Merge branch 'improvement/JAL-4250_secondary_structure_annotation_antialias' into...

[jalview.git] / src / jalview / analysis / ParseProperties.java

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 3347800..94b7b99 100644 (file)
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -20,12 +20,12 @@
  */
 package jalview.analysis;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
+import com.stevesoft.pat.Regex;
+
 public class ParseProperties
 {
   /**
@@ -57,9 +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,
@@ -86,9 +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);
@@ -135,18 +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);