basic methods for adding scores extracted from description

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