X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=b1a8b8bb2cbc279772ba7c5bca5158274fd8c232;hb=54b44faea7413a39963c535fa728b6e415dfe989;hp=e0c327f769e17409f8dbf9f3df67102b55bc068a;hpb=49057b644ae4dc904a3245b695ba86678ac01ede;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index e0c327f..b1a8b8b 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,
@@ -107,12 +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;
     int ap = annotationPanel.adjustPanelHeight();
     annotationPanel.repaint();
     Dimension d = calculateIdWidth();
@@ -138,16 +140,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
   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();
 
@@ -170,7 +170,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     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;
@@ -219,19 +219,24 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
         }
         else
         {
-          int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-              seqCanvas.getSize().width);
-          if (start < av.getStartRes() || start > (av.getStartRes() + cwidth))
-          {
-            vscroll.setValue(start / cwidth);
-            av.startRes = vscroll.getValue() * cwidth;
-          }
+          scrollToWrappedVisible(start);
         }
     }
 
     repaint();
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
+
   public OverviewPanel getOverviewPanel()
   {
     return overviewPanel;
@@ -247,7 +252,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     if (!av.wrapAlignment)
     {
       annotationSpaceFillerHolder.setVisible(b);
-      annotationScroller.setVisible(b);
+      annotationPanel.setVisible(b);
     }
     validate();
     repaint();
@@ -264,12 +269,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
 
     if (wrap)
     {
-      annotationScroller.setVisible(false);
+      annotationPanel.setVisible(false);
       annotationSpaceFillerHolder.setVisible(false);
     }
     else if (av.showAnnotation)
     {
-      annotationScroller.setVisible(true);
+      annotationPanel.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
     }
 
@@ -306,14 +311,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       }
       setScrollValues(hscroll.getValue(), vscroll.getValue()+1);
     }
+
     repaint();
     return true;
   }
 
   public boolean scrollRight(boolean right)
   {
-
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
@@ -381,6 +386,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     av.setEndSeq(endSeq);
     hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
     vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
+
+    if(overviewPanel!=null)
+          overviewPanel.setBoxPosition();
   }
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -513,7 +521,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
   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();
 
@@ -548,11 +555,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
       //  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);