X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=1a552d7b1c2498ef54939ae7e4c191b0d2d786a5;hb=63e93122d1722a69e997a9ac64502ef74c4a7a17;hp=f28fa0573c5d30957b01291e2168177d330bed6b;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index f28fa05..1a552d7 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,25 +1,34 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
-import jalview.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class SeqsetUtils
 {
@@ -43,7 +52,7 @@ public class SeqsetUtils
       sqinfo.put("Description", seq.getDescription());
     }
     Vector sfeat = new Vector();
-    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+    SequenceFeature[] sfarray = seq.getSequenceFeatures();
     if (sfarray != null && sfarray.length > 0)
     {
       for (int i = 0; i < sfarray.length; i++)
@@ -53,7 +62,7 @@ public class SeqsetUtils
     }
     sqinfo.put("SeqFeatures", sfeat);
     sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
-            : new Vector());
+            : new Vector<PDBEntry>());
     sqinfo.put("datasetSequence",
             (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                     : new Sequence("THISISAPLACEHOLDER", ""));
@@ -81,7 +90,7 @@ public class SeqsetUtils
     Integer start = (Integer) sqinfo.get("Start");
     Integer end = (Integer) sqinfo.get("End");
     Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
-    Vector pdbid = (Vector) sqinfo.get("PdbId");
+    Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
     String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
     if (oldname == null)
@@ -208,8 +217,7 @@ public class SeqsetUtils
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
           boolean quiet)
   {
-    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
-            sequences);
+    SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
     Vector unmatched = new Vector();
@@ -267,8 +275,7 @@ public class SeqsetUtils
     int msflen = 0;
     for (int i = 0, j = sequences.length; i < j; i++)
     {
-      String tempseq = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars,
+      String tempseq = AlignSeq.extractGaps(Comparison.GapChars,
               sequences[i].getSequenceAsString());
 
       if (tempseq.length() == 0)