From 5e9f96e1f022c55e192abfe52a5ddfead40e35e8 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 24 Oct 2007 10:58:20 +0000 Subject: [PATCH] javadoc --- src/jalview/io/JPredFile.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) 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 -- 1.7.10.2