concise files can now be read as a normal alignment, and will be displayed with annot...

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index a7e4e70..b003e6a 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -36,8 +36,8 @@ import jalview.datamodel.*;
  * Automagic translation happens for annotation called 'JNETPRED' (translated to Secondary Structure Prediction), or 'JNETCONF' (translates to 'Prediction Confidence').
  * Numeric scores are differentiated from symbolic by being parseable into a float vector. They are put in Scores.
  * Symscores gets the others.
- * JNetAnnotationMaker translates the data parsed by this object into annotation on an alignment.
- *
+ * JNetAnnotationMaker translates the data parsed by this object into annotation on an alignment. It is automatically called
+ * but can be used to transfer the annotation onto a sequence in another alignment (and insert gaps where necessary)
  * @author jprocter
  * @version $Revision$
  */
@@ -293,6 +293,26 @@ public class JPredFile
 
       seqs.addElement(newSeq);
     }
+    if (seqs.size()>0)
+    {
+      // try to make annotation for a prediction only input (default if no alignment is given)
+      Alignment tal = new Alignment(this.getSeqsAsArray());
+      try {
+        JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition, true);
+      } catch (Exception e)
+      {
+        tal = null;
+        IOException ex = new IOException("Couldn't parse concise annotation for prediction profile. ("+e.getMessage()+")");
+        ex.setStackTrace(e.getStackTrace());
+        throw ex;
+      }
+      this.annotations = new Vector();
+      AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
+      for (int aai = 0; aan!=null && aai<aan.length; aai++)
+      {
+        annotations.addElement(aan[aai]);
+      }
+    } 
   }
 
   /**