JAL-4091 JAL-4147 - revised annotation label display so consecutive runs of rows...

diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 92ed9be..0f0cf68 100644 (file)
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -156,8 +156,15 @@ public class AnnotationSorter
       {
         return showAutocalcAbove ? 1 : -1;
       }
-      int sequenceOrder = compareSequences(o1, o2);
-      return sequenceOrder == 0 ? compareLabels(o1, o2) : sequenceOrder;
+      int computedOrder = compareSequences(o1, o2);
+      if (computedOrder==0) {
+        computedOrder = compareLabels(o1, o2);
+      }
+      if (computedOrder==0)
+      {
+        computedOrder = compareDescriptions(o1,o2);
+      }
+      return computedOrder;
     }
 
     @Override
@@ -358,6 +365,29 @@ public class AnnotationSorter
     }
     String label1 = o1.label;
     String label2 = o2.label;
+    return compareString(label1,label2);
+  }
+
+  /**
+   * Non-case-sensitive comparison of annotation descriptions. Returns zero if either
+   * argument is null.
+   * 
+   * @param o1
+   * @param o2
+   * @return
+   */
+  private int compareDescriptions(AlignmentAnnotation o1, AlignmentAnnotation o2)
+  {
+    if (o1 == null || o2 == null)
+    {
+      return 0;
+    }
+    String label1 = o1.description;
+    String label2 = o2.description;
+    return compareString(label1,label2);
+  }
+  private int compareString(String label1, String label2)
+  {
     if (label1 == null && label2 == null)
     {
       return 0;

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index c01a6f3..0ccd6c2 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1087,6 +1087,7 @@ public class AnnotationLabels extends JPanel
     g.translate(0, getScrollOffset());
     g.setColor(Color.black);
     SequenceI lastSeqRef = null;
+    String lastLabel = null;
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
@@ -1111,6 +1112,7 @@ public class AnnotationLabels extends JPanel
     {
       hasHiddenRows = false;
       int olY = 0;
+      int nexAA = 0;
       for (int i = 0; i < aa.length; i++)
       {
         visible = true;
@@ -1120,6 +1122,9 @@ public class AnnotationLabels extends JPanel
           continue;
         }
         olY = y;
+        // look ahead to next annotation
+        for (nexAA=i+1; nexAA<aa.length && !aa[nexAA].visible; nexAA++)
+          ;
         y += aa[i].height;
         if (clip)
         {
@@ -1167,6 +1172,24 @@ public class AnnotationLabels extends JPanel
         }
         String label = aa[i].label;
         boolean vertBar = false;
+        if ((lastLabel != null && lastLabel.equals(label)))
+        {
+          label = aa[i].description;
+        }
+        else
+        {
+          if (nexAA < aa.length && label.equals(aa[nexAA].label)) // &&
+                                                                  // aa[nexY].sequenceRef==aa[i].sequenceRef)
+          {
+            lastLabel = label;
+            // next label is the same as this label
+            label = aa[i].description;
+          }
+          else
+          {
+            lastLabel = label;
+          }
+        }
         if (aa[i].sequenceRef != null)
         {
           if (aa[i].sequenceRef != lastSeqRef)
@@ -1250,8 +1273,8 @@ public class AnnotationLabels extends JPanel
         {
           if (vertBar)
           {
-            g.drawLine(20, y + offset, 20, y - aa[i].height);
-            g.drawLine(20, y + offset, x - 20, y + offset);
+            g.drawLine(width-3, y + offset-fontHeight, width-3, (int)(y - 1.5*aa[i].height-offset-fontHeight));
+            // g.drawLine(20, y + offset, x - 20, y + offset);
 
           }
           g.drawString(label, x, y + offset);