JAL-2629 update spikes/mungo to latest

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

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2b21e5e..921ab2a 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -27,6 +28,7 @@ import jalview.datamodel.SequenceI;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 public class SeqsetUtils
@@ -34,7 +36,7 @@ public class SeqsetUtils
 
   /**
    * Store essential properties of a sequence in a hashtable for later recovery
-   * Keys are Name, Start, End, SeqFeatures, PdbId
+   * Keys are Name, Start, End, SeqFeatures, PdbId, HMM
    * 
    * @param seq
    *          SequenceI
@@ -50,15 +52,11 @@ public class SeqsetUtils
     {
       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);
@@ -72,6 +70,10 @@ public class SeqsetUtils
               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                       : new Sequence("THISISAPLACEHOLDER", ""));
     }
+    if (seq.hasHMMProfile())
+    {
+      sqinfo.put("HMM", seq.getHMM());
+    }
     return sqinfo;
   }
 
@@ -95,10 +97,12 @@ 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");
     if (oldname == null)
     {
       namePresent = false;
@@ -118,14 +122,9 @@ 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)
     {
@@ -142,6 +141,10 @@ public class SeqsetUtils
       sq.setDatasetSequence(seqds);
     }
 
+    if (hmm != null)
+    {
+      sq.setHMM(new HiddenMarkovModel(hmm, sq));
+    }
     return namePresent;
   }