X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=81bddc2ebd637e7908687360a56e373447ce83e1;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=9943a22d967687a2d6fecfdd10c8877bae2bf2b2;hpb=4c6cd08af580ff73cfce39bec34ae4658a4b4b34;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 9943a22..81bddc2 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);
     }
 
@@ -142,8 +143,8 @@ public class AlignmentSorter
     }
 
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    List<SequenceI> asq;
-    synchronized (asq = align.getSequences())
+    List<SequenceI> asq = align.getSequences();
+    synchronized (asq)
     {
       for (int i = 0; i < len; i++)
       {
@@ -178,10 +179,10 @@ public class AlignmentSorter
   public static void setOrder(AlignmentI align, SequenceI[] seqs)
   {
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    List<SequenceI> algn;
-    synchronized (algn = align.getSequences())
+    List<SequenceI> algn = align.getSequences();
+    synchronized (algn)
     {
-      List<SequenceI> tmp = new ArrayList<SequenceI>();
+      List<SequenceI> tmp = new ArrayList<>();
 
       for (int i = 0; i < seqs.length; i++)
       {
@@ -278,7 +279,7 @@ public class AlignmentSorter
   {
     // MAINTAINS ORIGNAL SEQUENCE ORDER,
     // ORDERS BY GROUP SIZE
-    List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> groups = new ArrayList<>();
 
     if (groups.hashCode() != lastGroupHash)
     {
@@ -314,7 +315,7 @@ public class AlignmentSorter
 
     // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
     // /////////////////////////////////////////////
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
 
     for (int i = 0; i < groups.size(); i++)
     {
@@ -356,7 +357,7 @@ public class AlignmentSorter
     // tmp2 = tmp.retainAll(mask);
     // return tmp2.addAll(mask.removeAll(tmp2))
 
-    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+    ArrayList<SequenceI> seqs = new ArrayList<>();
     int i, idx;
     boolean[] tmask = new boolean[mask.size()];
 
@@ -415,7 +416,8 @@ public class AlignmentSorter
     }
     else
     {
-      setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+      setReverseOrder(align,
+              vectorSubsetToArray(tmp, align.getSequences()));
     }
   }
 
@@ -434,7 +436,7 @@ public class AlignmentSorter
   {
     int nSeq = align.getHeight();
 
-    List<SequenceI> tmp = new ArrayList<SequenceI>();
+    List<SequenceI> tmp = new ArrayList<>();
 
     tmp = _sortByTree(tree.getTopNode(), 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()));
     }
   }
 
@@ -586,7 +586,7 @@ public class AlignmentSorter
 
     for (int i = 0; i < alignment.length; i++)
     {
-      ids[i] = (new Float(alignment[i].getName().substring(8)))
+      ids[i] = (Float.valueOf(alignment[i].getName().substring(8)))
               .floatValue();
     }
 
@@ -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.
@@ -729,14 +708,15 @@ public class AlignmentSorter
     if (method != FEATURE_SCORE && method != FEATURE_LABEL
             && method != FEATURE_DENSITY)
     {
-      String msg = String
-              .format("Implementation Error - sortByFeature method must be either '%s' or '%s'",
-                      FEATURE_SCORE, FEATURE_DENSITY);
+      String msg = String.format(
+              "Implementation Error - sortByFeature method must be either '%s' or '%s'",
+              FEATURE_SCORE, FEATURE_DENSITY);
       System.err.println(msg);
       return;
     }
 
-    flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol, endCol);
+    flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol,
+            endCol);
 
     SequenceI[] seqs = alignment.getSequencesArray();
 
@@ -755,8 +735,8 @@ public class AlignmentSorter
        * get sequence residues overlapping column region
        * and features for residue positions and specified types
        */
-      String[] types = featureTypes == null ? null : featureTypes
-              .toArray(new String[featureTypes.size()]);
+      String[] types = featureTypes == null ? null
+              : featureTypes.toArray(new String[featureTypes.size()]);
       List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
               endCol + 1, types);