X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5d91b36cc01a05cb016ff0edc167d0764c592275;hb=3f91bb1385ab9ac8fdd15e3bc9378f5b554e1642;hp=fd918fc709fffdf48390fb8a80f70c36d5614799;hpb=4956fb78f7222e84d0d7008a6b91146d6c61d151;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index fd918fc..5d91b36 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.io.FastaFile;
 import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
@@ -53,11 +54,7 @@ public class Alignment implements AlignmentI
 
   protected char gapCharacter = '-';
 
-  protected int type = NUCLEOTIDE;
-
-  public static final int PROTEIN = 0;
-
-  public static final int NUCLEOTIDE = 1;
+  private boolean nucleotide = true;
 
   public boolean hasRNAStructure = false;
 
@@ -65,6 +62,8 @@ public class Alignment implements AlignmentI
 
   HiddenSequences hiddenSequences;
 
+  HiddenColumns hiddenCols;
+
   public Hashtable alignmentProperties;
 
   private List<AlignedCodonFrame> codonFrameList;
@@ -73,16 +72,10 @@ public class Alignment implements AlignmentI
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
     hiddenSequences = new HiddenSequences(this);
-    codonFrameList = new ArrayList<AlignedCodonFrame>();
+    hiddenCols = new HiddenColumns();
+    codonFrameList = new ArrayList<>();
 
-    if (Comparison.isNucleotide(seqs))
-    {
-      type = NUCLEOTIDE;
-    }
-    else
-    {
-      type = PROTEIN;
-    }
+    nucleotide = Comparison.isNucleotide(seqs);
 
     sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
 
@@ -135,7 +128,7 @@ public class Alignment implements AlignmentI
   public Alignment(SeqCigar[] alseqs)
   {
     SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
-            gapCharacter, new ColumnSelection(), null);
+            gapCharacter, new HiddenColumns(), null);
     initAlignment(seqs);
   }
 
@@ -195,14 +188,7 @@ public class Alignment implements AlignmentI
     return AlignmentUtils.getSequencesByName(this);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public SequenceI getSequenceAt(int i)
   {
@@ -216,8 +202,32 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
+  public SequenceI getSequenceAtAbsoluteIndex(int i)
+  {
+    SequenceI seq = null;
+    if (getHiddenSequences().getSize() > 0)
+    {
+      seq = getHiddenSequences().getHiddenSequence(i);
+      if (seq == null)
+      {
+        // didn't find the sequence in the hidden sequences, get it from the
+        // alignment
+        int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+        seq = getSequenceAt(index);
+      }
+    }
+    else
+    {
+      seq = getSequenceAt(i);
+    }
+    return seq;
+  }
+
   /**
-   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+   * this currently does not recalculate whether or not the alignment is
+   * nucleotide, so mixed alignments may have undefined behaviour.
    * 
    * @param snew
    */
@@ -226,18 +236,21 @@ public class Alignment implements AlignmentI
   {
     if (dataset != null)
     {
+
       // maintain dataset integrity
-      if (snew.getDatasetSequence() != null)
-      {
-        getDataset().addSequence(snew.getDatasetSequence());
-      }
-      else
+      SequenceI dsseq = snew.getDatasetSequence();
+      if (dsseq == null)
       {
         // derive new sequence
         SequenceI adding = snew.deriveSequence();
-        getDataset().addSequence(adding.getDatasetSequence());
         snew = adding;
+        dsseq = snew.getDatasetSequence();
+      }
+      if (getDataset().findIndex(dsseq) == -1)
+      {
+        getDataset().addSequence(dsseq);
       }
+
     }
     if (sequences == null)
     {
@@ -287,13 +300,23 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void finalize()
+  public void finalize() throws Throwable
   {
     if (getDataset() != null)
     {
       getDataset().removeAlignmentRef();
     }
 
+    nullReferences();
+    super.finalize();
+  }
+
+  /**
+   * Defensively nulls out references in case this object is not garbage
+   * collected
+   */
+  void nullReferences()
+  {
     dataset = null;
     sequences = null;
     groups = null;
@@ -302,41 +325,34 @@ public class Alignment implements AlignmentI
   }
 
   /**
-   * decrement the alignmentRefs counter by one and call finalize if it goes to
-   * zero.
+   * decrement the alignmentRefs counter by one and null references if it goes
+   * to zero.
+   * 
+   * @throws Throwable
    */
-  private void removeAlignmentRef()
+  private void removeAlignmentRef() throws Throwable
   {
     if (--alignmentRefs == 0)
     {
-      finalize();
+      nullReferences();
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(SequenceI s)
   {
-    deleteSequence(findIndex(s));
+    synchronized (sequences)
+    {
+      deleteSequence(findIndex(s));
+    }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(int i)
   {
-    if (i > -1 && i < getHeight())
+    synchronized (sequences)
     {
-      synchronized (sequences)
+      if (i > -1 && i < getHeight())
       {
         sequences.remove(i);
         hiddenSequences.adjustHeightSequenceDeleted(i);
@@ -344,23 +360,36 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public void deleteHiddenSequence(int i)
+  {
+    synchronized (sequences)
+    {
+      if (i > -1 && i < getHeight())
+      {
+        sequences.remove(i);
+      }
+    }
+  }
+
   /*
    * (non-Javadoc)
    * 
    * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
-  public SequenceGroup findGroup(SequenceI s)
+  public SequenceGroup findGroup(SequenceI seq, int position)
   {
     synchronized (groups)
     {
-      for (int i = 0; i < this.groups.size(); i++)
+      for (SequenceGroup sg : groups)
       {
-        SequenceGroup sg = groups.get(i);
-
-        if (sg.getSequences(null).contains(s))
+        if (sg.getSequences(null).contains(seq))
         {
-          return sg;
+          if (position >= sg.getStartRes() && position <= sg.getEndRes())
+          {
+            return sg;
+          }
         }
       }
     }
@@ -376,7 +405,7 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
+    ArrayList<SequenceGroup> temp = new ArrayList<>();
 
     synchronized (groups)
     {
@@ -427,7 +456,7 @@ public class Alignment implements AlignmentI
             return;
           }
         }
-        sg.setContext(this);
+        sg.setContext(this, true);
         groups.add(sg);
       }
     }
@@ -504,7 +533,7 @@ public class Alignment implements AlignmentI
       }
       for (SequenceGroup sg : groups)
       {
-        sg.setContext(null);
+        sg.setContext(null, false);
       }
       groups.clear();
     }
@@ -520,7 +549,7 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(g);
         groups.remove(g);
-        g.setContext(null);
+        g.setContext(null, false);
       }
     }
   }
@@ -645,7 +674,7 @@ public class Alignment implements AlignmentI
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   @Override
-  public int findIndex(SearchResults results)
+  public int findIndex(SearchResultsI results)
   {
     int i = 0;
 
@@ -660,22 +689,19 @@ public class Alignment implements AlignmentI
     return -1;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public int getHeight()
   {
     return sequences.size();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+  @Override
+  public int getAbsoluteHeight()
+  {
+    return sequences.size() + getHiddenSequences().getSize();
+  }
+
   @Override
   public int getWidth()
   {
@@ -761,6 +787,12 @@ public class Alignment implements AlignmentI
     return true;
   }
 
+  @Override
+  public boolean isHidden(int alignmentIndex)
+  {
+    return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+  }
+
   /**
    * Delete all annotations, including auto-calculated if the flag is set true.
    * Returns true if at least one annotation was deleted, else false.
@@ -961,29 +993,9 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setNucleotide(boolean b)
-  {
-    if (b)
-    {
-      type = NUCLEOTIDE;
-    }
-    else
-    {
-      type = PROTEIN;
-    }
-  }
-
-  @Override
   public boolean isNucleotide()
   {
-    if (type == NUCLEOTIDE)
-    {
-      return true;
-    }
-    else
-    {
-      return false;
-    }
+    return nucleotide;
   }
 
   @Override
@@ -1002,6 +1014,10 @@ public class Alignment implements AlignmentI
     }
     else if (dataset == null && data != null)
     {
+      if (data == this)
+      {
+        throw new IllegalArgumentException("Circular dataset reference");
+      }
       if (!(data instanceof Alignment))
       {
         throw new Error(
@@ -1039,6 +1055,7 @@ public class Alignment implements AlignmentI
   private void resolveAndAddDatasetSeq(SequenceI currentSeq,
           Set<SequenceI> seqs, boolean createDatasetSequence)
   {
+    SequenceI alignedSeq = currentSeq;
     if (currentSeq.getDatasetSequence() != null)
     {
       currentSeq = currentSeq.getDatasetSequence();
@@ -1054,7 +1071,7 @@ public class Alignment implements AlignmentI
     {
       return;
     }
-    List<SequenceI> toProcess = new ArrayList<SequenceI>();
+    List<SequenceI> toProcess = new ArrayList<>();
     toProcess.add(currentSeq);
     while (toProcess.size() > 0)
     {
@@ -1073,12 +1090,19 @@ public class Alignment implements AlignmentI
         {
           if (dbr.getMap() != null && dbr.getMap().getTo() != null)
           {
+            if (dbr.getMap().getTo() == alignedSeq)
+            {
+              /*
+               * update mapping to be to the newly created dataset sequence
+               */
+              dbr.getMap().setTo(currentSeq);
+            }
             if (dbr.getMap().getTo().getDatasetSequence() != null)
             {
-              throw new Error("Implementation error: Map.getTo() for dbref"
-                      + dbr + " is not a dataset sequence.");
-              // TODO: if this happens, could also rewrite the reference to
-              // point to new dataset sequence
+              throw new Error(
+                      "Implementation error: Map.getTo() for dbref " + dbr
+                              + " from " + curDs.getName()
+                              + " is not a dataset sequence.");
             }
             // we recurse to add all forward references to dataset sequences via
             // DBRefs/etc
@@ -1100,7 +1124,7 @@ public class Alignment implements AlignmentI
       return;
     }
     // try to avoid using SequenceI.equals at this stage, it will be expensive
-    Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
 
     for (int i = 0; i < getHeight(); i++)
     {
@@ -1306,6 +1330,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
+  public HiddenColumns getHiddenColumns()
+  {
+    return hiddenCols;
+  }
+
+  @Override
   public CigarArray getCompactAlignment()
   {
     synchronized (sequences)
@@ -1379,7 +1409,7 @@ public class Alignment implements AlignmentI
     {
       return null;
     }
-    List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> cframes = new ArrayList<>();
     for (AlignedCodonFrame acf : getCodonFrames())
     {
       if (acf.involvesSequence(seq))
@@ -1456,7 +1486,7 @@ public class Alignment implements AlignmentI
     if (sqs != null)
     {
       // avoid self append deadlock by
-      List<SequenceI> toappendsq = new ArrayList<SequenceI>();
+      List<SequenceI> toappendsq = new ArrayList<>();
       synchronized (sqs)
       {
         for (SequenceI addedsq : sqs)
@@ -1566,7 +1596,6 @@ public class Alignment implements AlignmentI
           String calcId, boolean autoCalc, SequenceI seqRef,
           SequenceGroup groupRef)
   {
-    assert (name != null);
     if (annotations != null)
     {
       for (AlignmentAnnotation annot : getAlignmentAnnotation())
@@ -1598,33 +1627,35 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
+    List<AlignmentAnnotation> aa = new ArrayList<>();
+    AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+    if (alignmentAnnotation != null)
     {
-      if (a.getCalcId() == calcId
-              || (a.getCalcId() != null && calcId != null && a.getCalcId()
-                      .equals(calcId)))
+      for (AlignmentAnnotation a : alignmentAnnotation)
       {
-        aa.add(a);
+        if (a.getCalcId() == calcId
+                || (a.getCalcId() != null && calcId != null && a
+                        .getCalcId().equals(calcId)))
+        {
+          aa.add(a);
+        }
       }
     }
     return aa;
   }
 
-  /**
-   * Returns an iterable collection of any annotations that match on given
-   * sequence ref, calcId and label (ignoring null values).
-   */
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     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))
+      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);
       }
@@ -1813,7 +1844,7 @@ public class Alignment implements AlignmentI
   @Override
   public String toString()
   {
-    return new FastaFile().print(getSequencesArray());
+    return new FastaFile().print(getSequencesArray(), true);
   }
 
   /**
@@ -1822,7 +1853,7 @@ public class Alignment implements AlignmentI
   @Override
   public Set<String> getSequenceNames()
   {
-    Set<String> names = new HashSet<String>();
+    Set<String> names = new HashSet<>();
     for (SequenceI seq : getSequences())
     {
       names.add(seq.getName());
@@ -1922,4 +1953,10 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  @Override
+  public void setHiddenColumns(HiddenColumns cols)
+  {
+    hiddenCols = cols;
+  }
 }