X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FRnamlFile.java;h=2948c92b5234f930d133cd5a844e7ddc047a94b5;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9f0c8d5518ee9da988c7177376422fdceefe6b1c;hpb=9e0407286fe32d01dfe4fea4d0bb6141f999f145;p=jalview.git

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index 9f0c8d5..2948c92 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -100,21 +100,29 @@ public class RnamlFile extends AlignFile
       _parse();
     } catch (ExceptionPermissionDenied pdx)
     {
-      errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
+      errormessage = MessageManager.formatMessage(
+              "exception.rnaml_couldnt_access_datasource",
+              new String[] { pdx.getMessage() });
       throw new IOException(pdx);
     } catch (ExceptionLoadingFailed lf)
     {
-      errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
+      errormessage = MessageManager.formatMessage(
+              "exception.ranml_couldnt_process_data",
+              new String[] { lf.getMessage() });
       throw new IOException(lf);
     } catch (ExceptionFileFormatOrSyntax iff)
     {
-        errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
+      errormessage = MessageManager.formatMessage(
+              "exception.ranml_invalid_file",
+              new String[] { iff.getMessage() });
       throw new IOException(iff);
     } catch (Exception x)
     {
       error = true;
-      errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
-      throw new IOException(errormessage , x);
+      errormessage = MessageManager.formatMessage(
+              "exception.ranml_problem_parsing_data",
+              new String[] { x.getMessage() });
+      throw new IOException(errormessage, x);
     }
   }
 
@@ -167,8 +175,11 @@ 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));