From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 27 Mar 2017 13:27:35 +0000 (+0100)
Subject: JAL-2416 class Javadoc updates prior to parsing changes
X-Git-Tag: Release_2_10_2~3^2~105^2~2^2~44
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2ef3e2f98a054c66f45c36bfdf62f085a28fc770;p=jalview.git

JAL-2416 class Javadoc updates prior to parsing changes
---

diff --git a/src/jalview/io/ScoreMatrixFile.java b/src/jalview/io/ScoreMatrixFile.java
index eee7d68..a332846 100644
--- a/src/jalview/io/ScoreMatrixFile.java
+++ b/src/jalview/io/ScoreMatrixFile.java
@@ -10,12 +10,26 @@ import java.util.StringTokenizer;
 /**
  * A class that can parse a file containing a substitution matrix and register
  * it for use in Jalview
+ * <p>
+ * Accepts 'NCBI' format (e.g.
+ * https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt), with the
+ * addition of a header line to provide a matrix name, e.g.
  * 
- * @author gmcarstairs
- *
+ * <pre>
+ * ScoreMatrix BLOSUM62
+ * </pre>
+ * 
+ * Also accepts 'aaindex' format (as described at
+ * http://www.genome.jp/aaindex/aaindex_help.html) with the minimum data
+ * required being
+ * 
+ * <pre>
+ * H accession number (used as score matrix identifier in Jalview)
+ * D description (used for tooltip in Jalview)
+ * M rows = symbolList
+ * and the substitution scores
+ * </pre>
  */
-// TODO modify the AlignFile / IdentifyFile pattern so that non-alignment files
-// like this are handled more naturally
 public class ScoreMatrixFile extends AlignFile implements
         AlignmentFileReaderI
 {
@@ -149,7 +163,8 @@ public class ScoreMatrixFile extends AlignFile implements
        * optionally with the symbol as the first column for readability
        */
       StringTokenizer scoreLine = new StringTokenizer(data, DELIMITERS);
-      if (scoreLine.countTokens() == size + 1)
+      int tokenCount = scoreLine.countTokens();
+      if (tokenCount == size + 1)
       {
         /*
          * check 'guide' symbol is the row'th letter of the alphabet