JAL-4095 slightly better threshold setting and todos for improvement

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index c3b44ce..b68ff01 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -57,6 +57,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactRange;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
@@ -69,6 +70,7 @@ 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
@@ -588,8 +590,9 @@ 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;
@@ -598,6 +601,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
         else
         {
+          GraphLine thr = aa[graphStretch].getThreshold();
           int currentX = getColumnForXPos(evt.getX());
           ContactListI forCurrentX = av.getContactList(aa[graphStretch],
                   currentX);
@@ -610,11 +614,54 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
             int fr, to;
             fr = Math.min(cXci.cStart, cXci.cEnd);
             to = Math.max(cXci.cStart, cXci.cEnd);
-            for (int c = fr; c <= to; c++)
+            // select corresponding range in segment under mouse
             {
-              av.getColumnSelection().addElement(c);
+              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;
+                }
+              }
             }
-            av.getColumnSelection().addElement(currentX);
           }
         }
       }
@@ -784,7 +831,7 @@ 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
@@ -1107,7 +1154,7 @@ 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)
@@ -1284,24 +1331,37 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
-      try
-      {
-        image = new BufferedImage(imgWidth,
-                ap.getAnnotationPanel().getHeight(),
-                BufferedImage.TYPE_INT_RGB);
-      } catch (OutOfMemoryError oom)
+      boolean tried = false;
+      image = null;
+      while (image == null && !tried)
       {
         try
         {
-          System.gc();
-        } catch (Exception x)
+          image = new BufferedImage(imgWidth,
+                  ap.getAnnotationPanel().getHeight(),
+                  BufferedImage.TYPE_INT_RGB);
+          tried = true;
+        } catch (IllegalArgumentException exc)
         {
+          System.err.println(
+                  "Serious issue with viewport geometry imgWidth requested was "
+                          + imgWidth);
+          return;
+        } catch (OutOfMemoryError oom)
+        {
+          try
+          {
+            System.gc();
+          } catch (Exception x)
+          {
+          }
+          ;
+          new OOMWarning(
+                  "Couldn't allocate memory to redraw screen. Please restart Jalview",
+                  oom);
+          return;
         }
-        ;
-        new OOMWarning(
-                "Couldn't allocate memory to redraw screen. Please restart Jalview",
-                oom);
-        return;
+
       }
       gg = (Graphics2D) image.getGraphics();