X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=39ee2cb7d71c089e8eb6b5f6e221463ba6e8bdc2;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=463b909ad8ef1c96ba00c06f208f1e056548e25d;hpb=3b239d86dc3a1bf3aa07c0ad3d38aeca57b54ada;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 463b909..39ee2cb 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -51,6 +51,8 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   boolean colourText = false;
 
+  HiddenMarkovModel hmm;
+
   /**
    * True if the group is defined as a group on the alignment, false if it is
    * just a selection.
@@ -100,6 +102,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private boolean ignoreGapsInConsensus = true;
 
+  private boolean ignoreBelowBackground = true;
+
   /**
    * consensus calculation property
    */
@@ -124,10 +128,18 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   AlignmentAnnotation conservation = null;
 
+  AlignmentAnnotation informationContent = null;
+
   private boolean showConsensusHistogram;
 
   private AnnotatedCollectionI context;
 
+  private boolean showHMMSequenceLogo;
+
+  private boolean normaliseHMMSequenceLogo;
+
+  private boolean showInformationHistogram;
+
   /**
    * Creates a new SequenceGroup object.
    */
@@ -199,6 +211,9 @@ public class SequenceGroup implements AnnotatedCollectionI
       showSequenceLogo = seqsel.showSequenceLogo;
       normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
       showConsensusHistogram = seqsel.showConsensusHistogram;
+      showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+      normaliseHMMSequenceLogo = seqsel.normaliseHMMSequenceLogo;
+      showInformationHistogram = seqsel.showInformationHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -207,6 +222,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+      ignoreBelowBackground = seqsel.ignoreBelowBackground;
       if (seqsel.conserve != null)
       {
         recalcConservation(); // safer than
@@ -548,7 +564,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public boolean recalcConservation(boolean defer)
   {
-    if (cs == null && consensus == null && conservation == null)
+    if (cs == null && consensus == null && conservation == null
+            && informationContent == null)
     {
       return false;
     }
@@ -559,6 +576,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
+      if (informationContent != null)
+      {
+        // _updateInformationRow(cnsns, sequences.size()); TODO don't know what
+        // to do here
+        upd = true;
+      }
       if (consensus != null)
       {
         _updateConsensusRow(cnsns, sequences.size());
@@ -654,6 +677,30 @@ public class SequenceGroup implements AnnotatedCollectionI
     // ignoreGapsInConsensusCalculation);
   }
 
+  private void _updateInformationRow(ProfilesI cnsns, long nseq)
+  {
+    if (consensus == null)
+    {
+      getConsensus();
+    }
+    consensus.label = "Consensus for " + getName();
+    consensus.description = "Percent Identity";
+    consensusData = cnsns;
+    // preserve width if already set
+    int aWidth = (consensus.annotations != null)
+            ? (endRes < consensus.annotations.length
+                    ? consensus.annotations.length : endRes + 1)
+            : endRes + 1;
+    consensus.annotations = null;
+    consensus.annotations = new Annotation[aWidth]; // should be alignment width
+
+    AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
+            ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+                                                            // container
+    // for
+    // ignoreGapsInConsensusCalculation);
+  }
+
   /**
    * @param s
    *          sequence to either add or remove from group
@@ -1187,6 +1234,20 @@ public class SequenceGroup implements AnnotatedCollectionI
     return ignoreGapsInConsensus;
   }
 
+  public void setIgnoreBelowBackground(boolean state)
+  {
+    if (this.ignoreBelowBackground != state)
+    {
+      ignoreBelowBackground = state;
+    }
+    ignoreBelowBackground = state;
+  }
+
+  public boolean getIgnoreBelowBackground()
+  {
+    return true;
+  }
+
   /**
    * @param showSequenceLogo
    *          indicates if a sequence logo is shown for consensus annotation
@@ -1457,4 +1518,44 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
   }
+
+  public boolean isShowInformationHistogram()
+  {
+    return showInformationHistogram;
+  }
+
+  public void setShowInformationHistogram(boolean state)
+  {
+    if (showInformationHistogram != state && informationContent != null)
+    {
+      this.showInformationHistogram = state;
+      // recalcConservation(); TODO don't know what to do here next
+    }
+    this.showInformationHistogram = state;
+
+  }
+
+  public boolean isShowHMMSequenceLogo()
+  {
+    // TODO Auto-generated method stub
+    return showHMMSequenceLogo;
+  }
+
+  public void setshowHMMSequenceLogo(boolean state)
+  {
+    showHMMSequenceLogo = state;
+
+  }
+
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    // TODO Auto-generated method stub
+    return normaliseHMMSequenceLogo;
+  }
+
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
 }