X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=6f9d84bfa54ce17b5e7189a6129a7a1a7235b905;hb=c9c74c082bdd9323850a864144dc8a9b36399157;hp=6d4e226000261c455d100309748fb9153620b954;hpb=b9fa0041e8f04f85f4f5357d2e2fe07e74d2172d;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 6d4e226..6f9d84b 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -92,11 +92,8 @@ public class AlignmentPanel extends GAlignmentPanel
 
     setScrollValues(0, 0);
 
-    annotationPanel.adjustPanelHeight();
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.
-                                        getPreferredSize());
+    adjustAnnotationHeight();
+
     setAnnotationVisible(av.getShowAnnotation());
 
     hscroll.addAdjustmentListener(this);
@@ -116,8 +113,7 @@ public class AlignmentPanel extends GAlignmentPanel
         switch (evt.getKeyCode())
         {
           case 27: // escape key
-            av.setSelectionGroup(null);
-            repaint();
+            alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);
 
             break;
 
@@ -165,7 +161,6 @@ public class AlignmentPanel extends GAlignmentPanel
             if(!av.cursorMode)
             {
               alignFrame.cut_actionPerformed(null);
-              seqPanel.seqCanvas.repaint();
             }
             else
               seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
@@ -179,7 +174,7 @@ public class AlignmentPanel extends GAlignmentPanel
             }
             break;
           case KeyEvent.VK_C:
-            if(av.cursorMode)
+            if(av.cursorMode && !evt.isControlDown())
             {
               seqPanel.setCursorColumn();
             }
@@ -418,6 +413,37 @@ public class AlignmentPanel extends GAlignmentPanel
     repaint();
   }
 
+  public void adjustAnnotationHeight()
+  {
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+          while(alignFrame.getHeight()==0)
+          {
+            Thread.yield();
+          }
+
+        int height = annotationPanel.adjustPanelHeight();
+
+        if (height > alignFrame.getHeight() / 2)
+        {
+          height = alignFrame.getHeight() / 2;
+        }
+
+        annotationScroller.setPreferredSize(
+            new Dimension(annotationScroller.getWidth(),
+                          height));
+
+        annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+            annotationSpaceFillerHolder.getWidth(),
+            height));
+
+        annotationPanel.repaint();
+      }
+    });
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -571,6 +597,7 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -588,10 +615,26 @@ public class AlignmentPanel extends GAlignmentPanel
 
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-            seqCanvas.getWidth());
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
+        if(offy>-1)
+        {
+          int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+              seqCanvas.getWidth());
+          av.setStartRes(offy * rowSize);
+          av.setEndRes( (offy + 1) * rowSize);
+        }
+        else
+        {
+          //This is only called if file loaded is a jar file that
+          //was wrapped when saved and user has wrap alignment true
+          //as preference setting
+          SwingUtilities.invokeLater(new Runnable()
+              {
+                public void run()
+                {
+                  setScrollValues(av.getStartRes(), av.getStartSeq());
+                }
+              });
+        }
       }
       else
       {
@@ -653,8 +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);
@@ -794,7 +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;
@@ -873,10 +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);
@@ -941,8 +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;
@@ -957,7 +1015,6 @@ public class AlignmentPanel extends GAlignmentPanel
         width = alignFrame.getWidth() - 22;
       }
       else
-
         width = seqPanel.getWidth() + idPanel.getWidth();
 
     }
@@ -1132,9 +1189,9 @@ public class AlignmentPanel extends GAlignmentPanel
                       if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
                         text.append(" " + features[f].getDescription());
 
-                      if (features[f].getStatus() != null && features[f].getStatus().length()>0)
+                      if (features[f].getValue("status") != null )
                       {
-                        text.append(" (" + features[f].getStatus() + ")");
+                        text.append(" (" + features[f].getValue("status") + ")");
                       }
                     }
                   }
@@ -1190,7 +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;
   }