X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=fabd0c69d178e483ab7c651245d888c183976d26;hb=8213e48c6973494f7a6e22e1a97290520a461d1b;hp=d8da4970bc3d8dcc6930a57cde99349d552caece;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index d8da497..fabd0c6 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,46 +1,35 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 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.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
-/**
- * <p>
- * Title:
- * </p>
- * 
- * <p>
- * Description:
- * </p>
- * 
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- * 
- * <p>
- * Company: Dundee University
- * </p>
- * 
- * @author not attributable
- * @version 1.0
- */
 public class SeqsetUtils
 {
 
@@ -62,20 +51,24 @@ public class SeqsetUtils
     {
       sqinfo.put("Description", seq.getDescription());
     }
-    Vector sfeat = new Vector();
-    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
-    if (sfarray != null && sfarray.length > 0)
+
+    Vector<SequenceFeature> sfeat = new Vector<SequenceFeature>();
+    List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
+    sfeat.addAll(sfs);
+
+    if (seq.getDatasetSequence() == null)
     {
-      for (int i = 0; i < sfarray.length; i++)
-      {
-        sfeat.addElement(sfarray[i]);
-      }
+      sqinfo.put("SeqFeatures", sfeat);
+      sqinfo.put("PdbId",
+              (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+                      : new Vector<PDBEntry>());
+    }
+    else
+    {
+      sqinfo.put("datasetSequence",
+              (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+                      : new Sequence("THISISAPLACEHOLDER", ""));
     }
-    sqinfo.put("SeqFeatures", sfeat);
-    sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
-            : new Vector());
-    sqinfo.put("datasetSequence", (seq.getDatasetSequence() != null) ? seq
-            .getDatasetSequence() : new Sequence("THISISAPLACEHOLDER", ""));
     return sqinfo;
   }
 
@@ -99,8 +92,9 @@ public class SeqsetUtils
     String oldname = (String) sqinfo.get("Name");
     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<SequenceFeature> sfeatures = (Vector<SequenceFeature>) sqinfo
+            .get("SeqFeatures");
+    Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
     String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
     if (oldname == null)
@@ -122,23 +116,22 @@ public class SeqsetUtils
       sq.setEnd(end.intValue());
     }
 
-    if ((sfeatures != null) && (sfeatures.size() > 0))
+    if (sfeatures != null && !sfeatures.isEmpty())
     {
-      SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
-      for (int is = 0, isize = sfeatures.size(); is < isize; is++)
-      {
-        sfarray[is] = (SequenceFeature) sfeatures.elementAt(is);
-      }
-      sq.setSequenceFeatures(sfarray);
+      sq.setSequenceFeatures(sfeatures);
     }
     if (description != null)
     {
       sq.setDescription(description);
     }
-    if ((seqds != null)
-            && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
-                    .getLength() == 0))
+    if ((seqds != null) && !(seqds.getName().equals("THISISAPLACEHOLDER")
+            && seqds.getLength() == 0))
     {
+      if (sfeatures != null)
+      {
+        System.err.println(
+                "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+      }
       sq.setDatasetSequence(seqds);
     }
 
@@ -260,8 +253,9 @@ public class SeqsetUtils
     if (unmatched.size() > 0 && !quiet)
     {
       System.err.println("Did not find matches for :");
-      for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out
-              .println(((SequenceI) i.nextElement()).getName()))
+      for (Enumeration i = unmatched.elements(); i
+              .hasMoreElements(); System.out
+                      .println(((SequenceI) i.nextElement()).getName()))
       {
         ;
       }
@@ -287,8 +281,8 @@ public class SeqsetUtils
     for (int i = 0, j = sequences.length; i < j; i++)
     {
       String tempseq = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, sequences[i]
-                      .getSequenceAsString());
+              jalview.util.Comparison.GapChars,
+              sequences[i].getSequenceAsString());
 
       if (tempseq.length() == 0)
       {