Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphaf...

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index e12cc3f..e146754 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;
@@ -150,6 +151,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   private MouseWheelListener[] _mwl;
 
+  private boolean notJustOne;
+
   /**
    * Creates a new AnnotationPanel object.
    * 
@@ -596,6 +599,7 @@ 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);
@@ -608,11 +612,48 @@ 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);
+            }
+            // and also select everything lower than the max range adjacent
+            // (kind of works)
+            {
+              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())
+              {
+                cval = forCurrentX.getContactAt(c);
+                if (// cr.getMin() <= cval &&
+                cval <= cr.getMax())
+                {
+                  av.getColumnSelection().addElement(c++);
+                }
+                else
+                {
+                  break;
+                }
+              }
             }
-            av.getColumnSelection().addElement(currentX);
           }
         }
       }
@@ -776,6 +817,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
          * mostly vertical drag
          */
         dragMode = DragMode.Resize;
+        notJustOne = evt.isShiftDown();
 
         /*
          * but could also be a matrix drag
@@ -816,7 +858,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           AlignmentAnnotation graphAnnotation = av.getAlignment()
                   .getAlignmentAnnotation()[graphStretch];
           int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
-          graphAnnotation.graphHeight = newHeight;
+          if (notJustOne)
+          {
+            for (AlignmentAnnotation similar : av.getAlignment()
+                    .findAnnotations(null, graphAnnotation.getCalcId(),
+                            graphAnnotation.label))
+            {
+              similar.graphHeight = newHeight;
+            }
+
+          }
+          else
+          {
+            graphAnnotation.graphHeight = newHeight;
+          }
           adjustPanelHeight();
           ap.paintAlignment(false, false);
         }
@@ -1097,14 +1152,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if (clist != null)
       {
         ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
-        ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset,
-                rowAndOffset);
+        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();
-
-        // ap.getStructureSelectionManager().mouseOverSequence(ann.sequenceRef,
-        // new int[] {column, ci.cStart,ci.cEnd}, -1, null)
+        int col = ann.sequenceRef.findPosition(column);
+        ap.getStructureSelectionManager()
+                .highlightPositionsOn(ann.sequenceRef, new int[][]
+                { new int[] { col, col },
+                    new int[]
+                    { ci.cStart, ci.cEnd } }, null);
       }
     }
     return tooltip;
@@ -1266,24 +1323,37 @@ 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();