JAL-3854 patched SeqSeqUtils.deUniquify to not use instanceOf - seems to work

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

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 329cbd8..4118124 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
@@ -28,6 +29,7 @@ import jalview.datamodel.SequenceI;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 public class SeqsetUtils
@@ -45,21 +47,17 @@ public class SeqsetUtils
   {
     Hashtable sqinfo = new Hashtable();
     sqinfo.put("Name", seq.getName());
-    sqinfo.put("Start", new Integer(seq.getStart()));
-    sqinfo.put("End", new Integer(seq.getEnd()));
+    sqinfo.put("Start", Integer.valueOf(seq.getStart()));
+    sqinfo.put("End", Integer.valueOf(seq.getEnd()));
     if (seq.getDescription() != null)
     {
       sqinfo.put("Description", seq.getDescription());
     }
-    Vector sfeat = new Vector();
-    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
-    if (sfarray != null && sfarray.length > 0)
-    {
-      for (int i = 0; i < sfarray.length; i++)
-      {
-        sfeat.addElement(sfarray[i]);
-      }
-    }
+
+    Vector<SequenceFeature> sfeat = new Vector<>();
+    List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
+    sfeat.addAll(sfs);
+
     if (seq.getDatasetSequence() == null)
     {
       sqinfo.put("SeqFeatures", sfeat);
@@ -73,10 +71,16 @@ public class SeqsetUtils
               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                       : new Sequence("THISISAPLACEHOLDER", ""));
     }
-    if (seq.isHMMConsensusSequence())
+    if (seq.hasHMMProfile())
     {
       sqinfo.put("HMM", seq.getHMM());
     }
+
+    if (seq.getAnnotation("Search Scores") != null)
+    {
+      sqinfo.put("Score", seq.getAnnotation("Search Scores"));
+    }
+
     return sqinfo;
   }
 
@@ -100,11 +104,15 @@ 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<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");
     HiddenMarkovModel hmm = (HiddenMarkovModel) sqinfo.get("HMM");
+    AlignmentAnnotation[] scores = (AlignmentAnnotation[]) sqinfo
+            .get("Score");
+
     if (oldname == null)
     {
       namePresent = false;
@@ -124,35 +132,36 @@ 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.");
+        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);
     }
 
     if (hmm != null)
     {
-      sq.setHMM(new HiddenMarkovModel(hmm));
-      sq.setIsHMMConsensusSequence(true);
+      sq.setHMM(new HiddenMarkovModel(hmm, sq));
+    }
+
+    if (scores != null)
+    {
+      for (AlignmentAnnotation score : scores)
+      {
+        sq.addAlignmentAnnotation(score);
+      }
     }
     return namePresent;
   }
@@ -251,8 +260,7 @@ public class SeqsetUtils
     while (keys.hasMoreElements())
     {
       Object key = keys.nextElement();
-      if (key instanceof String)
-      {
+      try {
         if ((msq = matcher.findIdMatch((String) key)) != null)
         {
           Hashtable sqinfo = (Hashtable) map.get(key);
@@ -267,13 +275,19 @@ public class SeqsetUtils
                     + "' in uniquified alignment");
           }
         }
+      } catch (ClassCastException ccastex) {
+        if (!quiet)
+        {
+          System.err.println("Unexpected object in SeqSet map : "+key.getClass());
+        }
       }
     }
     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()))
       {
         ;
       }