Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / gui / AnnotationPanel.java

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8e04048..8a957bc 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -737,7 +737,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         if (evt.isControlDown()
                 && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
         {
-          int c = fr - 1;
+          int c = fr;
           ContactRange cr = forCurrentX.getRangeFor(fr, to);
           double cval;
           // TODO: could use GraphLine instead of arbitrary picking
@@ -747,7 +747,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           // controls feathering - what other elements in row/column
           // should we select
           double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15;
-          while (c > 0)
+          while (c >= 0)
           {
             cval = forCurrentX.getContactAt(c);
             if (// cr.getMin() <= cval &&
@@ -1078,12 +1078,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
               cma.graphHeight);
       ContactGeometry.contactInterval lastXci = lastXcgeom
-              .mapFor(rowIndex[1], rowIndex[1] - deltaY);
+              .mapFor(rowIndex[1], rowIndex[1] + deltaY);
 
       ContactGeometry cXcgeom = new ContactGeometry(forToX,
               cma.graphHeight);
       ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
-              rowIndex[1] - deltaY);
+              rowIndex[1] + deltaY);
 
       // mark rectangular region formed by drag
       jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
@@ -1247,7 +1247,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         row = i;
         res[0] = row;
-        res[1] = height - yPos;
+        res[1] = yPos-lheight;
         break;
       }
     }
@@ -1301,6 +1301,10 @@ 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)
+      {
+        return null;
+      }
       ContactListI clist = av.getContactList(ann, column);
       if (clist != null)
       {
@@ -1503,7 +1507,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           tried = true;
         } catch (IllegalArgumentException exc)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Serious issue with viewport geometry imgWidth requested was "
                           + imgWidth);
           return;
@@ -1646,7 +1650,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               && (fadedImage == null || fadedImage.getWidth() != imgWidth
                       || fadedImage.getHeight() != image.getHeight()))
       {
-        // System.err.println("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);