X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=7daee5518c9c3a956f7322496d7516fc53335105;hb=49685e6426d5ac136dce4907196751680c667670;hp=dabd47aa83ea04bb904a2f4299850331c03c0c44;hpb=712d1fca4bfa7e91d667e9931fb67fbc99a5f369;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index dabd47a..7daee55 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 /**
  * PredFile.java
  * JalviewX / Vamsas Project
@@ -30,9 +29,15 @@ import java.util.*;
 import jalview.datamodel.*;
 
 /**
- * DOCUMENT ME!
- *
- * @author $author$
+ * Parser for the JPred/JNet concise format. This is a series of CSV lines,
+ * each line is either a sequence (QUERY), a sequence profile (align;), or
+ * jnet prediction annotation (anything else). 
+ * 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. 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 $Revision$
  */
 public class JPredFile
@@ -57,7 +62,10 @@ public class JPredFile
   {
     super(inFile, type);
   }
-
+  public JPredFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
   /**
    * DOCUMENT ME!
    *
@@ -287,6 +295,25 @@ 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.\n"+e);
+        throw ex;
+      }
+      this.annotations = new Vector();
+      AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
+      for (int aai = 0; aan!=null && aai<aan.length; aai++)
+      {
+        annotations.addElement(aan[aai]);
+      }
+    } 
   }
 
   /**
@@ -321,7 +348,7 @@ public class JPredFile
     catch (java.io.IOException e)
     {
       System.err.println("Exception " + e);
-      e.printStackTrace();
+      // e.printStackTrace(); not java 1.1 compatible!
     }
   }