X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=59cb4bba01f851e4cacbbeab3f84b1cefd23657c;hb=3a7dc7069f6983ef56b5440b57cd3e62eeb383c7;hp=854b39ddec8e171b014ed6a2261b1e0abe09107a;hpb=d595e9cf7672de6d60165b536bc3def4b31f2352;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 854b39d..59cb4bb 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -26,9 +26,13 @@ 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.Arrays;
 import java.util.List;
 import java.util.Map;
 
@@ -40,51 +44,80 @@ 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 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;
 
+  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;
 
@@ -96,24 +129,29 @@ 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;
-
-  /**
-   * consensus calculation property
-   */
   private boolean showSequenceLogo = false;
 
-  /**
-   * flag indicating if logo should be rendered normalised
-   */
   private boolean normaliseSequenceLogo;
 
   /*
+   * properties for HMM information annotation
+   */
+  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;
@@ -121,31 +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<>();
   }
 
   /**
@@ -182,10 +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<>();
@@ -197,6 +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);
@@ -210,9 +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;
@@ -221,15 +260,29 @@ public class SequenceGroup implements AnnotatedCollectionI
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
-      ignoreBelowBackground = seqsel.ignoreBelowBackground;
+      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;
@@ -511,6 +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)
@@ -554,8 +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
@@ -564,7 +620,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public boolean recalcConservation(boolean defer)
   {
     if (cs == null && consensus == null && conservation == null
-            && information == null)
+            && hmmInformation == null)
     {
       return false;
     }
@@ -575,14 +631,14 @@ 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);
-        _updateInformationRow(info, sequences.size());
+                hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
+        _updateInformationRow(info);
         upd = true;
       }
       if (consensus != null)
@@ -659,8 +715,6 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public ProfilesI consensusData = null;
 
-  public ProfilesI informationData = null;
-
   private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
@@ -687,35 +741,30 @@ 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, ignoreBelowBackground, showSequenceLogo, nseq); // TODO:
-                                                                        // setting
-                                                            // container
-    // for
-    // ignoreGapsInInformationCalculation);
+    hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+    AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
+            endRes + 1);
   }
 
   /**
@@ -753,6 +802,8 @@ public class SequenceGroup implements AnnotatedCollectionI
     synchronized (sequences)
     {
       sequences.remove(s);
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+              sequences.size() + 1, sequences.size());
 
       if (recalc)
       {
@@ -785,11 +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);
+    
+
+
   }
 
   /**
@@ -799,7 +855,9 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void setEndRes(int i)
   {
+    int before = endRes;
     endRes = i;
+    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
   }
 
   /**
@@ -1166,32 +1224,19 @@ 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);
   }
 
   /**
@@ -1247,9 +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
         {
@@ -1282,16 +1328,22 @@ 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 true;
+    return hmmIgnoreBelowBackground;
+  }
+
+  public void setInfoLetterHeight(boolean state)
+  {
+    hmmUseInfoLetterHeight = state;
+  }
+
+  public boolean isUseInfoLetterHeight()
+  {
+    return hmmUseInfoLetterHeight;
   }
 
   /**
@@ -1389,39 +1441,16 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<>();
-    if (calcId == null)
-    {
-      return aa;
-    }
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
-    {
-      if (calcId.equals(a.getCalcId()))
-      {
-        aa.add(a);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), calcId);
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if ((calcId == null || (ann.getCalcId() != null
-              && ann.getCalcId().equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null
-                      && ann.sequenceRef == seq))
-              && (label == null
-                      || (ann.label != null && ann.label.equals(label))))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   /**
@@ -1432,17 +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);
   }
 
   /**
@@ -1452,7 +1472,10 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     synchronized (sequences)
     {
+      int before = sequences.size();
       sequences.clear();
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+              sequences.size());
     }
   }
 
@@ -1569,41 +1592,67 @@ 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;
+  }
+
+  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;
   }
 
 }