X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=8371036cbdb2bece1d7d4894781f00f45b4c92ef;hb=refs%2Fheads%2Ffeatures%2FJAL-2465_No-mapping_Jmol-structures-loaded-via-url;hp=a6f2bf4e440035d98d59796921356e9baca65736;hpb=a6875ff6ca7894443c98b1d068f78ea25c5bfc87;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a6f2bf4..8371036 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -185,14 +185,7 @@ 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 +199,28 @@ 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 +335,21 @@ 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 +357,18 @@ 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 +686,19 @@ 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 +784,12 @@ 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 +1011,10 @@ 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(
@@ -1610,10 +1635,6 @@ 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 +1642,11 @@ 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);
       }