X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=e1193c92505d13694f6348c8478de23b5b0c9952;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=82021ac9ef6837eac663f6a8fb3a604ce3d9ae16;hpb=5830c6b18969d8eb7801b9df28ea9fb2c4dd5152;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 82021ac..e1193c9 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;
@@ -66,10 +68,12 @@ import jalview.renderer.AwtRenderPanelI;
 import jalview.renderer.ContactGeometry;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.MappableContactMatrixI;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 
 /**
@@ -599,73 +603,210 @@ 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());
+    if (rowIndex == null)
+    {
+      jalview.bin.Console
+              .error("IMPLEMENTATION ERROR: matrix click out of range.");
+      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)
+    {
+      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);
+      if (cXci != null)
+      {
+        /**
+         * 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);
+
+        // double click selects the whole group
+        if (evt.getClickCount() == 2)
         {
-          GraphLine thr = aa[graphStretch].getThreshold();
-          int currentX = getColumnForXPos(evt.getX());
-          ContactListI forCurrentX = av.getContactList(aa[graphStretch],
-                  currentX);
-          if (forCurrentX != null)
+          ContactMatrixI matrix = av.getContactMatrix(clicked);
+
+          if (matrix != null)
           {
-            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
+            // simplest approach is to select all group containing column
+            if (matrix.hasGroups())
             {
+              SequenceI rseq = clicked.sequenceRef;
+              BitSet grp = new BitSet();
+              grp.or(matrix.getGroupsFor(currentX));
+              // TODO: cXci needs to be mapped to real groups
               for (int c = fr; c <= to; c++)
               {
-                av.getColumnSelection().addElement(c);
+                BitSet additionalGrp = matrix.getGroupsFor(c);
+                grp.or(additionalGrp);
               }
-              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;
-              while (c > 0)
+
+              HiddenColumns hc = av.getAlignment().getHiddenColumns();
+              ColumnSelection cs = av.getColumnSelection();
+
+              for (int p = grp.nextSetBit(0); p >= 0; p = grp
+                      .nextSetBit(p + 1))
               {
-                cval = forCurrentX.getContactAt(c);
-                if (// cr.getMin() <= cval &&
-                cval <= cr.getMax())
+                if (matrix instanceof MappableContactMatrixI)
                 {
-                  av.getColumnSelection().addElement(c--);
+                  // find the end of this run of set bits
+                  int nextp = grp.nextClearBit(p) - 1;
+                  int[] pos = ((MappableContactMatrixI) matrix)
+                          .getMappedPositionsFor(rseq, p, nextp);
+                  p = nextp;
+
+                  if (pos != null)
+                  {
+                    for (int pos_p = pos[0]; pos_p <= pos[1]; pos_p++)
+                    {
+                      int col = rseq.findIndex(pos_p) - 1;
+                      if (col >= 0 && (!av.hasHiddenColumns()
+                              || hc.isVisible(col)))
+                      {
+                        cs.addElement(col);
+                      }
+                    }
+                  }
                 }
                 else
                 {
-                  break;
+                  int offp = (rseq != null)
+                          ? rseq.findIndex(rseq.getStart() - 1 + p)
+                          : p;
+
+                  if (!av.hasHiddenColumns() || hc.isVisible(offp))
+                  {
+                    cs.addElement(offp);
+                  }
                 }
               }
-              c = to;
-              while (c < forCurrentX.getContactHeight())
+            }
+            // 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
+          {
+            int[] rng = forCurrentX.getMappedPositionsFor(fr, to);
+            if (rng != null)
+            {
+              av.getColumnSelection().addRangeOfElements(rng, true);
+            }
+            av.getColumnSelection().addElement(currentX);
+          }
+          // PAE SPECIFIC
+          // and also select everything lower than the max range adjacent
+          // (kind of works)
+          if (evt.isControlDown()
+                  && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+          {
+            int c = fr;
+            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)
               {
-                cval = forCurrentX.getContactAt(c);
-                if (// cr.getMin() <= cval &&
-                cval <= cr.getMax())
+                int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+                if (cols != null)
                 {
-                  av.getColumnSelection().addElement(c++);
+                  av.getColumnSelection().addRangeOfElements(cols, true);
                 }
                 else
                 {
                   break;
                 }
               }
+              c--;
+            }
+            c = to;
+            while (c < forCurrentX.getContactHeight())
+            {
+              cval = forCurrentX.getContactAt(c);
+              if (// cr.getMin() <= cval &&
+              cval <= thresh)
+              {
+                int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+                if (cols != null)
+                {
+                  av.getColumnSelection().addRangeOfElements(cols, true);
+                }
+              }
+              else
+              {
+                break;
+              }
+              c++;
+
             }
           }
+
         }
       }
     }
-    else
-    {
-      ap.getScalePanel().mousePressed(evt);
-    }
+    ap.paintAlignment(false, false);
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
+    av.sendSelection();
+    return true;
   }
 
   /**
@@ -740,7 +881,10 @@ 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
@@ -924,12 +1068,13 @@ 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
@@ -945,55 +1090,47 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (forFromX != null && forToX != null)
     {
-      ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
+      // 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 = lastXcgeom
-              .mapFor(rowIndex[1], rowIndex[1] - deltaY);
-
-      ContactGeometry cXcgeom = new ContactGeometry(forToX,
-              cma.graphHeight);
-      ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
-              rowIndex[1] - deltaY);
+      ContactGeometry.contactInterval lastXci = xcgeom.mapFor(rowIndex[1]);
+      ContactGeometry.contactInterval cXci = xcgeom
+              .mapFor(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);
-      for (int c = fr; c <= to; c++)
-      {
-        if (cma.sequenceRef != null)
-        {
-          int col = cma.sequenceRef.findIndex(c);
-          av.getColumnSelection().addElement(col);
-        }
-        else
-        {
-          av.getColumnSelection().addElement(c);
-        }
-      }
-      fr = Math.min(cXci.cStart, cXci.cEnd);
-      to = Math.max(cXci.cStart, cXci.cEnd);
-      System.err.println("Marking " + fr + " to " + to);
-      for (int c = fr; c <= to; c++)
+      fr = Math.min(lastXci.cStart, cXci.cStart);
+      to = Math.max(lastXci.cEnd, cXci.cEnd);
+      int[] mappedPos = forFromX.getMappedPositionsFor(fr, to);
+      if (mappedPos != null)
       {
-        if (cma.sequenceRef != null)
-        {
-          int col = cma.sequenceRef.findIndex(c);
-          av.getColumnSelection().addElement(col);
-        }
-        else
+        jalview.bin.Console.trace("Marking " + fr + " to " + to
+                + " mapping to sequence positions " + mappedPos[0] + " to "
+                + mappedPos[1]);
+        for (int pair = 0; pair < mappedPos.length; pair += 2)
         {
-          av.getColumnSelection().addElement(c);
+          for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
+          // {
+          // if (cma.sequenceRef != null)
+          // {
+          // int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+          // av.getColumnSelection().addElement(col);
+          // }
+          // else
+          {
+            av.getColumnSelection().addElement(c - 1);
+          }
         }
       }
       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);
@@ -1098,7 +1235,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         row = i;
         res[0] = row;
-        res[1] = height - yPos;
+        res[1] = yPos - lheight;
         break;
       }
     }
@@ -1152,20 +1289,43 @@ 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)
       {
         ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
         ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
         ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
-        tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
-                + " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
+        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);
+        tooltip = tooltipb.toString();
         int col = ann.sequenceRef.findPosition(column);
+        int[][] highlightPos;
+        int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd);
+        if (mappedPos != null)
+        {
+          highlightPos = new int[1 + mappedPos.length][2];
+          highlightPos[0] = new int[] { col, col };
+          for (int p = 0, h = 0; p < mappedPos.length; h++, p += 2)
+          {
+            highlightPos[h][0] = ann.sequenceRef
+                    .findPosition(mappedPos[p] - 1);
+            highlightPos[h][1] = ann.sequenceRef
+                    .findPosition(mappedPos[p + 1] - 1);
+          }
+        }
+        else
+        {
+          highlightPos = new int[][] { new int[] { col, col } };
+        }
         ap.getStructureSelectionManager()
-                .highlightPositionsOn(ann.sequenceRef, new int[][]
-                { new int[] { col, col },
-                    new int[]
-                    { ci.cStart, ci.cEnd } }, null);
+                .highlightPositionsOn(ann.sequenceRef, highlightPos, null);
       }
     }
     return tooltip;
@@ -1317,8 +1477,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
-            + 1) * av.getCharWidth();
+    updateFadedImageWidth();
     if (imgWidth < 1)
     {
       return;
@@ -1339,7 +1498,7 @@ 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;
@@ -1386,6 +1545,13 @@ 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
    */
@@ -1475,7 +1641,8 @@ 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);
@@ -1561,6 +1728,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public int getFadedImageWidth()
   {
+    updateFadedImageWidth();
     return imgWidth;
   }