From: jprocter <Jim Procter>
Date: Wed, 24 Oct 2007 10:58:20 +0000 (+0000)
Subject: javadoc
X-Git-Tag: Release_2_4~237
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5e9f96e1f022c55e192abfe52a5ddfead40e35e8;p=jalview.git

javadoc
---

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index dabd47a..a7e4e70 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -30,9 +30,15 @@ import java.util.*;
 import jalview.datamodel.*;
 
 /**
- * DOCUMENT ME!
+ * 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.
  *
- * @author $author$
+ * @author jprocter
  * @version $Revision$
  */
 public class JPredFile