X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=fcb61092786c947fdfb978596634d25de4a5d13f;hb=c2e5d3d1ebe3b283bdde15637c590721cd6c5637;hp=2546d41314bb2ae1aa1c22c407c0337599b4a942;hpb=571d15a897c11bdc2dda76ce03686604596f220d;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2546d41..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);
   }
 
@@ -335,30 +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);
@@ -366,6 +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)
    * 
@@ -784,7 +790,7 @@ public class Alignment implements AlignmentI
   @Override
   public boolean isHidden(int alignmentIndex)
   {
-    return (getHiddenSequences().getHiddenSequence(alignmentIndex) == null);
+    return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
   }
 
   /**
@@ -1008,6 +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(
@@ -1320,6 +1330,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
+  public HiddenColumns getHiddenColumns()
+  {
+    return hiddenCols;
+  }
+
+  @Override
   public CigarArray getCompactAlignment()
   {
     synchronized (sequences)
@@ -1628,10 +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)
@@ -1639,9 +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);
       }
@@ -1939,4 +1953,10 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  @Override
+  public void setHiddenColumns(HiddenColumns cols)
+  {
+    hiddenCols = cols;
+  }
 }