X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=0f6901d018a510e3ae4909f71daa407de87f297a;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=844c1abfaa242c082fa7ad624df27783e2bd4421;hpb=c5443fe79c3846608bdaad1e548ba80ca65317ac;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 844c1ab..0f6901d 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -108,7 +108,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     public int adjustPanelHeight()
     {
         // setHeight of panels
-        image = null;
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
         int height = 0;
 
@@ -168,6 +167,15 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
         Annotation[] anot = aa[activeRow].annotations;
 
+        if (anot.length < av.getColumnSelection().getMax())
+        {
+          Annotation[] temp = new Annotation[av.getColumnSelection().getMax()+2 ];
+          System.arraycopy(anot, 0, temp, 0, anot.length);
+          anot = temp;
+          aa[activeRow].annotations = anot;
+        }
+
+
         if (evt.getActionCommand().equals(REMOVE))
         {
             for (int i = 0; i < av.getColumnSelection().size(); i++)
@@ -280,7 +288,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     public void mousePressed(MouseEvent evt)
     {
 
-
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
         if(aa==null)
           return;
@@ -350,6 +357,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
+        if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
         min = res;
         max = res;
 
@@ -431,6 +441,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
+        if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
         SequenceGroup sg = av.getSelectionGroup();
 
         if (res < min)
@@ -488,6 +501,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         if (aa == null)
         {
+          this.setToolTipText(null);
             return;
         }
 
@@ -509,12 +523,20 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             }
         }
 
+        if(row==-1)
+       {
+         this.setToolTipText(null);
+         return;
+       }
+
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
         if(av.hasHiddenColumns)
           res = av.getColumnSelection().adjustForHiddenColumns(res);
 
-        if (row > -1 && res<aa[row].annotations.length)
+        if ( aa[row].annotations!=null
+             && row > -1
+             && res < (int) aa[row].annotations.length)
         {
             if(aa[row].graphGroup>-1)
             {
@@ -530,18 +552,23 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 this.setToolTipText(tip.toString() + "</html>");
               }
             }
-            else if(aa[row].annotations[res] != null)
+            else if(aa[row].annotations[res] != null
+                    && aa[row].annotations[res].description!=null)
               this.setToolTipText(aa[row].annotations[res].description);
 
             if(aa[row].annotations[res]!=null)
             {
               StringBuffer text = new StringBuffer("Sequence position " +
-                                                   (res + 1) + "  " +
-                                                   aa[row].annotations[res].description);
+                                                   (res + 1));
+
+              if (aa[row].annotations[res].description != null)
+                text.append("  " + aa[row].annotations[res].description);
 
               ap.alignFrame.statusBar.setText(text.toString());
             }
         }
+        else
+          this.setToolTipText(null);
     }
 
     /**
@@ -654,6 +681,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     {
       if(av.updatingConsensus || av.updatingConservation)
       {
+        if(image==null)
+         {
+           return;
+         }
         //We'll keep a record of the old image,
         //and draw a faded image until the calculation
         //has completed
@@ -745,7 +776,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 }
             }
 
-            if (av.updatingConsensus && aa[i].label.equals("Consensus"))
+            if (av.updatingConsensus && aa[i]==av.consensus)
             {
               y += av.charHeight;
 
@@ -1022,7 +1053,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
                 default:
                   g.setColor(Color.gray);
-                  if(!av.wrapAlignment || endRes==av.endRes)
                   g.fillRect(lastSSX, y + 6 + iconOffset,
                              (x*av.charWidth) - lastSSX, 2);