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fix for JAL-701 - ensure '<' appears in tooltip in application and allow html tags...
authorjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 18 Aug 2011 11:02:45 +0000 (12:02 +0100)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Thu, 18 Aug 2011 11:17:01 +0000 (12:17 +0100)
src/jalview/datamodel/AlignmentAnnotation.java patch | blob | history
src/jalview/gui/AnnotationLabels.java patch | blob | history

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 236e8ee..483c821 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -813,6 +813,12 @@ public class AlignmentAnnotation
   {
     if (seqname && this.sequenceRef != null)
     {
+      int i=description.toLowerCase().indexOf("<html>");
+      if (i>-1)
+      {
+        // move the html tag to before the sequence reference.
+        return "<html>"+sequenceRef.getName()+" : "+description.substring(i+6);
+      }
       return sequenceRef.getName() + " : " + description;
     }
     return description;
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 6626016..7278901 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -18,6 +18,7 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.regex.Pattern;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
@@ -404,24 +405,46 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
     {
       AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
-
-      StringBuffer desc = new StringBuffer("<html>");
-
+      
+      StringBuffer desc = new StringBuffer();
       if (aa.description != null
               && !aa.description.equals("New description"))
       {
-        desc.append(aa.getDescription(true));
-        if (aa.hasScore)
-          desc.append("<br>");
+        // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips
+        desc.append(aa.getDescription(true).trim());
+        // check to see if the description is an html fragment.
+        if (desc.length()<6 || (desc.substring(0,6).toLowerCase().indexOf("<html>")<0))
+        {
+          // clean the description ready for embedding in html
+          desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("&lt;"));        
+          desc.insert(0, "<html>");
+        } else {
+               // remove terminating html if any
+               int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf("</html>");
+               if (i>-1) {
+                 desc.setLength(desc.length()-7+i);
+               }
+        }
+        if (aa.hasScore())
+        {
+          desc.append("<br/>");
+        }
+        
+        
+      } else {
+        // begin the tooltip's html fragment
+        desc.append("<html>");
       }
       if (aa.hasScore())
       {
-        desc.append("Score: " + aa.score);
+        // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value).
+        desc.append(" Score: " + aa.score);
       }
 
-      if (desc.length() != 6)
+      if (desc.length() > 6)
       {
         desc.append("</html>");
+        System.err.println(desc.toString());
         this.setToolTipText(desc.toString());
       }
       else