X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=0431708b7344400a3e7433313ae6f71cbd36e5e7;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=4b9427c510a080a95077bbe2be632f625742e631;hpb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 4b9427c..0431708 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -26,6 +26,7 @@ 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;
@@ -44,11 +45,10 @@ import java.util.Map;
 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
-  // quick fix for JAL-2665
+  // 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);
 
@@ -66,48 +66,58 @@ public class SequenceGroup implements AnnotatedCollectionI
   String groupName;
 
   String description;
-
+  
   Conservation conserve;
 
+  Conservation conservationData;
+
+  ProfilesI consensusProfiles;
+
+  ProfilesI hmmProfiles;
+
   boolean displayBoxes = true;
 
   boolean displayText = true;
 
   boolean colourText = false;
 
-  /**
-   * True if the group is defined as a group on the alignment, false if it is
-   * just a selection.
+  /*
+   * 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<>();
+  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 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;
 
@@ -119,24 +129,27 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public Color textColour2 = Color.white;
 
-  /**
-   * consensus calculation property
+  /*
+   * properties for consensus annotation
    */
   private boolean ignoreGapsInConsensus = true;
 
-  private boolean ignoreBelowBackground = true;
+  private boolean showSequenceLogo = false;
 
-  private boolean infoLetterHeight = false;
+  private boolean normaliseSequenceLogo;
 
-  /**
-   * consensus calculation property
+  /*
+   * properties for HMM information annotation
    */
-  private boolean showSequenceLogo = false;
+  private boolean hmmIgnoreBelowBackground = true;
 
-  /**
-   * flag indicating if logo should be rendered normalised
-   */
-  private boolean normaliseSequenceLogo;
+  private boolean hmmUseInfoLetterHeight;
+
+  private boolean hmmShowSequenceLogo;
+
+  private boolean hmmNormaliseSequenceLogo;
+
+  private boolean hmmShowHistogram;
 
   /*
    * visibility of rows or represented rows covered by group
@@ -146,31 +159,28 @@ public class SequenceGroup implements AnnotatedCollectionI
   /*
    * visibility of columns intersecting this group
    */
-  private boolean hidecols = false;
+  private boolean hidecols;
 
   AlignmentAnnotation consensus = null;
 
   AlignmentAnnotation conservation = null;
 
-  AlignmentAnnotation information = null;
-
+  private AlignmentAnnotation hmmInformation;
+  
   private boolean showConsensusHistogram;
-
+  
   private AnnotatedCollectionI context;
 
-  private boolean showHMMSequenceLogo;
-
-  private boolean normaliseHMMSequenceLogo;
-
-  private boolean showInformationHistogram;
 
   /**
-   * 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<>();
   }
 
   /**
@@ -207,10 +217,13 @@ 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<>();
@@ -222,6 +235,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayBoxes = seqsel.displayBoxes;
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
+      
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
       cs = new ResidueShader((ResidueShader) seqsel.cs);
@@ -235,9 +249,9 @@ public class SequenceGroup implements AnnotatedCollectionI
       showSequenceLogo = seqsel.showSequenceLogo;
       normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
       showConsensusHistogram = seqsel.showConsensusHistogram;
-      showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
-      normaliseHMMSequenceLogo = seqsel.normaliseHMMSequenceLogo;
-      showInformationHistogram = seqsel.showInformationHistogram;
+      hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
+      hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
+      hmmShowHistogram = seqsel.hmmShowHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -246,16 +260,29 @@ public class SequenceGroup implements AnnotatedCollectionI
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
-      ignoreBelowBackground = seqsel.ignoreBelowBackground;
-      infoLetterHeight = seqsel.infoLetterHeight;
+      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;
@@ -270,16 +297,15 @@ public class SequenceGroup implements AnnotatedCollectionI
     for (int i = 0, ipos = 0; i < inorder.length; i++)
     {
       SequenceI seq = inorder[i];
-
-      seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
-      if (seqs[ipos] != null)
+      SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+      if (seqipos != null)
       {
-        seqs[ipos].setDescription(seq.getDescription());
-        seqs[ipos].setDBRefs(seq.getDBRefs());
-        seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        seqipos.setDescription(seq.getDescription());
+        seqipos.setDBRefs(seq.getDBRefs());
+        seqipos.setSequenceFeatures(seq.getSequenceFeatures());
         if (seq.getDatasetSequence() != null)
         {
-          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+          seqipos.setDatasetSequence(seq.getDatasetSequence());
         }
 
         if (seq.getAnnotation() != null)
@@ -293,7 +319,7 @@ public class SequenceGroup implements AnnotatedCollectionI
             if (alann != null)
             {
               boolean found = false;
-              for (int pos = 0; pos < alann.length; pos++)
+              for (int pos = 0, np = alann.length; pos < np; pos++)
               {
                 if (alann[pos] == tocopy)
                 {
@@ -311,7 +337,7 @@ public class SequenceGroup implements AnnotatedCollectionI
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
-            seqs[ipos].addAlignmentAnnotation(newannot);
+            seqipos.addAlignmentAnnotation(newannot);
           }
         }
         ipos++;
@@ -582,8 +608,9 @@ 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
@@ -592,7 +619,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public boolean recalcConservation(boolean defer)
   {
     if (cs == null && consensus == null && conservation == null
-            && information == null)
+            && hmmInformation == null)
     {
       return false;
     }
@@ -603,15 +630,14 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
-      if (information != null)
+      if (hmmInformation != null)
       {
-        HiddenMarkovModel hmm = information.sequenceRef.getHMM();
+        HiddenMarkovModel hmm = hmmInformation.sequenceRef.getHMM();
 
         ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
                 (endRes + 1) - startRes, startRes, endRes + 1,
-                showHMMSequenceLogo, ignoreBelowBackground,
-                infoLetterHeight);
-        _updateInformationRow(info, sequences.size());
+                hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
+        _updateInformationRow(info);
         upd = true;
       }
       if (consensus != null)
@@ -688,8 +714,6 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public ProfilesI consensusData = null;
 
-  public ProfilesI informationData = null;
-
   private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
@@ -716,35 +740,30 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * Recalculates the information content on the HMM annotation.
+   * Recalculates the information content on the HMM annotation
    * 
    * @param cnsns
-   * @param nseq
    */
-  private void _updateInformationRow(ProfilesI cnsns, long nseq)
+  private void _updateInformationRow(ProfilesI cnsns)
   {
-    if (information == null)
+    if (hmmInformation == null)
     {
-      getInformation();
+      createInformationAnnotation();
     }
-    information.description = MessageManager
+    hmmInformation.description = MessageManager
             .getString("label.information_description");
-    informationData = cnsns;
+    setHmmProfiles(cnsns);
     // preserve width if already set
-    int aWidth = (information.annotations != null)
-            ? (endRes < information.annotations.length
-                    ? information.annotations.length : endRes + 1)
+    int aWidth = (hmmInformation.annotations != null)
+            ? (endRes < hmmInformation.annotations.length
+                    ? hmmInformation.annotations.length : endRes + 1)
             : endRes + 1;
-    information.annotations = null;
-    information.annotations = new Annotation[aWidth]; // should be alignment
+    hmmInformation.annotations = null;
+    hmmInformation.annotations = new Annotation[aWidth]; // should be alignment
                                                       // width
-    information.calcId = "HMM";
-    AAFrequency.completeInformation(information, cnsns, startRes,
-            endRes + 1, nseq, 0f); // TODO:
-                                                                        // setting
-                                                            // container
-    // for
-    // ignoreGapsInInformationCalculation);
+    hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+    AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
+            endRes + 1);
   }
 
   /**
@@ -816,13 +835,16 @@ 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)
   {
     int before = startRes;
-    startRes = i;
-    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+   startRes= Math.max(0,newStart); // sanity check for negative start column positions
+   changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+    
+
+
   }
 
   /**
@@ -1201,32 +1223,19 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * 
-   * @return information content annotation.
+   * Creates the Hidden Markov Model annotation for this group
    */
-  public AlignmentAnnotation getInformation()
+  void createInformationAnnotation()
   {
-    // TODO get or calculate and get information annotation row for this group
-    int aWidth = this.getWidth();
-    // pointer
-    // possibility
-    // here.
-    if (aWidth < 0)
-    {
-      return null;
-    }
-    if (information == null)
-    {
-      information = new AlignmentAnnotation("", "", new Annotation[1], 0f,
-              6.25f, AlignmentAnnotation.BAR_GRAPH);
-      information.hasText = true;
-      information.autoCalculated = false;
-      information.groupRef = this;
-      information.label = getName();
-      information.description = "Information content, measured in bits";
-      information.calcId = "HMM";
-    }
-    return information;
+    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);
   }
 
   /**
@@ -1282,9 +1291,10 @@ 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
         {
@@ -1317,30 +1327,22 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public void setIgnoreBelowBackground(boolean state)
   {
-    if (this.ignoreBelowBackground != state)
-    {
-      ignoreBelowBackground = state;
-    }
-    ignoreBelowBackground = state;
+    hmmIgnoreBelowBackground = state;
   }
 
-  public boolean getIgnoreBelowBackground()
+  public boolean isIgnoreBelowBackground()
   {
-    return ignoreBelowBackground;
+    return hmmIgnoreBelowBackground;
   }
 
   public void setInfoLetterHeight(boolean state)
   {
-    if (this.infoLetterHeight != state)
-    {
-      infoLetterHeight = state;
-    }
-    infoLetterHeight = state;
+    hmmUseInfoLetterHeight = state;
   }
 
-  public boolean getInfoLetterHeight()
+  public boolean isUseInfoLetterHeight()
   {
-    return infoLetterHeight;
+    return hmmUseInfoLetterHeight;
   }
 
   /**
@@ -1589,84 +1591,67 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public boolean isShowInformationHistogram()
   {
-    return showInformationHistogram;
+    return hmmShowHistogram;
   }
 
   public void setShowInformationHistogram(boolean state)
   {
-    if (showInformationHistogram != state && information != null)
+    if (hmmShowHistogram != state && hmmInformation != null)
     {
-      this.showInformationHistogram = state;
+      this.hmmShowHistogram = state;
       // recalcConservation(); TODO don't know what to do here next
     }
-    this.showInformationHistogram = state;
-
+    this.hmmShowHistogram = state;
   }
 
   public boolean isShowHMMSequenceLogo()
   {
-    // TODO Auto-generated method stub
-    return showHMMSequenceLogo;
+    return hmmShowSequenceLogo;
   }
 
-  public void setshowHMMSequenceLogo(boolean state)
+  public void setShowHMMSequenceLogo(boolean state)
   {
-    showHMMSequenceLogo = state;
-
+    hmmShowSequenceLogo = state;
   }
 
   public boolean isNormaliseHMMSequenceLogo()
   {
-    // TODO Auto-generated method stub
-    return normaliseHMMSequenceLogo;
+    return hmmNormaliseSequenceLogo;
   }
 
   public void setNormaliseHMMSequenceLogo(boolean state)
   {
-    normaliseSequenceLogo = state;
+    hmmNormaliseSequenceLogo = state;
   }
 
-  /**
-   * Returns all HMM consensus sequences. This will not return real sequences
-   * with HMMs. If remove is set to true, the consensus sequences will be
-   * removed from the alignment.
-   */
-  @Override // TODO make this more efficient.
-  public List<SequenceI> getHMMConsensusSequences(boolean remove)
+  public ProfilesI getConsensusData()
   {
-    List<SequenceI> seqs = new ArrayList<>();
-    int position = 0;
-    int seqsRemoved = 0;
-    boolean endReached = false;
+    return consensusProfiles;
+  }
 
-    while (!endReached)
-    {
-      SequenceI seq = sequences.get(position);
-      if (seq.isHMMConsensusSequence())
-      {
-        if (remove)
-        {
-          sequences.remove(position);
-          seqsRemoved++;
-          seq.setPreviousPosition(seqsRemoved + position - 1);
-        }
-        else
-        {
-          position++;
-        }
-        seqs.add(seq);
-      }
-      else
-      {
-        position++;
-      }
+  public ProfilesI getHmmProfiles()
+  {
+    return hmmProfiles;
+  }
 
-      if (position >= sequences.size())
+  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())
       {
-        endReached = true;
+        result.add(seq);
       }
     }
-    return seqs;
+    return result;
   }
 
 }