Merge branch 'develop' into features/hmmer

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

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2b21e5e..6f037e5 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;
@@ -34,7 +35,7 @@ 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
@@ -72,6 +73,10 @@ public class SeqsetUtils
               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                       : new Sequence("THISISAPLACEHOLDER", ""));
     }
+    if (seq.isHMMConsensusSequence())
+    {
+      sqinfo.put("HMM", seq.getHMM());
+    }
     return sqinfo;
   }
 
@@ -99,6 +104,7 @@ public class SeqsetUtils
     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;
@@ -142,6 +148,11 @@ public class SeqsetUtils
       sq.setDatasetSequence(seqds);
     }
 
+    if (hmm != null)
+    {
+      sq.setHMM(new HiddenMarkovModel(hmm));
+      sq.setIsHMMConsensusSequence(true);
+    }
     return namePresent;
   }