,8 +696,14 @@ public class AlignmentPanel extends GAlignmentPanel
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
+      int maxwidth = av.alignment.getWidth();
+
+      if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+      int max = maxwidth /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +
+          1;
 
 
       vscroll.setMaximum(max);
@@ -839,7 +843,7 @@ public class AlignmentPanel extends GAlignmentPanel
     for (int i = startSeq; i < endSeq; i++)
     {
       if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().sequences.contains(
+          av.getSelectionGroup().getSequences(false).contains(
               av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
@@ -918,10 +922,15 @@ public class AlignmentPanel extends GAlignmentPanel
 
     int idWidth = calculateIdWidth().width + 4;
 
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+
     int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
         idWidth);
 
-    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
+    int totalHeight = cHeight * (maxwidth / resWidth + 1);
 
     pg.setColor(Color.white);
     pg.fillRect(0, 0, pwidth, pheight);
@@ -986,8 +995,12 @@ public class AlignmentPanel extends GAlignmentPanel
 
   void makeAlignmentImage(int type, File file)
   {
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+
     int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
+    int width = idPanel.getWidth() + (maxwidth * av.charWidth);
     if (idPanel.getWidth() == 0)
     {
       width += calculateIdWidth().getWidth() + 4;
@@ -1002,7 +1015,6 @@ public class AlignmentPanel extends GAlignmentPanel
         width = alignFrame.getWidth() - 22;
       }
       else
-
         width = seqPanel.getWidth() + idPanel.getWidth();
 
     }
@@ -1235,7 +1247,12 @@ public class AlignmentPanel extends GAlignmentPanel
         + hgap
         + annotationHeight;
 
-    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+
+    int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
 
     return height;
   }