X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=b5cefe0baa860082d1fa6093782270c5cf839e69;hb=refs%2Fheads%2Ffeatures%2FJAL-2446NCList;hp=9943a22d967687a2d6fecfdd10c8877bae2bf2b2;hpb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 9943a22..b5cefe0 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -108,8 +108,9 @@ public class AlignmentSorter
             true);
     for (int i = 0; i < nSeq; i++)
     {
-      scores[i] = (float) PIDModel.computePID(align.getSequenceAt(i)
-              .getSequenceAsString(), refSeq, pidParams);
+      scores[i] = (float) PIDModel.computePID(
+              align.getSequenceAt(i).getSequenceAsString(), refSeq,
+              pidParams);
       seqs[i] = align.getSequenceAt(i);
     }
 
@@ -415,7 +416,8 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align,
+              vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
@@ -450,12 +452,9 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err
-                .println("WARNING: tmp.size()="
-                        + tmp.size()
-                        + " != nseq="
-                        + nSeq
-                        + " in getOrderByTree - tree contains sequences not in alignment");
+        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+                + nSeq
+                + " in getOrderByTree - tree contains sequences not in alignment");
       }
     }
 
@@ -491,7 +490,8 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align,
+              vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
@@ -681,27 +681,6 @@ public class AlignmentSorter
 
   public static String FEATURE_DENSITY = "density";
 
-  private static boolean containsIgnoreCase(final String lab,
-          final List<String> labs)
-  {
-    if (labs == null)
-    {
-      return true;
-    }
-    if (lab == null)
-    {
-      return false;
-    }
-    for (String label : labs)
-    {
-      if (lab.equalsIgnoreCase(label))
-      {
-        return true;
-      }
-    }
-    return false;
-  }
-
   /**
    * Sort sequences by feature score or density, optionally restricted by
    * feature types, feature groups, or alignment start/end positions.