X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=59cb4bba01f851e4cacbbeab3f84b1cefd23657c;hb=3a7dc7069f6983ef56b5440b57cd3e62eeb383c7;hp=9a408e31dda4dfdce5d63638009bb6884a8cc3ab;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 9a408e3..59cb4bb 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -22,14 +22,19 @@ package jalview.datamodel;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+import jalview.workers.InformationThread;
 
 import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
-import java.util.Vector;
 
 /**
  * Collects a set contiguous ranges on a set of sequences
@@ -39,13 +44,36 @@ import java.util.Vector;
  */
 public class SequenceGroup implements AnnotatedCollectionI
 {
+  // TODO ideally this event notification functionality should be separated into
+  // a subclass of ViewportProperties similarly to ViewportRanges.
+  // Done here as a quick fix for JAL-2665
+  public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
+  
+  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
+  public void addPropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
+
+  public void removePropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
+  // end of event notification functionality initialisation
+
   String groupName;
 
   String description;
-
+  
   Conservation conserve;
 
-  Vector aaFrequency;
+  Conservation conservationData;
+
+  ProfilesI consensusProfiles;
+
+  ProfilesI hmmProfiles;
 
   boolean displayBoxes = true;
 
@@ -53,33 +81,43 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   boolean colourText = false;
 
-  /**
+  /*
+   * true if the group is defined as a group on the alignment, false if it is
+   * just a selection
+   */
+  boolean isDefined = false;
+
+  /*
    * after Olivier's non-conserved only character display
    */
   boolean showNonconserved = false;
 
-  /**
-   * group members
+  /*
+   * sequences in the group
    */
-  private List<SequenceI> sequences = new ArrayList<SequenceI>();
+  private List<SequenceI> sequences;
 
-  /**
+  /*
    * representative sequence for this group (if any)
    */
   private SequenceI seqrep = null;
 
   int width = -1;
 
-  /**
-   * Colourscheme applied to group if any
+  /*
+   * colour scheme applied to group if any
    */
-  public ColourSchemeI cs;
+  public ResidueShaderI cs;
 
-  // start column (base 0)
-  int startRes = 0;
+  /**
+   * start column (base 0)
+   */
+  private int startRes = 0;
 
-  // end column (base 0)
-  int endRes = 0;
+  /**
+   *  end column (base 0)
+   */
+  private int endRes = 0;
 
   public Color outlineColour = Color.black;
 
@@ -91,35 +129,58 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public Color textColour2 = Color.white;
 
-  /**
-   * consensus calculation property
+  /*
+   * properties for consensus annotation
    */
   private boolean ignoreGapsInConsensus = true;
 
-  /**
-   * consensus calculation property
-   */
   private boolean showSequenceLogo = false;
 
-  /**
-   * flag indicating if logo should be rendered normalised
-   */
   private boolean normaliseSequenceLogo;
 
-  /**
-   * @return the includeAllConsSymbols
+  /*
+   * properties for HMM information annotation
    */
-  public boolean isShowSequenceLogo()
-  {
-    return showSequenceLogo;
-  }
+  private boolean hmmIgnoreBelowBackground = true;
+
+  private boolean hmmUseInfoLetterHeight;
+
+  private boolean hmmShowSequenceLogo;
+
+  private boolean hmmNormaliseSequenceLogo;
+
+  private boolean hmmShowHistogram;
+
+  /*
+   * visibility of rows or represented rows covered by group
+   */
+  private boolean hidereps = false;
+
+  /*
+   * visibility of columns intersecting this group
+   */
+  private boolean hidecols;
+
+  AlignmentAnnotation consensus = null;
+
+  AlignmentAnnotation conservation = null;
+
+  private AlignmentAnnotation hmmInformation;
+  
+  private boolean showConsensusHistogram;
+  
+  private AnnotatedCollectionI context;
+
 
   /**
-   * Creates a new SequenceGroup object.
+   * Constructor, assigning a generated default name of "JGroup:" with object
+   * hashcode appended
    */
   public SequenceGroup()
   {
     groupName = "JGroup:" + this.hashCode();
+    cs = new ResidueShader();
+    sequences = new ArrayList<>();
   }
 
   /**
@@ -140,12 +201,13 @@ public class SequenceGroup implements AnnotatedCollectionI
           ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
           boolean colourText, int start, int end)
   {
+    this();
     this.sequences = sequences;
     this.groupName = groupName;
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
-    this.cs = scheme;
+    this.cs = new ResidueShader(scheme);
     startRes = start;
     endRes = end;
     recalcConservation();
@@ -155,12 +217,16 @@ public class SequenceGroup implements AnnotatedCollectionI
    * copy constructor
    * 
    * @param seqsel
+   * @param keepsequences
+   *          if false do not add sequences from seqsel to new instance
    */
   public SequenceGroup(SequenceGroup seqsel)
   {
+    this();
+
     if (seqsel != null)
     {
-      sequences = new ArrayList<SequenceI>();
+      sequences = new ArrayList<>();
       sequences.addAll(seqsel.sequences);
       if (seqsel.groupName != null)
       {
@@ -169,15 +235,23 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayBoxes = seqsel.displayBoxes;
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
+      
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
-      cs = seqsel.cs;
+      cs = new ResidueShader((ResidueShader) seqsel.cs);
       if (seqsel.description != null)
       {
         description = new String(seqsel.description);
       }
       hidecols = seqsel.hidecols;
       hidereps = seqsel.hidereps;
+      showNonconserved = seqsel.showNonconserved;
+      showSequenceLogo = seqsel.showSequenceLogo;
+      normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
+      showConsensusHistogram = seqsel.showConsensusHistogram;
+      hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
+      hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
+      hmmShowHistogram = seqsel.hmmShowHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -186,14 +260,34 @@ public class SequenceGroup implements AnnotatedCollectionI
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+      hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
+      hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
       if (seqsel.conserve != null)
       {
+        // todo avoid doing this if we don't actually want derived calculations
+        // !
         recalcConservation(); // safer than
         // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
       }
     }
   }
 
+  /**
+   * Constructor that copies the given list of sequences
+   * 
+   * @param seqs
+   */
+  public SequenceGroup(List<SequenceI> seqs)
+  {
+    this();
+    this.sequences.addAll(seqs);
+  }
+
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
   public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
   {
     int iSize = sequences.size();
@@ -310,7 +404,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     else
     {
-      List<SequenceI> allSequences = new ArrayList<SequenceI>();
+      List<SequenceI> allSequences = new ArrayList<>();
       for (SequenceI seq : sequences)
       {
         allSequences.add(seq);
@@ -470,6 +564,8 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (s != null && !sequences.contains(s))
       {
         sequences.add(s);
+        changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+                sequences.size() - 1, sequences.size());
       }
 
       if (recalc)
@@ -513,8 +609,9 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * calculate residue conservation for group - but only if necessary. returns
-   * true if the calculation resulted in a visible change to group
+   * Recalculates column consensus, conservation, and HMM annotation for the
+   * group (as applicable). Returns true if the calculation resulted in a
+   * visible change to group.
    * 
    * @param defer
    *          when set, colourschemes for this group are not refreshed after
@@ -522,7 +619,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public boolean recalcConservation(boolean defer)
   {
-    if (cs == null && consensus == null && conservation == null)
+    if (cs == null && consensus == null && conservation == null
+            && hmmInformation == null)
     {
       return false;
     }
@@ -531,8 +629,18 @@ public class SequenceGroup implements AnnotatedCollectionI
     boolean upd = false;
     try
     {
-      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+      ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
+      if (hmmInformation != null)
+      {
+        HiddenMarkovModel hmm = hmmInformation.sequenceRef.getHMM();
+
+        ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
+                (endRes + 1) - startRes, startRes, endRes + 1,
+                hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
+        _updateInformationRow(info);
+        upd = true;
+      }
       if (consensus != null)
       {
         _updateConsensusRow(cnsns, sequences.size());
@@ -547,8 +655,8 @@ public class SequenceGroup implements AnnotatedCollectionI
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName, 3, sequences,
-                startRes, endRes + 1);
+        Conservation c = new Conservation(groupName, sequences, startRes,
+                endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
         if (conservation != null)
@@ -594,8 +702,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     conservation.description = "Conservation for group " + getName()
             + " less than " + consPercGaps + "% gaps";
     // preserve width if already set
-    int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
-            : endRes + 1)
+    int aWidth = (conservation.annotations != null)
+            ? (endRes < conservation.annotations.length
+                    ? conservation.annotations.length
+                    : endRes + 1)
             : endRes + 1;
     conservation.annotations = null;
     conservation.annotations = new Annotation[aWidth]; // should be alignment
@@ -603,9 +713,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public Hashtable[] consensusData = null;
+  public ProfilesI consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
+  private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
     {
@@ -615,8 +725,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     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)
+    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
@@ -629,6 +741,33 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
+   * Recalculates the information content on the HMM annotation
+   * 
+   * @param cnsns
+   */
+  private void _updateInformationRow(ProfilesI cnsns)
+  {
+    if (hmmInformation == null)
+    {
+      createInformationAnnotation();
+    }
+    hmmInformation.description = MessageManager
+            .getString("label.information_description");
+    setHmmProfiles(cnsns);
+    // preserve width if already set
+    int aWidth = (hmmInformation.annotations != null)
+            ? (endRes < hmmInformation.annotations.length
+                    ? hmmInformation.annotations.length : endRes + 1)
+            : endRes + 1;
+    hmmInformation.annotations = null;
+    hmmInformation.annotations = new Annotation[aWidth]; // should be alignment
+                                                      // width
+    hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+    AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
+            endRes + 1);
+  }
+
+  /**
    * @param s
    *          sequence to either add or remove from group
    * @param recalc
@@ -663,6 +802,8 @@ public class SequenceGroup implements AnnotatedCollectionI
     synchronized (sequences)
     {
       sequences.remove(s);
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+              sequences.size() + 1, sequences.size());
 
       if (recalc)
       {
@@ -695,11 +836,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Set the first column selected by this group. Runs from 0<=i<N_cols
    * 
-   * @param i
+   * @param newStart
    */
-  public void setStartRes(int i)
+  public void setStartRes(int newStart)
   {
-    startRes = i;
+    int before = startRes;
+   startRes= Math.max(0,newStart); // sanity check for negative start column positions
+   changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+    
+
+
   }
 
   /**
@@ -709,7 +855,9 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void setEndRes(int i)
   {
+    int before = endRes;
     endRes = i;
+    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
   }
 
   /**
@@ -950,11 +1098,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of rows or represented rows covered by group
-   */
-  private boolean hidereps = false;
-
-  /**
    * set visibility of sequences covered by (if no sequence representative is
    * defined) or represented by this group.
    * 
@@ -976,11 +1119,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of columns intersecting this group
-   */
-  private boolean hidecols = false;
-
-  /**
    * set intended visibility of columns covered by this group
    * 
    * @param visibility
@@ -1014,7 +1152,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
-    sgroup.sequences = new ArrayList<SequenceI>();
+    sgroup.sequences = new ArrayList<>();
     for (int s = 0; insect != null && s < insect.length; s++)
     {
       if (map == null || map.containsKey(insect[s]))
@@ -1042,13 +1180,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.showNonconserved = displayNonconserved;
   }
 
-  AlignmentAnnotation consensus = null, conservation = null;
-
-  /**
-   * flag indicating if consensus histogram should be rendered
-   */
-  private boolean showConsensusHistogram;
-
   /**
    * set this alignmentAnnotation object as the one used to render consensus
    * annotation
@@ -1093,6 +1224,22 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
+   * Creates the Hidden Markov Model annotation for this group
+   */
+  void createInformationAnnotation()
+  {
+    hmmInformation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+            6.25f, AlignmentAnnotation.BAR_GRAPH);
+    hmmInformation.hasText = true;
+    hmmInformation.autoCalculated = false;
+    hmmInformation.groupRef = this;
+    hmmInformation.label = getName();
+    hmmInformation.description = MessageManager
+            .getString("label.information_description");
+    hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+  }
+
+  /**
    * set this alignmentAnnotation object as the one used to render consensus
    * annotation
    * 
@@ -1145,9 +1292,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       if (consensus.annotations[i] != null)
       {
-        if (consensus.annotations[i].description.charAt(0) == '[')
+        String desc = consensus.annotations[i].description;
+        if (desc.length() > 1 && desc.charAt(0) == '[')
         {
-          seqs.append(consensus.annotations[i].description.charAt(1));
+          seqs.append(desc.charAt(1));
         }
         else
         {
@@ -1178,6 +1326,26 @@ public class SequenceGroup implements AnnotatedCollectionI
     return ignoreGapsInConsensus;
   }
 
+  public void setIgnoreBelowBackground(boolean state)
+  {
+    hmmIgnoreBelowBackground = state;
+  }
+
+  public boolean isIgnoreBelowBackground()
+  {
+    return hmmIgnoreBelowBackground;
+  }
+
+  public void setInfoLetterHeight(boolean state)
+  {
+    hmmUseInfoLetterHeight = state;
+  }
+
+  public boolean isUseInfoLetterHeight()
+  {
+    return hmmUseInfoLetterHeight;
+  }
+
   /**
    * @param showSequenceLogo
    *          indicates if a sequence logo is shown for consensus annotation
@@ -1241,7 +1409,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     // TODO add in other methods like 'getAlignmentAnnotation(String label),
     // etc'
-    ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
     synchronized (sequences)
     {
       for (SequenceI seq : sequences)
@@ -1273,38 +1441,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
-    {
-      if (a.getCalcId() == calcId)
-      {
-        aa.add(a);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
-  /**
-   * Returns a list of annotations that match the specified sequenceRef, calcId
-   * and label, ignoring null values.
-   * 
-   * @return list of AlignmentAnnotation objects
-   */
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
-              && ann.sequenceRef != null && ann.sequenceRef == seq
-              && ann.label != null && ann.label.equals(label))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   /**
@@ -1315,17 +1461,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public boolean hasAnnotation(String calcId)
   {
-    if (calcId != null && !"".equals(calcId))
-    {
-      for (AlignmentAnnotation a : getAlignmentAnnotation())
-      {
-        if (a.getCalcId() == calcId)
-        {
-          return true;
-        }
-      }
-    }
-    return false;
+    return AlignmentAnnotation
+            .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   /**
@@ -1335,20 +1472,52 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
+      int before = sequences.size();
       sequences.clear();
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+              sequences.size());
     }
   }
 
-  private AnnotatedCollectionI context;
+  /**
+   * Sets the alignment or group context for this group, and whether it is
+   * defined as a group
+   * 
+   * @param ctx
+   *          the context for the group
+   * @param defined
+   *          whether the group is defined on the alignment or is just a
+   *          selection
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
+   */
+  public void setContext(AnnotatedCollectionI ctx, boolean defined)
+  {
+    setContext(ctx);
+    this.isDefined = defined;
+  }
 
   /**
-   * set the alignment or group context for this group
+   * Sets the alignment or group context for this group
    * 
-   * @param context
+   * @param ctx
+   *          the context for the group
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
    */
-  public void setContext(AnnotatedCollectionI context)
+  public void setContext(AnnotatedCollectionI ctx)
   {
-    this.context = context;
+    AnnotatedCollectionI ref = ctx;
+    while (ref != null)
+    {
+      if (ref == this || ref.getContext() == ctx)
+      {
+        throw new IllegalArgumentException(
+                "Circular reference in SequenceGroup.context");
+      }
+      ref = ref.getContext();
+    }
+    this.context = ctx;
   }
 
   /*
@@ -1361,4 +1530,129 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     return context;
   }
+
+  public boolean isDefined()
+  {
+    return isDefined;
+  }
+
+  public void setColourScheme(ColourSchemeI scheme)
+  {
+    if (cs == null)
+    {
+      cs = new ResidueShader();
+    }
+    cs.setColourScheme(scheme);
+  }
+
+  public void setGroupColourScheme(ResidueShaderI scheme)
+  {
+    cs = scheme;
+  }
+
+  public ColourSchemeI getColourScheme()
+  {
+    return cs == null ? null : cs.getColourScheme();
+  }
+
+  public ResidueShaderI getGroupColourScheme()
+  {
+    return cs;
+  }
+
+  @Override
+  public boolean isNucleotide()
+  {
+    if (context != null)
+    {
+      return context.isNucleotide();
+    }
+    return false;
+  }
+
+  /**
+   * @param seq
+   * @return true if seq is a member of the group
+   */
+
+  public boolean contains(SequenceI seq1)
+  {
+    return sequences.contains(seq1);
+  }
+
+  /**
+   * @param seq
+   * @param apos
+   * @return true if startRes<=apos and endRes>=apos and seq is in the group
+   */
+  public boolean contains(SequenceI seq, int apos)
+  {
+    return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
+  }
+
+  public boolean isShowInformationHistogram()
+  {
+    return hmmShowHistogram;
+  }
+
+  public void setShowInformationHistogram(boolean state)
+  {
+    if (hmmShowHistogram != state && hmmInformation != null)
+    {
+      this.hmmShowHistogram = state;
+      // recalcConservation(); TODO don't know what to do here next
+    }
+    this.hmmShowHistogram = state;
+  }
+
+  public boolean isShowHMMSequenceLogo()
+  {
+    return hmmShowSequenceLogo;
+  }
+
+  public void setShowHMMSequenceLogo(boolean state)
+  {
+    hmmShowSequenceLogo = state;
+  }
+
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    return hmmNormaliseSequenceLogo;
+  }
+
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    hmmNormaliseSequenceLogo = state;
+  }
+
+  public ProfilesI getConsensusData()
+  {
+    return consensusProfiles;
+  }
+
+  public ProfilesI getHmmProfiles()
+  {
+    return hmmProfiles;
+  }
+
+  public void setHmmProfiles(ProfilesI hmmProfiles)
+  {
+    this.hmmProfiles = hmmProfiles;
+  }
+
+  @Override
+  public List<SequenceI> getHmmSequences()
+  {
+    List<SequenceI> result = new ArrayList<>();
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      SequenceI seq = sequences.get(i);
+      if (seq.hasHMMProfile())
+      {
+        result.add(seq);
+      }
+    }
+    return result;
+  }
+
 }