JAL-2349 handle matrix_clicked on mouse_release rather than mouse_pressed so click...

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index b112383..c7751e3 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -601,130 +601,154 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           firstDragX = mouseDragLastX;
           firstDragY = mouseDragLastY;
         }
-        else
+      }
+    }
+    else
+    {
+      // no row (or row that can be adjusted) was pressed. Simulate a ruler click
+      ap.getScalePanel().mousePressed(evt);
+    }
+  }
+
+  /**
+   * checks whether the annotation row under the mouse click evt's handles the
+   * event
+   * 
+   * @param evt
+   * @return false if evt was not handled
+   */
+  boolean matrix_clicked(MouseEvent evt)
+  {
+    int[] rowIndex = getRowIndexAndOffset(evt.getY(),
+            av.getAlignment().getAlignmentAnnotation());
+    int yOffset = rowIndex[1];
+
+    if (rowIndex == null)
+    {
+      System.err.println("IMPLEMENTATION ERROR: matrix click out of range.");
+    }
+    AlignmentAnnotation clicked = av.getAlignment()
+            .getAlignmentAnnotation()[rowIndex[0]];
+    if (clicked.graph != AlignmentAnnotation.CONTACT_MAP)
+    {
+      return false;
+    }
+
+    // TODO - use existing threshold to select related sections of matrix
+    GraphLine thr = clicked.getThreshold();
+
+    int currentX = getColumnForXPos(evt.getX());
+    ContactListI forCurrentX = av.getContactList(clicked, currentX);
+    if (forCurrentX != null)
+    {
+      ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
+              clicked.graphHeight);
+      ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
+              yOffset);
+      /**
+       * start and end range corresponding to the row range under the mouse at
+       * column currentX
+       */
+      int fr, to;
+      fr = Math.min(cXci.cStart, cXci.cEnd);
+      to = Math.max(cXci.cStart, cXci.cEnd);
+
+      if (evt.isControlDown())
+      {
+        ContactMatrixI matrix = av.getContactMatrix(clicked);
+
+        if (matrix != null)
         {
-          GraphLine thr = aa[graphStretch].getThreshold();
-          
-          int currentX = getColumnForXPos(evt.getX());
-          ContactListI forCurrentX = av.getContactList(aa[graphStretch],
-                  currentX);
-          if (forCurrentX != null)
+          // simplest approach is to select all group containing column
+          if (matrix.hasGroups())
           {
-            ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
-                    aa[graphStretch].graphHeight);
-            ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
-                    yOffset);
-            /**
-             * start and end range corresponding to the row range under the
-             * mouse at column currentX
-             */
-            int fr, to;
-            fr = Math.min(cXci.cStart, cXci.cEnd);
-            to = Math.max(cXci.cStart, cXci.cEnd);
-
-            if (evt.isControlDown())
+            SequenceI rseq = clicked.sequenceRef;
+            BitSet grp = matrix.getGroupsFor(currentX);
+            for (int c = fr; c <= to; c++)
             {
-              ContactMatrixI matrix = av.getContactMatrix(aa[graphStretch]);
-              
-              if (matrix != null)
-              {
-                // simplest approach is to select all group containing column
-                if (matrix.hasGroups())
-                {
-                  SequenceI rseq = aa[graphStretch].sequenceRef;
-                  BitSet grp = matrix.getGroupsFor(currentX);
-                  for (int c=fr;c<=to; c++)
-                  {
-                    BitSet additionalGrp = matrix.getGroupsFor(c);
-                    grp.or(additionalGrp);
-                  }
-                  HiddenColumns hc = av.getAlignment().getHiddenColumns();
-                  for (int p = grp.nextSetBit(0); p >= 0; p = grp
-                          .nextSetBit(p + 1))
-                  {
-                    int offp = (rseq != null)
-                            ? rseq.findIndex(rseq.getStart() - 1 + p)
-                            : p;
-
-                    if (!av.hasHiddenColumns() || hc.isVisible(offp))
-                    {
-                      av.getColumnSelection().addElement(offp);
-                    }
-                  }
-                }
-                // possible alternative for interactive selection - threshold
-                // gives 'ceiling' for forming a cluster
-                // when a row+column is selected, farthest common ancestor less
-                // than thr is used to compute cluster
+              BitSet additionalGrp = matrix.getGroupsFor(c);
+              grp.or(additionalGrp);
+            }
+            HiddenColumns hc = av.getAlignment().getHiddenColumns();
+            for (int p = grp.nextSetBit(0); p >= 0; p = grp
+                    .nextSetBit(p + 1))
+            {
+              int offp = (rseq != null)
+                      ? rseq.findIndex(rseq.getStart() - 1 + p)
+                      : p;
 
+              if (!av.hasHiddenColumns() || hc.isVisible(offp))
+              {
+                av.getColumnSelection().addElement(offp);
               }
             }
+          }
+          // possible alternative for interactive selection - threshold
+          // gives 'ceiling' for forming a cluster
+          // when a row+column is selected, farthest common ancestor less
+          // than thr is used to compute cluster
+
+        }
+      }
+      else
+      {
+        // select corresponding range in segment under mouse
+        {
+          for (int c = fr; c <= to; c++)
+          {
+            av.getColumnSelection().addElement(c);
+          }
+          av.getColumnSelection().addElement(currentX);
+        }
+        // PAE SPECIFIC
+        // and also select everything lower than the max range adjacent
+        // (kind of works)
+        if (PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+        {
+          int c = fr - 1;
+          ContactRange cr = forCurrentX.getRangeFor(fr, to);
+          double cval;
+          // TODO: could use GraphLine instead of arbitrary picking
+          // TODO: could report mean/median/variance for partitions
+          // (contiguous selected vs unselected regions and inter-contig
+          // regions)
+          // controls feathering - what other elements in row/column
+          // should we select
+          double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15;
+          while (c > 0)
+          {
+            cval = forCurrentX.getContactAt(c);
+            if (// cr.getMin() <= cval &&
+            cval <= thresh)
+            {
+              av.getColumnSelection().addElement(c--);
+            }
             else
             {
-              // select corresponding range in segment under mouse
-              {
-                for (int c = fr; c <= to; c++)
-                {
-                  av.getColumnSelection().addElement(c);
-                }
-                av.getColumnSelection().addElement(currentX);
-              }
-              // PAE SPECIFIC
-              // and also select everything lower than the max range adjacent
-              // (kind of works)
-              if (PAEContactMatrix.PAEMATRIX
-                      .equals(aa[graphStretch].getCalcId()))
-              {
-                int c = fr - 1;
-                ContactRange cr = forCurrentX.getRangeFor(fr, to);
-                double cval;
-                // TODO: could use GraphLine instead of arbitrary picking
-                // TODO: could report mean/median/variance for partitions
-                // (contiguous selected vs unselected regions and inter-contig
-                // regions)
-                // controls feathering - what other elements in row/column
-                // should we select
-                double thresh = cr.getMean()
-                        + (cr.getMax() - cr.getMean()) * .15;
-                while (c > 0)
-                {
-                  cval = forCurrentX.getContactAt(c);
-                  if (// cr.getMin() <= cval &&
-                  cval <= thresh)
-                  {
-                    av.getColumnSelection().addElement(c--);
-                  }
-                  else
-                  {
-                    break;
-                  }
-                }
-                c = to;
-                while (c < forCurrentX.getContactHeight())
-                {
-                  cval = forCurrentX.getContactAt(c);
-                  if (// cr.getMin() <= cval &&
-                  cval <= thresh)
-                  {
-                    av.getColumnSelection().addElement(c++);
-                  }
-                  else
-                  {
-                    break;
-                  }
-                }
-              }
+              break;
+            }
+          }
+          c = to;
+          while (c < forCurrentX.getContactHeight())
+          {
+            cval = forCurrentX.getContactAt(c);
+            if (// cr.getMin() <= cval &&
+            cval <= thresh)
+            {
+              av.getColumnSelection().addElement(c++);
+            }
+            else
+            {
+              break;
             }
           }
         }
       }
     }
-    else
-    {
-      ap.getScalePanel().mousePressed(evt);
-    }
-  }
+    ap.paintAlignment(false, false);
 
+    return true;
+  }
   /**
    * Construct and display a context menu at the right-click position
    * 
@@ -797,7 +821,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       ap.adjustAnnotationHeight();
     }
     dragMode = DragMode.Undefined;
-    ap.getScalePanel().mouseReleased(evt);
+    if (!matrix_clicked(evt))
+    {
+      ap.getScalePanel().mouseReleased(evt);
+    }
 
     /*
      * isPopupTrigger is set in mouseReleased on Windows