X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=8c935992ed529e658cc29d37de942ccc87518a7f;hb=37a5dfc3c72a42689e90ad8a0e118e8855d9868b;hp=ed88418c0ecf42a60cc4c258c38e6c2c7e5fb887;hpb=1ed150e97b6a7df6ebe5cf92ead96cd147a58b7e;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index ed88418..8c93599 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -63,13 +63,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     scalePanel = new ScalePanel(av, this);
     idwidthAdjuster = new IdwidthAdjuster(this);
     annotationPanel = new AnnotationPanel(this);
+
+    sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);
+
     alabels = new AnnotationLabels(this);
 
     setAnnotationVisible(av.showAnnotation);
 
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-    annotationScroller.add(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
@@ -93,7 +95,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     idPanel.idCanvas.setSize(d);
 
     hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
-    annotationScroller.setSize(annotationPanel.getSize());
 
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
@@ -107,13 +108,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   {
     // set idCanvas bufferedImage to null
     // to prevent drawing old image
-    idPanel.idCanvas.image =null;
+    idPanel.idCanvas.image = null;
     FontMetrics fm = getFontMetrics(av.getFont());
 
     scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
     idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
 
-annotationPanel.image = null;
+    annotationPanel.image = null;
     int ap = annotationPanel.adjustPanelHeight();
     annotationPanel.repaint();
     Dimension d = calculateIdWidth();
@@ -139,16 +140,14 @@ annotationPanel.image = null;
 
   Dimension calculateIdWidth()
   {
-    Frame frame = new Frame();
-    frame.addNotify();
-    Graphics g = frame.getGraphics();
-    if (g == null)
+    if (av.nullFrame == null)
     {
-      Frame f = new Frame();
-      f.addNotify();
-      g = f.getGraphics();
+      av.nullFrame = new Frame();
+      av.nullFrame.addNotify();
     }
 
+    Graphics g = av.nullFrame.getGraphics();
+
     FontMetrics fm = g.getFontMetrics(av.font);
     AlignmentI al = av.getAlignment();
 
@@ -171,7 +170,7 @@ annotationPanel.image = null;
     i = 0;
     if (al.getAlignmentAnnotation() != null)
     {
-      fm = g.getFontMetrics(frame.getFont());
+      fm = g.getFontMetrics(av.nullFrame.getFont());
       while (i < al.getAlignmentAnnotation().length)
       {
         String label = al.getAlignmentAnnotation()[i].label;
@@ -253,7 +252,7 @@ annotationPanel.image = null;
     if (!av.wrapAlignment)
     {
       annotationSpaceFillerHolder.setVisible(b);
-      annotationScroller.setVisible(b);
+      annotationPanel.setVisible(b);
     }
     validate();
     repaint();
@@ -270,12 +269,12 @@ annotationPanel.image = null;
 
     if (wrap)
     {
-      annotationScroller.setVisible(false);
+      annotationPanel.setVisible(false);
       annotationSpaceFillerHolder.setVisible(false);
     }
     else if (av.showAnnotation)
     {
-      annotationScroller.setVisible(true);
+      annotationPanel.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
     }
 
@@ -342,30 +341,38 @@ annotationPanel.image = null;
 
   public void setScrollValues(int x, int y)
   {
+    int width = av.alignment.getWidth();
+    int height = av.alignment.getHeight();
+
+    if(av.hasHiddenColumns)
+     width = av.getColumnSelection().findColumnPosition(width);
+
     av.setStartRes(x);
     av.setStartSeq(y);
-    av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1);
+
+    av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) -1);
 
     hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
     vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
 
-    if (hextent > av.alignment.getWidth())
+    if (hextent > width)
     {
-      hextent = av.alignment.getWidth();
+      hextent = width;
     }
-    if (vextent > av.alignment.getHeight())
+
+    if (vextent > height)
     {
-      vextent = av.alignment.getHeight();
+      vextent = height;
     }
 
-    if (hextent + x > av.getAlignment().getWidth())
+    if ( (hextent + x) > width)
     {
-      x = av.getAlignment().getWidth() - hextent;
+      x = width - hextent;
     }
 
-    if (vextent + y > av.getAlignment().getHeight())
+    if ( (vextent + y) > height)
     {
-      y = av.getAlignment().getHeight() - vextent;
+      y = height - vextent;
     }
 
     if (y < 0)
@@ -390,6 +397,7 @@ annotationPanel.image = null;
 
     if(overviewPanel!=null)
           overviewPanel.setBoxPosition();
+
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -478,9 +486,15 @@ annotationPanel.image = null;
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.
-          getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;
+      int maxwidth = av.alignment.getWidth();
+
+      if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+      int max = maxwidth /
+          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +
+          1;
+
       vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
       vscroll.setVisibleAmount(1);
@@ -522,7 +536,6 @@ annotationPanel.image = null;
   BorderLayout borderLayout10 = new BorderLayout();
   protected Panel hscrollFillerPanel = new Panel();
   BorderLayout borderLayout11 = new BorderLayout();
-  public Panel annotationScroller = new Panel();
   BorderLayout borderLayout4 = new BorderLayout();
   BorderLayout borderLayout2 = new BorderLayout();
 
@@ -557,11 +570,9 @@ annotationPanel.image = null;
       //  this.setPreferredSize(new Dimension(220, 166));
       seqPanelHolder.setBackground(Color.white);
       idPanelHolder.setBackground(Color.white);
-      annotationScroller.setLayout(borderLayout2);
       sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
       sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
       seqPanelHolder.add(vscroll, BorderLayout.EAST);
-      sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
 
       //  Panel3.add(secondaryPanelHolder,  BorderLayout.SOUTH);
       this.add(idPanelHolder, BorderLayout.WEST);