X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FParseProperties.java;h=629a8a3454d89144e211ebc3841e6591c65ee1a2;hb=11ec9d4540710b65b82b8b901de07b441c130887;hp=38d83715cbc65538e04c74ac66e6893f0504fdd1;hpb=d07fe6a0891b57a9d707e356f7769395ce94b0da;p=jalview.git

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 38d8371..629a8a3 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -20,9 +20,11 @@
  */
 package jalview.analysis;
 
-import com.stevesoft.pat.Regex;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import com.stevesoft.pat.Regex;
 
 public class ParseProperties
 {
@@ -55,9 +57,9 @@ public class ParseProperties
   public int getScoresFromDescription(String ScoreName,
           String ScoreDescriptions, String regex, boolean repeat)
   {
-    return getScoresFromDescription(new String[]
-    { ScoreName }, new String[]
-    { ScoreDescriptions }, regex, repeat);
+    return getScoresFromDescription(new String[] { ScoreName },
+            new String[]
+            { ScoreDescriptions }, regex, repeat);
   }
 
   public int getScoresFromDescription(String[] ScoreNames,
@@ -84,9 +86,8 @@ public class ParseProperties
    *          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,
-          boolean repeat)
+  public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames,
+          String[] ScoreDescriptions, String regex, boolean repeat)
   {
     int count = 0;
     Regex pattern = new Regex(regex);
@@ -101,7 +102,9 @@ public class ParseProperties
       ScoreNames = tnames;
       String descrbase = ScoreDescriptions[onamelen - 1];
       if (descrbase == null)
+      {
         descrbase = "Score parsed from (" + regex + ")";
+      }
       tnames = new String[pattern.numSubs() + 1];
       System.arraycopy(ScoreDescriptions, 0, tnames, 0,
               ScoreDescriptions.length);
@@ -116,7 +119,9 @@ public class ParseProperties
     {
       String descr = seqs[i].getDescription();
       if (descr == null)
+      {
         continue;
+      }
       int pos = 0;
       boolean added = false;
       int reps = 0;
@@ -136,11 +141,12 @@ public class ParseProperties
             continue;
           }
           // add score to sequence annotation.
-          AlignmentAnnotation an = new AlignmentAnnotation(ScoreNames[cols]
-                  + ((reps > 0) ? "_" + reps : ""),
+          AlignmentAnnotation an = new AlignmentAnnotation(
+                  ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""),
                   ScoreDescriptions[cols], null);
           an.setScore(score);
-          System.out.println("Score: " + ScoreNames[cols] + "=" + score); // DEBUG
+          System.out.println(seqs[i].getName() + " score: '"
+                  + ScoreNames[cols] + "' = " + score); // DEBUG
           an.setSequenceRef(seqs[i]);
           seqs[i].addAlignmentAnnotation(an);
           al.addAnnotation(an);