From: jprocter <Jim Procter>
Date: Fri, 21 Dec 2007 15:05:33 +0000 (+0000)
Subject: javadoc and bugfix
X-Git-Tag: Release_2_4~164
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a3f3ef6087f2be16d21bf2db97bd8e22e0c3f2b3;p=jalview.git

javadoc and bugfix
---

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 43460d6..587e501 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -30,14 +30,14 @@ public class ParseProperties
     this.al = al;
   }
 
-  public int getScoresFromDescription(String ScoreName, String ScoreDescriptions, String regex)
+  public int getScoresFromDescription(String ScoreName, String ScoreDescriptions, String regex, boolean repeat)
   {
-    return getScoresFromDescription(new String[] { ScoreName }, new String[] { ScoreDescriptions}, regex);
+    return getScoresFromDescription(new String[] { ScoreName }, new String[] { ScoreDescriptions}, regex, repeat);
   }
 
-  public int getScoresFromDescription(String[] ScoreNames, String[] ScoreDescriptions, String regex) 
+  public int getScoresFromDescription(String[] ScoreNames, String[] ScoreDescriptions, String regex, boolean repeat) 
   {
-    return getScoresFromDescription(al.getSequencesArray(), ScoreNames, ScoreDescriptions, regex);
+    return getScoresFromDescription(al.getSequencesArray(), ScoreNames, ScoreDescriptions, regex, repeat);
   }
   /**
    * Extract scores for sequences by applying regex to description string.
@@ -45,9 +45,10 @@ public class ParseProperties
    * @param ScoreNames labels for each numeric field in regex match
    * @param ScoreDescriptions description for each numeric field in regex match
    * @param regex Regular Expression string for passing to <code>new com.stevesoft.patt.Regex(regex)</code>
+   * @param repeat true means the regex will be applied multiple times along the description string of each sequence
    * @return total number of sequences that matched the regex
    */
-  public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames, String[] ScoreDescriptions, String regex) 
+  public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames, String[] ScoreDescriptions, String regex, boolean repeat) 
   {
     int count=0;
     Regex pattern = new Regex(regex);
@@ -76,9 +77,11 @@ public class ParseProperties
       String descr = seqs[i].getDescription();
       if (descr==null)
         continue;
-      if (pattern.search(descr))
+      int pos=0;
+      boolean added=false;
+      while ((repeat || pos==0) && pattern.searchFrom(descr, pos))
       {
-        boolean added=false;
+        pos = pattern.matchedTo();
         for (int cols=0; cols<pattern.numSubs(); cols++)
         {
           String sstring = pattern.stringMatched(cols+1);
@@ -100,10 +103,11 @@ public class ParseProperties
           al.addAnnotation(an);
           added=true;
         }
-        if (added)
-          count++;
       }
-      
+      if (added)
+      {
+        count++;
+      }
     }
     return count; 
   }
@@ -120,9 +124,9 @@ public class ParseProperties
     Alignment al = new Alignment(seqs);
     ParseProperties pp = new ParseProperties(al);
     String regex = ".*([-0-9.+]+)";
-    System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex)+" for "+regex);
+    System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex, true)+" for "+regex);
     regex = ".*([-0-9.+]+).+([-0-9.+]+).*";
-    System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex)+" for "+regex);
+    System.out.println("Matched "+pp.getScoresFromDescription("my Score", "my Score Description",regex, true)+" for "+regex);
     System.out.println("Finished.");
   }
 }