X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=a4a38f98fce7e525a23ce6edd9dbe425ad520b45;hb=76b5c58c65413e8b239dbf71999f500600ef0f95;hp=4a7a05d074c1a0ed0cca93d0ea36de6de7dad31e;hpb=94e3d91558ad96de545821aeb548934f8c8353a3;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 4a7a05d..a4a38f9 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -32,8 +32,6 @@ import java.io.*;
 
 import javax.swing.*;
 
-import org.biojava.dasobert.eventmodel.*;
-
 
 /**
  * DOCUMENT ME!
@@ -42,7 +40,7 @@ import org.biojava.dasobert.eventmodel.*;
  * @version $Revision$
  */
 public class AlignmentPanel extends GAlignmentPanel
-    implements AdjustmentListener, Printable, FeatureListener
+    implements AdjustmentListener, Printable
 {
   public AlignViewport av;
   OverviewPanel overviewPanel;
@@ -115,8 +113,7 @@ public class AlignmentPanel extends GAlignmentPanel
         switch (evt.getKeyCode())
         {
           case 27: // escape key
-            av.setSelectionGroup(null);
-            repaint();
+            alignFrame.deselectAllSequenceMenuItem_actionPerformed(null);
 
             break;
 
@@ -164,7 +161,6 @@ public class AlignmentPanel extends GAlignmentPanel
             if(!av.cursorMode)
             {
               alignFrame.cut_actionPerformed(null);
-              seqPanel.seqCanvas.repaint();
             }
             else
               seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown());
@@ -178,7 +174,7 @@ public class AlignmentPanel extends GAlignmentPanel
             }
             break;
           case KeyEvent.VK_C:
-            if(av.cursorMode)
+            if(av.cursorMode && !evt.isControlDown())
             {
               seqPanel.setCursorColumn();
             }
@@ -239,21 +235,44 @@ public class AlignmentPanel extends GAlignmentPanel
               ex.printStackTrace();
             }
             break;
+          case KeyEvent.VK_H:
+          {
+            boolean toggleSeqs = !evt.isControlDown();
+            boolean toggleCols = !evt.isShiftDown();
+
+            boolean hide = false;
+
+            SequenceGroup sg = av.getSelectionGroup();
+            if(toggleSeqs)
+             {
+               if(sg != null && sg.getSize(false) != av.alignment.getHeight())
+               {
+                 alignFrame.hideSelSequences_actionPerformed(null);
+                 hide = true;
+               }
+               else if (!(toggleCols && av.colSel.getSelected().size() > 0))
+                 alignFrame.showAllSeqs_actionPerformed(null);
+             }
+
+             if (toggleCols)
+             {
+               if(av.colSel.getSelected().size() > 0)
+               {
+                 alignFrame.hideSelColumns_actionPerformed(null);
+                 if(!toggleSeqs)
+                   av.selectionGroup = sg;
+               }
+               else if(!hide)
+                 alignFrame.showAllColumns_actionPerformed(null);
+             }
+            break;
+          }
 
         }
       }
     });
   }
 
-  public void comeBackLater(FeatureEvent evt)
-  {}
-
-  public void newFeatures(FeatureEvent evt)
-  {
-    seqPanel.seqCanvas.fr.findAllFeatures();
-    repaint();
-  }
-
   /**
    * DOCUMENT ME!
    */
@@ -610,6 +629,7 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+
     int oldX = av.getStartRes();
     int oldY = av.getStartSeq();
 
@@ -627,10 +647,26 @@ 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
       {
@@ -692,8 +728,14 @@ 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);
@@ -833,7 +875,7 @@ 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;
@@ -912,10 +954,15 @@ 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);
@@ -980,8 +1027,12 @@ 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;
@@ -996,7 +1047,6 @@ public class AlignmentPanel extends GAlignmentPanel
         width = alignFrame.getWidth() - 22;
       }
       else
-
         width = seqPanel.getWidth() + idPanel.getWidth();
 
     }
@@ -1229,7 +1279,12 @@ 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;
   }