X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=fcb61092786c947fdfb978596634d25de4a5d13f;hb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;hp=a6f2bf4e440035d98d59796921356e9baca65736;hpb=a6875ff6ca7894443c98b1d068f78ea25c5bfc87;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a6f2bf4..fcb6109 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -62,6 +62,8 @@ public class Alignment implements AlignmentI
 
   HiddenSequences hiddenSequences;
 
+  HiddenColumns hiddenCols;
+
   public Hashtable alignmentProperties;
 
   private List<AlignedCodonFrame> codonFrameList;
@@ -70,6 +72,7 @@ public class Alignment implements AlignmentI
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
     hiddenSequences = new HiddenSequences(this);
+    hiddenCols = new HiddenColumns();
     codonFrameList = new ArrayList<AlignedCodonFrame>();
 
     nucleotide = Comparison.isNucleotide(seqs);
@@ -125,7 +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);
   }
 
@@ -185,14 +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)
   {
@@ -206,6 +202,28 @@ 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. Note
    * this currently does not recalculate whether or not the alignment is
@@ -320,30 +338,21 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * 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);
@@ -351,6 +360,18 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public void deleteHiddenSequence(int i)
+  {
+    synchronized (sequences)
+    {
+      if (i > -1 && i < getHeight())
+      {
+        sequences.remove(i);
+      }
+    }
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -668,22 +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()
   {
@@ -769,6 +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.
@@ -990,6 +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(
@@ -1302,6 +1330,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
+  public HiddenColumns getHiddenColumns()
+  {
+    return hiddenCols;
+  }
+
+  @Override
   public CigarArray getCompactAlignment()
   {
     synchronized (sequences)
@@ -1610,10 +1644,6 @@ public class Alignment implements AlignmentI
     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)
@@ -1621,9 +1651,11 @@ public class Alignment implements AlignmentI
     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))
+      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);
       }
@@ -1921,4 +1953,10 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  @Override
+  public void setHiddenColumns(HiddenColumns cols)
+  {
+    hiddenCols = cols;
+  }
 }