Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index ca2b6d4..009a290 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -27,6 +27,7 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -82,6 +83,10 @@ public class Sequence extends ASequence implements SequenceI
 
   private String vamsasId;
 
+  HiddenMarkovModel hmm;
+
+  boolean isHMMConsensusSequence = false;
+
   private DBModList<DBRefEntry> dbrefs; // controlled access
 
   /**
@@ -361,6 +366,11 @@ public class Sequence extends ASequence implements SequenceI
         this.addPDBId(new PDBEntry(pdb));
       }
     }
+    if (seq.getHMM() != null)
+    {
+      this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
+    }
+
   }
 
   @Override
@@ -472,18 +482,19 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the sequence name, with '/start-end' appended if jvsuffix is true
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public String getDisplayId(boolean jvsuffix)
   {
-    StringBuffer result = new StringBuffer(name);
-    if (jvsuffix)
+    if (!jvsuffix)
     {
-      result.append("/" + start + "-" + end);
+      return name;
     }
+    StringBuilder result = new StringBuilder(name);
+    result.append("/").append(start).append("-").append(end);
 
     return result.toString();
   }
@@ -522,6 +533,7 @@ public class Sequence extends ASequence implements SequenceI
   public void setStart(int start)
   {
     this.start = start;
+    sequenceChanged();
   }
 
   /**
@@ -696,8 +708,8 @@ public class Sequence extends ASequence implements SequenceI
   public void setGeneLoci(String speciesId, String assemblyId,
           String chromosomeId, MapList map)
   {
-    addDBRef(new DBRefEntry(speciesId, assemblyId,
-            DBRefEntry.CHROMOSOME + ":" + chromosomeId, new Mapping(map)));
+    addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId,
+            new Mapping(map)));
   }
 
   /**
@@ -713,41 +725,9 @@ public class Sequence extends ASequence implements SequenceI
     {
       for (final DBRefEntry ref : refs)
       {
-        if (ref.isChromosome())
+        if (ref instanceof GeneLociI)
         {
-          return new GeneLociI()
-          {
-            @Override
-            public String getSpeciesId()
-            {
-              return ref.getSource();
-            }
-
-            @Override
-            public String getAssemblyId()
-            {
-              // DEV NOTE: DBRefEntry is reused here to hold chromosomal locus
-              // of a gene sequence.
-              // source=species, version=assemblyId, accession=chromosome, map =
-              // positions.
-
-              return ref.getVersion();
-            }
-
-            @Override
-            public String getChromosomeId()
-            {
-              // strip off "chromosome:" prefix to chrId
-              return ref.getAccessionId()
-                      .substring(DBRefEntry.CHROMOSOME.length() + 1);
-            }
-
-            @Override
-            public MapList getMap()
-            {
-              return ref.getMap().getMap();
-            }
-          };
+          return (GeneLociI) ref;
         }
       }
     }
@@ -1099,7 +1079,8 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public ContiguousI findPositions(int fromColumn, int toColumn)
   {
-    if (toColumn < fromColumn || fromColumn < 1)
+    fromColumn = Math.max(fromColumn, 1);
+    if (toColumn < fromColumn)
     {
       return null;
     }
@@ -1612,7 +1593,7 @@ public class Sequence extends ASequence implements SequenceI
       _isNa = Comparison.isNucleotide(this);
     }
     return !_isNa;
-  };
+  }
 
   /*
    * (non-Javadoc)
@@ -1834,7 +1815,8 @@ public class Sequence extends ASequence implements SequenceI
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
+        String id = ann.getCalcId();
+        if (id != null && id.equals(calcId)
                 && ann.label != null && ann.label.equals(label))
         {
           result.add(ann);
@@ -1954,6 +1936,34 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel hmm)
+  {
+    this.hmm = hmm;
+  }
+
+  @Override
+  public boolean hasHMMAnnotation()
+  {
+    if (this.annotation == null) {
+      return false;
+    }
+    for (AlignmentAnnotation ann : annotation)
+    {
+      if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
   /**
    * {@inheritDoc}
    */
@@ -1967,15 +1977,6 @@ public class Sequence extends ASequence implements SequenceI
 
     List<SequenceFeature> result = getFeatures().findFeatures(startPos,
             endPos, types);
-    if (datasetSequence != null)
-    {
-      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
-              types);
-    }
-    else
-    {
-      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
-    }
 
     /*
      * if end column is gapped, endPos may be to the right, 
@@ -2127,4 +2128,10 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     return 0;
   }
+
+  @Override
+  public boolean hasHMMProfile()
+  {
+    return hmm != null;
+  }
 }