From c3b91c81342d21498ffcb4639c3597a25aa2753c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 4 Oct 2018 14:54:40 +0100
Subject: [PATCH] JAL-3132 status message for sequence and/or graph group
 annotation

---
 src/jalview/gui/AnnotationLabels.java      |   55 ++++++++++++++++++++++++++--
 src/jalview/gui/IdPanel.java               |    8 ++--
 test/jalview/gui/AnnotationLabelsTest.java |   48 ++++++++++++++++++++++++
 3 files changed, 105 insertions(+), 6 deletions(-)

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 0ff6b73..6da6cc3 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -674,16 +674,65 @@ public class AnnotationLabels extends JPanel
     if (selectedRow > -1 && ap.av.getAlignment()
             .getAlignmentAnnotation().length > selectedRow)
     {
-      AlignmentAnnotation aa = ap.av.getAlignment()
-              .getAlignmentAnnotation()[selectedRow];
+      AlignmentAnnotation[] anns = ap.av.getAlignment()
+              .getAlignmentAnnotation();
+      AlignmentAnnotation aa = anns[selectedRow];
 
       String desc = getTooltip(aa);
       this.setToolTipText(desc);
-      ap.alignFrame.setStatus(aa.label);
+      String msg = getStatusMessage(aa, anns);
+      ap.alignFrame.setStatus(msg);
     }
   }
 
   /**
+   * Constructs suitable text to show in the status bar when over an annotation
+   * label, containing the associated sequence name (if any), and the annotation
+   * labels (or all labels for a graph group annotation)
+   * 
+   * @param aa
+   * @param anns
+   * @return
+   */
+  static String getStatusMessage(AlignmentAnnotation aa,
+          AlignmentAnnotation[] anns)
+  {
+    if (aa == null)
+    {
+      return null;
+    }
+
+    StringBuilder msg = new StringBuilder(32);
+    if (aa.sequenceRef != null)
+    {
+      msg.append(aa.sequenceRef.getName()).append(" : ");
+    }
+
+    if (aa.graphGroup == -1)
+    {
+      msg.append(aa.label);
+    }
+    else if (anns != null)
+    {
+      boolean first = true;
+      for (int i = anns.length - 1; i >= 0; i--)
+      {
+        if (anns[i].graphGroup == aa.graphGroup)
+        {
+          if (!first)
+          {
+            msg.append(", ");
+          }
+          msg.append(anns[i].label);
+          first = false;
+        }
+      }
+    }
+
+    return msg.toString();
+  }
+
+  /**
    * Answers a tooltip, formatted as html, containing the annotation description
    * (prefixed by associated sequence id if applicable), and the annotation
    * (non-positional) score if it has one. Answers null if neither description
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 579229c..e29330e 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -110,10 +110,12 @@ public class IdPanel extends JPanel
       /*
        * mouse is over an annotation label in wrapped mode
        */
-      AlignmentAnnotation annotation = av.getAlignment()
-              .getAlignmentAnnotation()[pos.annotationIndex];
+      AlignmentAnnotation[] anns = av.getAlignment()
+              .getAlignmentAnnotation();
+      AlignmentAnnotation annotation = anns[pos.annotationIndex];
       setToolTipText(AnnotationLabels.getTooltip(annotation));
-      alignPanel.alignFrame.setStatus(annotation.label);
+      alignPanel.alignFrame.setStatus(
+              AnnotationLabels.getStatusMessage(annotation, anns));
     }
     else
     {
diff --git a/test/jalview/gui/AnnotationLabelsTest.java b/test/jalview/gui/AnnotationLabelsTest.java
index 31839a9..616a1a6 100644
--- a/test/jalview/gui/AnnotationLabelsTest.java
+++ b/test/jalview/gui/AnnotationLabelsTest.java
@@ -102,4 +102,52 @@ public class AnnotationLabelsTest
     ann.sequenceRef = null;
     assertNull(AnnotationLabels.getTooltip(ann));
   }
+
+  @Test(groups = "Functional")
+  public void testGetStatusMessage()
+  {
+    assertNull(AnnotationLabels.getStatusMessage(null, null));
+
+    /*
+     * simple label
+     */
+    AlignmentAnnotation aa = new AlignmentAnnotation("IUPredWS Short",
+            "Protein disorder", null);
+    assertEquals(AnnotationLabels.getStatusMessage(aa, null),
+            "IUPredWS Short");
+
+    /*
+     * with sequence ref
+     */
+    aa.setSequenceRef(new Sequence("FER_CAPAA", "MIGRKQL"));
+    assertEquals(AnnotationLabels.getStatusMessage(aa, null),
+            "FER_CAPAA : IUPredWS Short");
+
+    /*
+     * with graph group (degenerate, one annotation only)
+     */
+    aa.graphGroup = 1;
+    AlignmentAnnotation aa2 = new AlignmentAnnotation("IUPredWS Long",
+            "Protein disorder", null);
+    assertEquals(
+            AnnotationLabels.getStatusMessage(aa, new AlignmentAnnotation[]
+            { aa, aa2 }), "FER_CAPAA : IUPredWS Short");
+
+    /*
+     * graph group with two members; note labels are appended in
+     * reverse order (matching rendering order on screen)
+     */
+    aa2.graphGroup = 1;
+    assertEquals(
+            AnnotationLabels.getStatusMessage(aa, new AlignmentAnnotation[]
+            { aa, aa2 }), "FER_CAPAA : IUPredWS Long, IUPredWS Short");
+
+    /*
+     * graph group with no sequence ref
+     */
+    aa.sequenceRef = null;
+    assertEquals(
+            AnnotationLabels.getStatusMessage(aa, new AlignmentAnnotation[]
+            { aa, aa2 }), "IUPredWS Long, IUPredWS Short");
+  }
 }
-- 
1.7.10.2