JAL-2629 moved HMM storage location to placeholder sequence

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 573e607..900209d 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -741,12 +741,10 @@ public class AAFrequency
    *          less than their background frequencies.
    * @return
    */
-  public static int[] getHMMProfileFor(AlignmentAnnotation aa, int column,
+  public static int[] getHMMProfileFor(HiddenMarkovModel hmm, int column,
           boolean removeBelowBackground)
   {
 
-    HiddenMarkovModel hmm;
-    hmm = aa.getHMM();
     if (hmm != null)
     {
       String alph = hmm.getAlphabetType();

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 31aeecc..e8e8d01 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -51,9 +51,9 @@ public class AlignmentAnnotation
 
   public static final int CDNA_PROFILE = 2;
 
-  private static long counter = 0;
+  HiddenMarkovModel hmm;
 
-  private HiddenMarkovModel hmm;
+  private static long counter = 0;
 
   /**
    * If true, this annotations is calculated every edit, eg consensus, quality
@@ -1506,23 +1506,13 @@ public class AlignmentAnnotation
     return graphMin < graphMax;
   }
 
-  /**
-   * Returns the HMM associated with this annotation.
-   * 
-   * @return
-   */
-  public HiddenMarkovModel getHMM()
+  public void setHMM(HiddenMarkovModel markov)
   {
-    return hmm;
+    hmm = markov;
   }
 
-  /**
-   * Sets the HMM associated with this annotation.
-   * 
-   * @param hmm
-   */
-  public void setHMM(HiddenMarkovModel hmm)
+  public HiddenMarkovModel getHMM()
   {
-    this.hmm = hmm;
+    return hmm;
   }
 }

diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index 40f106e..96a5a6f 100644 (file)
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -1069,7 +1069,7 @@ public class HiddenMarkovModel
         if ("x".equals(character) || "X".equals(character))
         {
           nodeIndex++;
-          if (nodeIndex <= nodes.size())
+          if (nodeIndex < nodes.size())
           {
             nodes.get(nodeIndex).setAlignmentColumn(col + 1);
             nodeLookup.put(col + 1, nodeIndex);

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index b0faf21..56a89a1 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -57,6 +57,8 @@ public class Sequence extends ASequence implements SequenceI
 
   int end;
 
+  HiddenMarkovModel hmm;
+
   Vector<PDBEntry> pdbIds;
 
   String vamsasId;
@@ -416,7 +418,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (pdbIds == null)
     {
-      pdbIds = new Vector<PDBEntry>();
+      pdbIds = new Vector<>();
       pdbIds.add(entry);
       return true;
     }
@@ -787,7 +789,7 @@ 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;
@@ -1048,7 +1050,7 @@ 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))
     {
@@ -1372,7 +1374,7 @@ 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)
@@ -1428,7 +1430,7 @@ public class Sequence extends ASequence implements SequenceI
     }
     synchronized (dbrefs)
     {
-      List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+      List<DBRefEntry> primaries = new ArrayList<>();
       DBRefEntry[] tmp = new DBRefEntry[1];
       for (DBRefEntry ref : dbrefs)
       {
@@ -1475,4 +1477,16 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel hmm)
+  {
+    this.hmm = hmm;
+  }
+
 }

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index e81553b..3298829 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -41,6 +41,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b14423c..0c951fa 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4683,12 +4683,30 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                                                             // pipeline
             hmmFile.parse();
             HiddenMarkovModel hmm = hmmFile.getHMM();
+            AlignmentAnnotation annotArray[] = getViewport().getAlignment()
+                    .getAlignmentAnnotation();
+
+            AlignmentAnnotation reference = null;
+            for (AlignmentAnnotation annot : annotArray)
+            {
+              if (annot.label.contains("Reference"))
+              {
+                reference = annot;
+              }
+            }
+
+            if (reference != null)
+            {
+              hmm.mapToReferenceAnnotation(reference);
+            }
+
             AlignmentAnnotation annotation = hmm.createAnnotation(
                     getViewport().getAlignment().getWidth());
             getViewport().getAlignment().addAnnotation(annotation);
-            annotation.setHMM(hmm);
             int length = getViewport().getAlignment().getWidth();
             Sequence consensus = hmm.getConsensusSequence(length);
+            consensus.setHMM(hmm);
+            annotation.setHMM(hmm);
             SequenceI[] consensusArr = new Sequence[] { consensus };
             AlignmentI newAlignment = new Alignment(consensusArr);
             newAlignment.append(getViewport().getAlignment());

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 7333075..745fb93 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -311,9 +311,9 @@ public abstract class AlignFile extends FileParse implements
    */
   protected void initData()
   {
-    seqs = new Vector<SequenceI>();
-    annotations = new Vector<AlignmentAnnotation>();
-    seqGroups = new ArrayList<SequenceGroup>();
+    seqs = new Vector<>();
+    annotations = new Vector<>();
+    seqGroups = new ArrayList<>();
     parseCalled = false;
   }
 
@@ -326,7 +326,7 @@ public abstract class AlignFile extends FileParse implements
   @Override
   public void setSeqs(SequenceI[] s)
   {
-    seqs = new Vector<SequenceI>();
+    seqs = new Vector<>();
 
     for (int i = 0; i < s.length; i++)
     {
@@ -397,7 +397,7 @@ public abstract class AlignFile extends FileParse implements
   {
     if (newickStrings == null)
     {
-      newickStrings = new Vector<String[]>();
+      newickStrings = new Vector<>();
     }
     newickStrings.addElement(new String[] { treeName, newickString });
   }
@@ -421,4 +421,16 @@ public abstract class AlignFile extends FileParse implements
   {
     seqs.add(seq);
   }
+
+  /**
+   * Used only for hmmer statistics, so should probably be removed at some
+   * point. TODO remove this
+   * 
+   * @return
+   */
+  public Vector<AlignmentAnnotation> getAnnotations()
+  {
+    return annotations;
+  }
+
 }

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 1f3d5a9..78b3a88 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.ProfilesI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.NucleotideColourScheme;
@@ -359,7 +360,8 @@ public class AnnotationRenderer
     //
     if (aa.label.startsWith("Information"))
     {
-      return AAFrequency.getHMMProfileFor(aa, column,
+      HiddenMarkovModel hmm = aa.getHMM();
+      return AAFrequency.getHMMProfileFor(hmm, column,
               av_ignoreBelowBackground); // TODO check if this follows standard
                                          // pipeline
     }

diff --git a/src/jalview/schemes/HMMERColourScheme.java b/src/jalview/schemes/HMMERColourScheme.java
index 09092a6..c9e081f 100644 (file)
--- a/src/jalview/schemes/HMMERColourScheme.java
+++ b/src/jalview/schemes/HMMERColourScheme.java
@@ -1,6 +1,5 @@
 package jalview.schemes;
 
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceCollectionI;
@@ -106,35 +105,19 @@ public class HMMERColourScheme extends ResidueColourScheme
   public void alignmentChanged(AnnotatedCollectionI collection,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    AlignmentAnnotation[] annArr = collection.getAlignmentAnnotation();
-    for (AlignmentAnnotation ann : annArr)
-    {
-      if (ann.label.indexOf("Information Content") > -1)
-      {
-        hmm = ann.getHMM();
-      }
-    }
-
+    SequenceI seq = collection.getSequences().get(0);
+    hmm = seq.getHMM();
   }
 
+
+
   @Override
   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     HiddenMarkovModel markov = null;
-    AlignmentAnnotation[] annArr = sg.getAlignmentAnnotation();
-    for (AlignmentAnnotation ann : annArr)
-    {
-      if (ann.label.indexOf("Information Content") > -1)
-      {
-        markov = ann.getHMM();
-      }
-    }
-    
-    
-    
-    
-
+    SequenceI seq = sg.getSequences().get(0);
+    markov = seq.getHMM();
     HMMERColourScheme colour = new HMMERColourScheme(markov);
     return colour;
 

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 646412f..4755bf6 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -249,11 +249,8 @@ public class AAFrequencyTest
             "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
     hmmFile.parse();
     HiddenMarkovModel hmm = hmmFile.getHMM();
-    AlignmentAnnotation aa = hmm.createAnnotation(80);
-    aa.setHMM(hmm);
-
     int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 };
-    int[] actual = AAFrequency.getHMMProfileFor(aa, 17, false);
+    int[] actual = AAFrequency.getHMMProfileFor(hmm, 17, false);
     for (int i = 0; i < actual.length; i++)
     {
       if (i == 2)
@@ -267,7 +264,7 @@ public class AAFrequencyTest
     }
 
     int[] expected2 = { 0, 4, 85, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
-    int[] actual2 = AAFrequency.getHMMProfileFor(aa, 2, true);
+    int[] actual2 = AAFrequency.getHMMProfileFor(hmm, 2, true);
     for (int i = 0; i < actual.length; i++)
     {
       if (i == 2)