From 9fe76dc8b685a5a48aeff77c7a9eaf862da3340e Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 26 Apr 2007 10:36:42 +0000
Subject: [PATCH] basic methods for adding scores extracted from description

---
 src/jalview/analysis/ParseProperties.java |   22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 015fcfe..c23cb3a 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -8,6 +8,14 @@ public class ParseProperties
 {
   /**
    * Methods for parsing free text properties on alignments and sequences.
+   * There are a number of ways we might want to do this:
+   * arbitrary regex. and an associated score name for the number that's extracted.
+   * Regex that provides both score and name.
+   * 
+   * We may also want to :
+   * - modify description to remove parsed numbers (this behaviour is dangerous since exporting the alignment would lose the original form then)
+   * - 
+   * 
    */
   /**
    * The alignment being operated on
@@ -18,7 +26,7 @@ public class ParseProperties
    * initialise a new property parser
    * @param al
    */
-  ParseProperties(AlignmentI al) {
+  public ParseProperties(AlignmentI al) {
     this.al = al;
   }
 
@@ -51,10 +59,10 @@ public class ParseProperties
       System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);
       String base = tnames[ScoreNames.length-1];
       ScoreNames = tnames;
-      String descrbase = ScoreDescriptions[ScoreNames.length-1];
+      String descrbase = ScoreDescriptions[onamelen-1];
       if (descrbase == null)
         descrbase = "Score parsed from ("+regex+")";
-      tnames = new String[pattern.numSubs()];
+      tnames = new String[pattern.numSubs()+1];
       System.arraycopy(ScoreDescriptions, 0, tnames, 0, ScoreDescriptions.length);
       ScoreDescriptions = tnames;
       for (int i=onamelen; i<ScoreNames.length; i++)
@@ -66,12 +74,14 @@ public class ParseProperties
     for (int i=0; i<seqs.length; i++)
     {
       String descr = seqs[i].getDescription();
+      if (descr==null)
+        continue;
       if (pattern.search(descr))
       {
         boolean added=false;
         for (int cols=0; cols<pattern.numSubs(); cols++)
         {
-          String sstring = pattern.stringMatched(cols);
+          String sstring = pattern.stringMatched(cols+1);
           float score;
           try {
             score = new Float(sstring).floatValue();
@@ -107,10 +117,10 @@ public class ParseProperties
     //seqs[4].setDescription("5 mydescription5");
     Alignment al = new Alignment(seqs);
     ParseProperties pp = new ParseProperties(al);
-    String regex = ".*([-0-9.+]+).*";
+    String regex = ".*([-0-9.+]+)";
     System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex)+" for "+regex);
     regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
     System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex)+" for "+regex);
-    
+    System.out.println("Finished.");
   }
 }
-- 
1.7.10.2