JAL-1950 JAL-2937 allow copy of group without sequences being also copied to cloned...

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index b7ec9f9..cffe0d9 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -88,11 +88,6 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private SequenceI seqrep;
 
-  /*
-   * HMM consensus sequence for group (if any)
-   */
-  private SequenceI hmmConsensus;
-
   private int width = -1;
 
   /*
@@ -134,7 +129,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   private boolean hmmUseInfoLetterHeight;
 
-  private boolean showHMMSequenceLogo;
+  private boolean hmmShowSequenceLogo;
 
   private boolean hmmNormaliseSequenceLogo;
 
@@ -203,11 +198,27 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public SequenceGroup(SequenceGroup seqsel)
   {
+    this(seqsel, true);
+  }
+
+  /**
+   * copy constructor
+   * 
+   * @param seqsel
+   * @param keepsequences
+   *          if false do not add sequences from seqsel to new instance
+   */
+  public SequenceGroup(SequenceGroup seqsel, boolean keepsequences)
+  {
     this();
+
     if (seqsel != null)
     {
       sequences = new ArrayList<>();
-      sequences.addAll(seqsel.sequences);
+      if (keepsequences)
+      {
+        sequences.addAll(seqsel.sequences);
+      }
       if (seqsel.groupName != null)
       {
         groupName = new String(seqsel.groupName);
@@ -228,7 +239,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       showSequenceLogo = seqsel.showSequenceLogo;
       normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
       showConsensusHistogram = seqsel.showConsensusHistogram;
-      showHMMSequenceLogo = seqsel.showHMMSequenceLogo;
+      hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
       hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
       hmmShowHistogram = seqsel.hmmShowHistogram;
       idColour = seqsel.idColour;
@@ -241,8 +252,10 @@ public class SequenceGroup implements AnnotatedCollectionI
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
       hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
       hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
-      if (seqsel.conservationData != null)
+      if (keepsequences && seqsel.conservationData != null)
       {
+        // todo avoid doing this if we don't actually want derived calculations
+        // !
         recalcConservation(); // safer than
         // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
       }
@@ -267,7 +280,8 @@ public class SequenceGroup implements AnnotatedCollectionI
     return showSequenceLogo;
   }
 
-  public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
+  public SequenceI[] getSelectionAsNewSequences(AlignmentI align,
+          boolean copyAnnotation)
   {
     int iSize = sequences.size();
     SequenceI[] seqs = new SequenceI[iSize];
@@ -281,15 +295,8 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (seqs[ipos] != null)
       {
         seqs[ipos].setDescription(seq.getDescription());
-        seqs[ipos].setDBRefs(seq.getDBRefs());
-        seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
-        seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
-        if (seq.getDatasetSequence() != null)
-        {
-          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
-        }
 
-        if (seq.getAnnotation() != null)
+        if (seq.getAnnotation() != null && copyAnnotation)
         {
           AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
           // Only copy annotation that is either a score or referenced by the
@@ -617,9 +624,8 @@ public class SequenceGroup implements AnnotatedCollectionI
 
         ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
                 (endRes + 1) - startRes, startRes, endRes + 1,
-                showHMMSequenceLogo, hmmIgnoreBelowBackground,
-                hmmUseInfoLetterHeight);
-        _updateInformationRow(info, sequences.size());
+                hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
+        _updateInformationRow(info);
         upd = true;
       }
       if (consensus != null)
@@ -720,12 +726,11 @@ 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 (hmmInformation == null)
     {
@@ -744,7 +749,7 @@ public class SequenceGroup implements AnnotatedCollectionI
                                                       // width
     hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
     AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
-            endRes + 1, nseq, 0f);
+            endRes + 1);
   }
 
   /**
@@ -1580,18 +1585,16 @@ public class SequenceGroup implements AnnotatedCollectionI
       // recalcConservation(); TODO don't know what to do here next
     }
     this.hmmShowHistogram = state;
-
   }
 
   public boolean isShowHMMSequenceLogo()
   {
-    return showHMMSequenceLogo;
+    return hmmShowSequenceLogo;
   }
 
-  public void setshowHMMSequenceLogo(boolean state)
+  public void setShowHMMSequenceLogo(boolean state)
   {
-    showHMMSequenceLogo = state;
-
+    hmmShowSequenceLogo = state;
   }
 
   public boolean isNormaliseHMMSequenceLogo()
@@ -1601,19 +1604,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public void setNormaliseHMMSequenceLogo(boolean state)
   {
-    normaliseSequenceLogo = state;
-  }
-
-  @Override
-  public SequenceI getHmmConsensus()
-  {
-    return hmmConsensus;
-  }
-
-  @Override
-  public void setHmmConsensus(SequenceI hmmSeq)
-  {
-    this.hmmConsensus = hmmSeq;
+    hmmNormaliseSequenceLogo = state;
   }
 
   public ProfilesI getConsensusData()
@@ -1631,4 +1622,19 @@ public class SequenceGroup implements AnnotatedCollectionI
     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;
+  }
+
 }