X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FParseProperties.java;h=94b7b997ecf8116fbd28fc7d7523542a51770685;hb=b254ce17e47c43d19804efa129367291a79b1315;hp=c580c77e645b145b1c2fe16dbd861c39a1e5a6ce;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index c580c77..94b7b99 100644
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -58,7 +58,8 @@ public class ParseProperties
           String ScoreDescriptions, String regex, boolean repeat)
   {
     return getScoresFromDescription(new String[] { ScoreName },
-            new String[] { ScoreDescriptions }, regex, repeat);
+            new String[]
+            { ScoreDescriptions }, regex, repeat);
   }
 
   public int getScoresFromDescription(String[] ScoreNames,
@@ -85,9 +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);
@@ -134,18 +134,18 @@ public class ParseProperties
           double score = Double.NaN;
           try
           {
-            score = new Double(sstring).doubleValue();
+            score = Double.valueOf(sstring).doubleValue();
           } catch (Exception e)
           {
             // don't try very hard to parse if regex was wrong.
             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(seqs[i].getName() + " score: '"
+          jalview.bin.Console.outPrintln(seqs[i].getName() + " score: '"
                   + ScoreNames[cols] + "' = " + score); // DEBUG
           an.setSequenceRef(seqs[i]);
           seqs[i].addAlignmentAnnotation(an);