JAL-1807 explicit imports (jalview.util)

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

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index d2b5b72..1a552d7 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,9 +20,15 @@
  */
 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
 {
@@ -46,7 +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++)
@@ -56,7 +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", ""));
@@ -84,7 +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)
@@ -211,8 +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();
@@ -270,8 +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)