Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index bd7d5fb..d8d27d0 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
@@ -762,30 +763,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseMoved(MouseEvent evt)
   {
+    int yPos = evt.getY();
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 
-    if (aa == null)
-    {
-      this.setToolTipText(null);
-      return;
-    }
-
-    int row = -1;
-    int height = 0;
-
-    for (int i = 0; i < aa.length; i++)
-    {
-      if (aa[i].visible)
-      {
-        height += aa[i].height;
-      }
-
-      if (evt.getY() < height)
-      {
-        row = i;
-        break;
-      }
-    }
+    int row = getRowIndex(yPos, aa);
 
     if (row == -1)
     {
@@ -795,6 +776,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     int column = (evt.getX() / av.getCharWidth())
             + av.getRanges().getStartRes();
+    column = Math.min(column, av.getRanges().getEndRes());
 
     if (av.hasHiddenColumns())
     {
@@ -806,8 +788,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (row > -1 && ann.annotations != null
             && column < ann.annotations.length)
     {
-      buildToolTip(ann, column, aa);
-      setStatusMessage(column, ann);
+      setToolTipText(buildToolTip(ann, column, aa));
+      String msg = getStatusMessage(av.getAlignment(), column, ann);
+      ap.alignFrame.setStatus(msg);
     }
     else
     {
@@ -817,15 +800,51 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * Builds a tooltip for the annotation at the current mouse position.
+   * Answers the index in the annotations array of the visible annotation at the
+   * given y position. This is done by adding the heights of visible annotations
+   * until the y position has been exceeded. Answers -1 if no annotations are
+   * visible, or the y position is below all annotations.
+   * 
+   * @param yPos
+   * @param aa
+   * @return
+   */
+  static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
+  {
+    if (aa == null)
+    {
+      return -1;
+    }
+    int row = -1;
+    int height = 0;
+
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
+        height += aa[i].height;
+      }
+
+      if (height > yPos)
+      {
+        row = i;
+        break;
+      }
+    }
+    return row;
+  }
+
+  /**
+   * Answers a tooltip for the annotation at the current mouse position
    * 
    * @param ann
    * @param column
    * @param anns
    */
-  void buildToolTip(AlignmentAnnotation ann, int column,
+  static String buildToolTip(AlignmentAnnotation ann, int column,
           AlignmentAnnotation[] anns)
   {
+    String tooltip = null;
     if (ann.graphGroup > -1)
     {
       StringBuilder tip = new StringBuilder(32);
@@ -847,35 +866,39 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if (tip.length() != 6)
       {
         tip.setLength(tip.length() - 4);
-        this.setToolTipText(tip.toString() + "</html>");
+        tooltip = tip.toString() + "</html>";
       }
     }
-    else if (ann.annotations[column] != null)
+    else if (column < ann.annotations.length
+            && ann.annotations[column] != null)
     {
       String description = ann.annotations[column].description;
       if (description != null && description.length() > 0)
       {
-        this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
+        tooltip = JvSwingUtils.wrapTooltip(true, description);
       }
       else
       {
-        this.setToolTipText(null); // no tooltip if null or empty description
+        tooltip = null; // no tooltip if null or empty description
       }
     }
     else
     {
       // clear the tooltip.
-      this.setToolTipText(null);
+      tooltip = null;
     }
+    return tooltip;
   }
 
   /**
-   * Constructs and displays the status bar message
+   * Constructs and returns the status bar message
    * 
+   * @param al
    * @param column
    * @param ann
    */
-  void setStatusMessage(int column, AlignmentAnnotation ann)
+  static String getStatusMessage(AlignmentI al, int column,
+          AlignmentAnnotation ann)
   {
     /*
      * show alignment column and annotation description if any
@@ -884,7 +907,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     text.append(MessageManager.getString("label.column")).append(" ")
             .append(column + 1);
 
-    if (ann.annotations[column] != null)
+    if (column < ann.annotations.length && ann.annotations[column] != null)
     {
       String description = ann.annotations[column].description;
       if (description != null && description.trim().length() > 0)
@@ -900,7 +923,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     SequenceI seqref = ann.sequenceRef;
     if (seqref != null)
     {
-      int seqIndex = av.getAlignment().findIndex(seqref);
+      int seqIndex = al.findIndex(seqref);
       if (seqIndex != -1)
       {
         text.append(", ").append(MessageManager.getString("label.sequence"))
@@ -910,7 +933,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           text.append(" ");
           String name;
-          if (av.getAlignment().isNucleotide())
+          if (al.isNucleotide())
           {
             name = ResidueProperties.nucleotideName
                     .get(String.valueOf(residue));
@@ -931,7 +954,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
 
-    ap.alignFrame.setStatus(text.toString());
+    return text.toString();
   }
 
   /**