JAL-2668 add tests for HMMER commands, annotation and io

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 44522a8..0da30ba 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,6 +22,7 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.DBRefEntryI;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
@@ -50,12 +51,20 @@ public class Sequence extends ASequence implements SequenceI
 
   private char[] sequence;
 
+  int previousPosition;
+
   String description;
 
   int start;
 
   int end;
 
+  boolean hasInfo;
+
+  HiddenMarkovModel hmm;
+
+  boolean isHMMConsensusSequence = false;
+
   Vector<PDBEntry> pdbIds;
 
   String vamsasId;
@@ -232,8 +241,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       char[] oseq = seq.getSequence();
       initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(),
-            seq.getEnd());
+              seq.getStart(), seq.getEnd());
     }
     description = seq.getDescription();
     if (seq != datasetSequence)
@@ -290,9 +298,12 @@ public class Sequence extends ASequence implements SequenceI
         this.addPDBId(new PDBEntry(pdb));
       }
     }
+    if (seq.getHMM() != null)
+    {
+      this.hmm = new HiddenMarkovModel(seq.getHMM());
+    }
   }
 
-
   @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -315,12 +326,11 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public synchronized void addSequenceFeature(SequenceFeature sf)
+  public synchronized boolean addSequenceFeature(SequenceFeature sf)
   {
-    if (sequenceFeatures==null && datasetSequence != null)
+    if (sequenceFeatures == null && datasetSequence != null)
     {
-      datasetSequence.addSequenceFeature(sf);
-      return;
+      return datasetSequence.addSequenceFeature(sf);
     }
     if (sequenceFeatures == null)
     {
@@ -331,7 +341,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       if (sequenceFeatures[i].equals(sf))
       {
-        return;
+        return false;
       }
     }
 
@@ -340,6 +350,7 @@ public class Sequence extends ASequence implements SequenceI
     temp[sequenceFeatures.length] = sf;
 
     sequenceFeatures = temp;
+    return true;
   }
 
   @Override
@@ -347,8 +358,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
-      if (datasetSequence!=null) {
-         datasetSequence.deleteFeature(sf);
+      if (datasetSequence != null)
+      {
+        datasetSequence.deleteFeature(sf);
       }
       return;
     }
@@ -416,7 +428,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (pdbIds == null)
     {
-      pdbIds = new Vector<PDBEntry>();
+      pdbIds = new Vector<>();
       pdbIds.add(entry);
       return true;
     }
@@ -787,7 +799,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public List<int[]> getInsertions()
   {
-    ArrayList<int[]> map = new ArrayList<int[]>();
+    ArrayList<int[]> map = new ArrayList<>();
     int lastj = -1, j = 0;
     int pos = start;
     int seqlen = sequence.length;
@@ -944,7 +956,17 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setDBRefs(DBRefEntry[] dbref)
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      datasetSequence.setDBRefs(dbref);
+      return;
+    }
     dbrefs = dbref;
+    if (dbrefs != null)
+    {
+      DBRefUtils.ensurePrimaries(this);
+    }
   }
 
   @Override
@@ -961,7 +983,12 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
-    // TODO add to dataset sequence instead if there is one?
+    if (datasetSequence != null)
+    {
+      datasetSequence.addDBRef(entry);
+      return;
+    }
+
     if (dbrefs == null)
     {
       dbrefs = new DBRefEntry[0];
@@ -989,12 +1016,23 @@ public class Sequence extends ASequence implements SequenceI
     temp[temp.length - 1] = entry;
 
     dbrefs = temp;
+
+    DBRefUtils.ensurePrimaries(this);
   }
 
   @Override
   public void setDatasetSequence(SequenceI seq)
   {
-    // TODO check for circular reference before setting?
+    if (seq == this)
+    {
+      throw new IllegalArgumentException(
+              "Implementation Error: self reference passed to SequenceI.setDatasetSequence");
+    }
+    if (seq != null && seq.getDatasetSequence() != null)
+    {
+      throw new IllegalArgumentException(
+              "Implementation error: cascading dataset sequences are not allowed.");
+    }
     datasetSequence = seq;
   }
 
@@ -1022,7 +1060,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (this.annotation == null)
     {
-      this.annotation = new Vector<AlignmentAnnotation>();
+      this.annotation = new Vector<>();
     }
     if (!this.annotation.contains(annotation))
     {
@@ -1067,7 +1105,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    Sequence seq=null;
+    Sequence seq = null;
     if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
@@ -1081,7 +1119,7 @@ public class Sequence extends ASequence implements SequenceI
       else
       {
         // Create a new, valid dataset sequence
-       createDatasetSequence();
+        createDatasetSequence();
       }
     }
     return new Sequence(this);
@@ -1091,6 +1129,10 @@ public class Sequence extends ASequence implements SequenceI
 
   private long _seqhash = 0;
 
+  /**
+   * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+   * true
+   */
   @Override
   public boolean isProtein()
   {
@@ -1101,7 +1143,7 @@ public class Sequence extends ASequence implements SequenceI
     if (_seqhash != sequence.hashCode())
     {
       _seqhash = sequence.hashCode();
-      _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+      _isNa = Comparison.isNucleotide(this);
     }
     return !_isNa;
   };
@@ -1125,9 +1167,9 @@ public class Sequence extends ASequence implements SequenceI
       dsseq.setDescription(description);
       // move features and database references onto dataset sequence
       dsseq.sequenceFeatures = sequenceFeatures;
-      sequenceFeatures=null;
+      sequenceFeatures = null;
       dsseq.dbrefs = dbrefs;
-      dbrefs=null;
+      dbrefs = null;
       // TODO: search and replace any references to this sequence with
       // references to the dataset sequence in Mappings on dbref
       dsseq.pdbIds = pdbIds;
@@ -1342,7 +1384,7 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
-    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
@@ -1385,21 +1427,20 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
-
   @Override
   public List<DBRefEntry> getPrimaryDBRefs()
   {
-    if (datasetSequence!=null)
+    if (datasetSequence != null)
     {
       return datasetSequence.getPrimaryDBRefs();
     }
-    if (dbrefs==null || dbrefs.length==0)
+    if (dbrefs == null || dbrefs.length == 0)
     {
       return Collections.emptyList();
     }
     synchronized (dbrefs)
     {
-      List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+      List<DBRefEntry> primaries = new ArrayList<>();
       DBRefEntry[] tmp = new DBRefEntry[1];
       for (DBRefEntry ref : dbrefs)
       {
@@ -1446,4 +1487,89 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel hmm)
+  {
+    this.hmm = hmm;
+  }
+
+  @Override
+  public void updateHMMMapping()
+  {
+    int node = 1;
+    int column = 0;
+    for (char residue : sequence)
+    {
+      if (!Comparison.isGap(residue))
+      {
+        hmm.setAlignmentColumn(node, column);
+        hmm.getNodeLookup().put(column, node);
+        node++;
+      }
+      else
+      {
+        hmm.getNodeLookup().remove(column);
+      }
+      column++;
+    }
+
+  }
+
+  @Override
+  public boolean isHMMConsensusSequence()
+  {
+    return isHMMConsensusSequence;
+  }
+
+  @Override
+  public void setIsHMMConsensusSequence(boolean isHMMConsensusSequence)
+  {
+    this.isHMMConsensusSequence = isHMMConsensusSequence;
+  }
+
+  @Override
+  public boolean hasHMMAnnotation()
+  {
+    return hasInfo;
+    /*
+    if (annotation == null)
+    {
+      return false;
+    }
+    
+    for (AlignmentAnnotation annot : annotation)
+    {
+      if (annot.label.contains("_HMM"))
+      {
+        return true;
+      }
+    }
+    return false;
+    */
+  }
+
+  @Override
+  public void setHasInfo(boolean status)
+  {
+    hasInfo = true;
+  }
+
+  @Override
+  public int getPreviousPosition()
+  {
+    return previousPosition;
+  }
+
+  @Override
+  public void setPreviousPosition(int previousPosition)
+  {
+    this.previousPosition = previousPosition;
+  }
+
 }