X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=f1a8af7f4eab439f57b57e748c03748f81e3f16c;hb=7d66757c0ac1b57953fb113cdae34dc94b03dd17;hp=e146754bdb7c3a2fa0d50f90bdab25564c6983db;hpb=5221c772a071266446c5c959f34ec89c8e874201;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index e146754..f1a8af7 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -41,6 +41,7 @@ import java.awt.event.MouseWheelListener;
 import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Collections;
 import java.util.List;
 
@@ -56,6 +57,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.ContactRange;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.HiddenColumns;
@@ -70,6 +72,7 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 
 /**
  * AnnotationPanel displays visible portion of annotation rows below unwrapped
@@ -589,79 +592,166 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (graphStretch != -1)
     {
 
-      if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)
+      if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)
       {
+        // data in row has position on y as well as x axis
         if (evt.isAltDown() || evt.isAltGraphDown())
         {
           dragMode = DragMode.MatrixSelect;
           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());
+    if (rowIndex == null)
+    {
+      jalview.bin.Console
+              .error("IMPLEMENTATION ERROR: matrix click out of range.");
+      return false;
+    }
+    int yOffset = rowIndex[1];
+
+    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);
-            int fr, to;
-            fr = Math.min(cXci.cStart, cXci.cEnd);
-            to = Math.max(cXci.cStart, cXci.cEnd);
-            // select corresponding range in segment under mouse
+            SequenceI rseq = clicked.sequenceRef;
+            BitSet grp = matrix.getGroupsFor(currentX);
+            for (int c = fr; c <= to; c++)
             {
-              for (int c = fr; c <= to; c++)
-              {
-                av.getColumnSelection().addElement(c);
-              }
-              av.getColumnSelection().addElement(currentX);
+              BitSet additionalGrp = matrix.getGroupsFor(c);
+              grp.or(additionalGrp);
             }
-            // and also select everything lower than the max range adjacent
-            // (kind of works)
+            HiddenColumns hc = av.getAlignment().getHiddenColumns();
+            for (int p = grp.nextSetBit(0); p >= 0; p = grp
+                    .nextSetBit(p + 1))
             {
-              int c = fr - 1;
-              ContactRange cr = forCurrentX.getRangeFor(fr, to);
-              double cval;
-              while (c > 0)
-              {
-                cval = forCurrentX.getContactAt(c);
-                if (// cr.getMin() <= cval &&
-                cval <= cr.getMax())
-                {
-                  av.getColumnSelection().addElement(c--);
-                }
-                else
-                {
-                  break;
-                }
-              }
-              c = to;
-              while (c < forCurrentX.getContactHeight())
+              int offp = (rseq != null)
+                      ? rseq.findIndex(rseq.getStart() - 1 + p)
+                      : p;
+
+              if (!av.hasHiddenColumns() || hc.isVisible(offp))
               {
-                cval = forCurrentX.getContactAt(c);
-                if (// cr.getMin() <= cval &&
-                cval <= cr.getMax())
-                {
-                  av.getColumnSelection().addElement(c++);
-                }
-                else
-                {
-                  break;
-                }
+                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
+            {
+              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);
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
+    av.sendSelection();
+    return true;
   }
 
   /**
@@ -736,7 +826,10 @@ 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
@@ -823,7 +916,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
          * but could also be a matrix drag
          */
         if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
-                .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER))
+                .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP))
         {
           /*
            * dragging in a matrix
@@ -920,12 +1013,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (rowIndex == null || toRowIndex == null)
     {
-      System.out.println("Drag out of range. needs to be clipped");
+      jalview.bin.Console.trace("Drag out of range. needs to be clipped");
 
     }
     if (rowIndex[0] != toRowIndex[0])
     {
-      System.out.println("Drag went to another row. needs to be clipped");
+      jalview.bin.Console
+              .trace("Drag went to another row. needs to be clipped");
     }
 
     // rectangular selection on matrix style annotation
@@ -952,13 +1046,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               rowIndex[1] - deltaY);
 
       // mark rectangular region formed by drag
-      System.err.println("Matrix Selection from last(" + fromXc + ",["
-              + lastXci.cStart + "," + lastXci.cEnd + "]) to cur(" + toXc
-              + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
+      jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
+              + ",[" + lastXci.cStart + "," + lastXci.cEnd + "]) to cur("
+              + toXc + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
       int fr, to;
       fr = Math.min(lastXci.cStart, lastXci.cEnd);
       to = Math.max(lastXci.cStart, lastXci.cEnd);
-      System.err.println("Marking " + fr + " to " + to);
+      jalview.bin.Console.trace("Marking " + fr + " to " + to);
       for (int c = fr; c <= to; c++)
       {
         if (cma.sequenceRef != null)
@@ -973,7 +1067,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
       fr = Math.min(cXci.cStart, cXci.cEnd);
       to = Math.max(cXci.cStart, cXci.cEnd);
-      System.err.println("Marking " + fr + " to " + to);
+      jalview.bin.Console.trace("Marking " + fr + " to " + to);
       for (int c = fr; c <= to; c++)
       {
         if (cma.sequenceRef != null)
@@ -989,7 +1083,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       fr = Math.min(lastX, currentX);
       to = Math.max(lastX, currentX);
 
-      System.err.println("Marking " + fr + " to " + to);
+      jalview.bin.Console.trace("Marking " + fr + " to " + to);
       for (int c = fr; c <= to; c++)
       {
         av.getColumnSelection().addElement(c);
@@ -1146,7 +1240,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       tooltip = ann.annotations[column].description;
     }
     // TODO abstract tooltip generator so different implementations can be built
-    if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
+    if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
     {
       ContactListI clist = av.getContactList(ann, column);
       if (clist != null)
@@ -1313,8 +1407,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
-            + 1) * av.getCharWidth();
+    updateFadedImageWidth();
     if (imgWidth < 1)
     {
       return;
@@ -1382,6 +1475,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     g.drawImage(image, 0, 0, this);
   }
 
+  public void updateFadedImageWidth()
+  {
+    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+            + 1) * av.getCharWidth();
+
+  }
+
   /**
    * set true to enable redraw timing debug output on stderr
    */
@@ -1557,6 +1657,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public int getFadedImageWidth()
   {
+    updateFadedImageWidth();
     return imgWidth;
   }