X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=f36872ee11724358c02b5a46b5ad4372271073a5;hb=a4fca83856b96df2fe8701bb5cc14c8d1d0a6b09;hp=cec2abcabe44a367208caa009544dc0ca7153ca9;hpb=77b038f418aea84563953ad94f839592317ea500;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index cec2abc..f36872e 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -108,6 +108,8 @@ public class Alignment
 
   public SequenceI[] getSequencesArray()
   {
+    if (sequences==null)
+      return null;
     SequenceI[] reply = new SequenceI[sequences.size()];
     for (int i = 0; i < sequences.size(); i++)
     {
@@ -188,7 +190,7 @@ public class Alignment
   public void finalize()
   {
     if(getDataset()!=null)
-      getDataset().finalize();
+      getDataset().removeAlignmentRef();
 
     dataset = null;
     sequences = null;
@@ -197,6 +199,16 @@ public class Alignment
     hiddenSequences = null;
   }
 
+  /**
+   * decrement the alignmentRefs counter by one and call finalize if it goes to zero.
+   */
+  private void removeAlignmentRef()
+  {
+    if (--alignmentRefs==0)
+    {
+      finalize();
+    }
+  }
 
   /**
    * DOCUMENT ME!
@@ -482,16 +494,15 @@ public class Alignment
     boolean swap=false;
     int tIndex = 0;
 
-    for (int i = 0; tIndex<temp.length && i < aSize; i++)
+    for (int i = 0; i < aSize; i++)
     {
       if (annotations[i] == aa)
       {
         swap=true;
         continue;
       }
-
-      temp[tIndex] = annotations[i];
-      tIndex++;
+      if (tIndex<temp.length)
+        temp[tIndex++] = annotations[i];
     }
 
     if (swap)
@@ -606,7 +617,7 @@ public class Alignment
       // Create a new dataset for this alignment.
       // Can only be done once, if dataset is not null
       // This will not be performed
-      Sequence[] seqs = new Sequence[getHeight()];
+      SequenceI[] seqs = new SequenceI[getHeight()];
       SequenceI currentSeq;
       for (int i = 0; i < getHeight(); i++)
       {
@@ -617,17 +628,7 @@ public class Alignment
         }
         else
         {
-          seqs[i] = new Sequence(currentSeq.getName(),
-                                 AlignSeq.extractGaps(
-                                     jalview.util.Comparison.GapChars,
-                                     currentSeq.getSequenceAsString()
-                                 ),
-                                 currentSeq.getStart(),
-                                 currentSeq.getEnd());
-          seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
-          seqs[i].setDescription(currentSeq.getDescription());
-          getSequenceAt(i).setSequenceFeatures(null);
-          getSequenceAt(i).setDatasetSequence(seqs[i]);
+          seqs[i] = currentSeq.createDatasetSequence();
         }
       }
 
@@ -637,6 +638,18 @@ public class Alignment
     {
       dataset = data;
     }
+    dataset.addAlignmentRef();
+  }
+  /**
+   * reference count for number of alignments referencing this one.
+   */
+  int alignmentRefs=0;
+  /**
+   * increase reference count to this alignment.
+   */
+  private void addAlignmentRef()
+  {
+    alignmentRefs++;
   }
 
   public Alignment getDataset()
@@ -726,5 +739,86 @@ public class Alignment
   {
     return alignmentProperties;
   }
+  AlignedCodonFrame[] codonFrameList=null;
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   */
+  public void addCodonFrame(AlignedCodonFrame codons)
+  {
+    if (codons==null)
+      return;
+    if (codonFrameList==null)
+    {
+      codonFrameList = new AlignedCodonFrame[] { codons };
+      return;
+    }
+    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
+    System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
+    t[codonFrameList.length] = codons;
+    codonFrameList = t;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+   */
+  public AlignedCodonFrame getCodonFrame(int index)
+  {
+    return codonFrameList[index];
+  }
 
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   */
+  public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+  {
+    if (seq==null || codonFrameList==null)
+      return null;
+    Vector cframes=new Vector();
+    for (int f=0;f<codonFrameList.length; f++)
+    {
+      if (codonFrameList[f].involvesSequence(seq))
+        cframes.addElement(codonFrameList[f]);
+    }
+    if (cframes.size()==0)
+      return null;
+    AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
+    cframes.copyInto(cfr);
+    return cfr;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#getCodonFrames()
+   */
+  public AlignedCodonFrame[] getCodonFrames()
+  {
+    return codonFrameList;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   */
+  public boolean removeCodonFrame(AlignedCodonFrame codons)
+  {
+    if (codons==null || codonFrameList==null)
+      return false;
+    boolean removed=false;
+    int i=0,iSize=codonFrameList.length;
+    while (i<iSize)
+    {
+      if (codonFrameList[i]==codons)
+      {
+        removed=true;
+        if (i+1<iSize)
+        {
+          System.arraycopy(codonFrameList,i+1,codonFrameList, i, iSize-i-1);
+        }
+        iSize--;
+      }
+      else
+      {
+        i++;
+      }
+    }
+    return removed;
+  }
 }