Merge branch 'features/JAL-3858_PAEsInProjects' into develop

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index e146754..b68ff01 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -70,6 +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
@@ -589,8 +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;
@@ -620,17 +622,23 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               }
               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 <= cr.getMax())
+                cval <= thresh)
                 {
                   av.getColumnSelection().addElement(c--);
                 }
@@ -644,7 +652,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               {
                 cval = forCurrentX.getContactAt(c);
                 if (// cr.getMin() <= cval &&
-                cval <= cr.getMax())
+                cval <= thresh)
                 {
                   av.getColumnSelection().addElement(c++);
                 }
@@ -823,7 +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
@@ -1146,7 +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)