X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=44370d40e97b2af574ef6e56b24a6c09d44ad561;hb=a28c9340eeadfdaa551a21b9dea1d0f1530126e3;hp=b46876a17d5e63c86b144d442420f1381f28e3bb;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index b46876a..44370d4 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -22,10 +22,8 @@ package jalview.appletgui;
 import java.awt.*;
 import java.awt.event.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.jbappletgui.*;
-import jalview.schemes.*;
 
 public class AlignmentPanel
     extends GAlignmentPanel implements AdjustmentListener
@@ -44,8 +42,13 @@ public class AlignmentPanel
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
+  boolean MAC = false;
+
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
+    if(System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
     alignFrame = af;
     this.av = av;
     seqPanel = new SeqPanel(av, this);
@@ -167,6 +170,9 @@ public class AlignmentPanel
     hscrollFillerPanel.setSize(d);
 
     alignFrame.pack();
+
+    if(overviewPanel!=null)
+          overviewPanel.updateOverviewImage();
   }
 
   public void setIdWidth(int w, int h)
@@ -198,14 +204,7 @@ public class AlignmentPanel
     while (i < al.getHeight() && al.getSequenceAt(i) != null)
     {
       SequenceI s = al.getSequenceAt(i);
-      if (av.getShowFullId())
-      {
-        id = s.getDisplayId();
-      }
-      else
-      {
-        id = s.getName();
-      }
+      id = s.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
 
       if (fm.stringWidth(id) > idWidth)
       {
@@ -266,21 +265,33 @@ public class AlignmentPanel
 
   public void setAnnotationVisible(boolean b)
   {
-    annotationSpaceFillerHolder.setVisible(b);
-    annotationScroller.setVisible(b);
+    if (!av.wrapAlignment)
+    {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationScroller.setVisible(b);
+    }
     validate();
     repaint();
   }
 
   public void setWrapAlignment(boolean wrap)
   {
+    av.startSeq = 0;
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
 
-    av.setShowAnnotation(!wrap);
-    annotationScroller.setVisible(!wrap);
-    annotationSpaceFillerHolder.setVisible(!wrap);
+    if (wrap)
+    {
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.showAnnotation)
+    {
+      annotationScroller.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
+    }
+
     idSpaceFillerPanel1.setVisible(!wrap);
 
     validate();
@@ -429,7 +440,7 @@ public class AlignmentPanel
       overviewPanel.setBoxPosition();
     }
 
-    if (av.getWrapAlignment() || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint || MAC)
     {
       repaint();
     }
@@ -459,13 +470,8 @@ public class AlignmentPanel
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
                                         annotationPanel.getSize().height);
-    alabels.setSize(d.width, annotationPanel.getSize().height);
 
-    alabels.repaint();
-    idPanel.idCanvas.repaint();
-    seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
     if (av.getWrapAlignment())
     {
@@ -481,5 +487,11 @@ public class AlignmentPanel
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
+    alabels.repaint();
+    idPanel.idCanvas.repaint();
+    seqPanel.seqCanvas.repaint();
+    scalePanel.repaint();
+    annotationPanel.repaint();
+
   }
 }