X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=65fd1100b8e8a7f2cdc33f1d1a90f80aaa3076bf;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=15ea2fcb94cb6b70db80f9929b493d1561a12c5a;hpb=427421de47dacacac55ac29deca78e2f0a1c5408;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 15ea2fc..65fd110 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,6 +20,8 @@
  */
 package jalview.analysis;
 
+import java.util.Locale;
+
 import jalview.analysis.scoremodels.PIDModel;
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
@@ -148,7 +150,8 @@ public class AlignSeq
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
-    seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type);
+    seqInit(s1, string1.toUpperCase(Locale.ROOT), s2,
+            string2.toUpperCase(Locale.ROOT), type);
   }
 
   /**
@@ -561,7 +564,7 @@ public class AlignSeq
         }
       }
 
-      output.append(NEWLINE);// .append(NEWLINE);
+      output.append(NEWLINE).append(NEWLINE);
     }
 
     pid = pid / (aseq1.length - count) * 100;
@@ -643,12 +646,14 @@ public class AlignSeq
     for (int j = 1; j < m; j++)
     {
       // What should these values be? 0 maybe
-      E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST, E[0][j - 1] - GAP_EXTEND_COST);
+      E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST,
+              E[0][j - 1] - GAP_EXTEND_COST);
       F[0][j] = -GAP_EXTEND_COST;
 
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
               s2str.charAt(j));
-      score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST, -GAP_EXTEND_COST);
+      score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST,
+              -GAP_EXTEND_COST);
 
       traceback[0][j] = 1;
     }
@@ -657,7 +662,8 @@ public class AlignSeq
     for (int i = 1; i < n; i++)
     {
       E[i][0] = -GAP_OPEN_COST;
-      F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST, F[i - 1][0] - GAP_EXTEND_COST);
+      F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST,
+              F[i - 1][0] - GAP_EXTEND_COST);
 
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
               s2str.charAt(0));
@@ -670,8 +676,10 @@ public class AlignSeq
     {
       for (int j = 1; j < m; j++)
       {
-        E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST, E[i][j - 1] - GAP_EXTEND_COST);
-        F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST, F[i - 1][j] - GAP_EXTEND_COST);
+        E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST,
+                E[i][j - 1] - GAP_EXTEND_COST);
+        F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST,
+                F[i - 1][j] - GAP_EXTEND_COST);
 
         float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
                 s2str.charAt(j));