From 4c36db52fa7bc52e22befa30abc8eabce5742e1b Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 5 Jun 2018 09:34:08 +0100
Subject: [PATCH 1/1] JAL-3011 include annotation scores in sequence id
 tooltip and sequence details report

---
 src/jalview/gui/CutAndPasteHtmlTransfer.java |    1 +
 src/jalview/io/SequenceAnnotationReport.java |   16 ++++++++++++++++
 2 files changed, 17 insertions(+)

diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index 2e51bce..1d7d1c9 100644
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -143,6 +143,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
   {
     textarea.setDocument(textarea.getEditorKit().createDefaultDocument());
     textarea.setText(text);
+    textarea.setCaretPosition(0);
   }
 
   @Override
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 6b82671..5ada355 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import jalview.api.FeatureColourI;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceFeature;
@@ -353,12 +354,27 @@ public class SequenceAnnotationReport
       sb.append("<br>").append(tmp);
       maxWidth = Math.max(maxWidth, tmp.length());
     }
+
     SequenceI ds = sequence;
     while (ds.getDatasetSequence() != null)
     {
       ds = ds.getDatasetSequence();
     }
 
+    /*
+     * add any annotation scores
+     */
+    AlignmentAnnotation[] anns = ds.getAnnotation();
+    for (int i = 0; anns != null && i < anns.length; i++)
+    {
+      AlignmentAnnotation aa = anns[i];
+      if (aa != null && aa.hasScore() && aa.sequenceRef != null)
+      {
+        sb.append("<br>").append(aa.label).append(": ")
+                .append(aa.getScore());
+      }
+    }
+
     if (showDbRefs)
     {
       maxWidth = Math.max(maxWidth, appendDbRefs(sb, ds, summary));
-- 
1.7.10.2