X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=e1193c92505d13694f6348c8478de23b5b0c9952;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=f01d7be2b06f0d698c99e376d7b98db1b178fa79;hpb=f047ab25cc45bfc9d130f67d2c56a940751d9c91;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index f01d7be..e1193c9 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -631,7 +631,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return false;
     }
     int yOffset = rowIndex[1];
-
+    AlignmentAnnotation[] allAnnotation = av.getAlignment()
+            .getAlignmentAnnotation();
+    if (allAnnotation == null || rowIndex[0] < 0
+            || rowIndex[0] >= allAnnotation.length)
+    {
+      return false;
+    }
     AlignmentAnnotation clicked = av.getAlignment()
             .getAlignmentAnnotation()[rowIndex[0]];
     if (clicked.graph != AlignmentAnnotation.CONTACT_MAP)
@@ -1084,13 +1090,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (forFromX != null && forToX != null)
     {
-      // FIXME will need two ContactGeometry objects when handling contact matrices with differing numbers of rows at each
+      // FIXME will need two ContactGeometry objects when handling contact
+      // matrices with differing numbers of rows at each
       // column
       ContactGeometry xcgeom = new ContactGeometry(forFromX,
               cma.graphHeight);
-      ContactGeometry.contactInterval lastXci = xcgeom
-              .mapFor(rowIndex[1]);
-      ContactGeometry.contactInterval cXci = xcgeom.mapFor(rowIndex[1] + deltaY);
+      ContactGeometry.contactInterval lastXci = xcgeom.mapFor(rowIndex[1]);
+      ContactGeometry.contactInterval cXci = xcgeom
+              .mapFor(rowIndex[1] + deltaY);
 
       // mark rectangular region formed by drag
       jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
@@ -1116,7 +1123,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           // }
           // else
           {
-            av.getColumnSelection().addElement(c-1);
+            av.getColumnSelection().addElement(c - 1);
           }
         }
       }
@@ -1228,7 +1235,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         row = i;
         res[0] = row;
-        res[1] = yPos-lheight;
+        res[1] = yPos - lheight;
         break;
       }
     }
@@ -1282,7 +1289,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     // TODO abstract tooltip generator so different implementations can be built
     if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
     {
-      if (rowAndOffset>=ann.graphHeight)
+      if (rowAndOffset >= ann.graphHeight)
       {
         return null;
       }
@@ -1293,9 +1300,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
         ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
         StringBuilder tooltipb = new StringBuilder();
-        tooltipb.append("Contact from ")
-        .append(clist.getPosition()).append(", [").append(ci.cStart).append(" - ").append(ci.cEnd).append("]").append("<br/>Mean:");
-        Format.appendPercentage(tooltipb, (float)cr.getMean(),2);
+        tooltipb.append("Contact from ").append(clist.getPosition())
+                .append(", [").append(ci.cStart).append(" - ")
+                .append(ci.cEnd).append("]").append("<br/>Mean:");
+        Format.appendPercentage(tooltipb, (float) cr.getMean(), 2);
         tooltip = tooltipb.toString();
         int col = ann.sequenceRef.findPosition(column);
         int[][] highlightPos;
@@ -1633,7 +1641,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               && (fadedImage == null || fadedImage.getWidth() != imgWidth
                       || fadedImage.getHeight() != image.getHeight()))
       {
-        // jalview.bin.Console.errPrintln("redraw faded image ("+(fadedImage==null ?
+        // jalview.bin.Console.errPrintln("redraw faded image
+        // ("+(fadedImage==null ?
         // "null image" : "") + " lastGood="+lastImageGood+")");
         fadedImage = new BufferedImage(imgWidth, image.getHeight(),
                 BufferedImage.TYPE_INT_RGB);