From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 26 Nov 2014 14:48:28 +0000 (+0000)
Subject: JAL-674 make RNAML-extracted secondary structure lines consistent with those from... 
X-Git-Tag: Jalview_2_9~121^2~7^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=753c25d4e1ef75ec8f8e2a5df67824c397584e01

JAL-674 make RNAML-extracted secondary structure lines consistent with those from Jmol
---

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index 9f0c8d5..c075fda 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -167,8 +167,11 @@ public class RnamlFile extends AlignFile
                         annot[k]).charAt(0), 0f);
       }
 
-      AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
-              current.getID(), ann);
+      AlignmentAnnotation align = new AlignmentAnnotation(
+              "Secondary Structure",
+              current.getID().trim().length() > 0 ? "Secondary Structure for "
+                      + current.getID()
+                      : "", ann);
 
       seqs[i].addAlignmentAnnotation(align);
       seqs[i].setRNA(result.get(i));