X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=1134857428850bf8e49716f31013e37c56b2c37b;hb=ddcce112558a130196ca384c4683b4f9b7d7d133;hp=3f9f03ff230b2d5d44282896a18bde9f4bd697b1;hpb=2acdd7fdaa575dd5238585ad86597f808b30d281;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3f9f03f..1134857 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -22,13 +22,14 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.io.FastaFile;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -47,8 +48,7 @@ public class Alignment implements AlignmentI
 
   protected List<SequenceI> sequences;
 
-  protected List<SequenceGroup> groups = java.util.Collections
-          .synchronizedList(new ArrayList<SequenceGroup>());
+  protected List<SequenceGroup> groups;
 
   protected char gapCharacter = '-';
 
@@ -60,20 +60,21 @@ public class Alignment implements AlignmentI
 
   public boolean hasRNAStructure = false;
 
-  /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
 
-  HiddenSequences hiddenSequences = new HiddenSequences(this);
+  HiddenSequences hiddenSequences;
 
   public Hashtable alignmentProperties;
 
-  private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+  private List<AlignedCodonFrame> codonFrameList;
 
   private void initAlignment(SequenceI[] seqs)
   {
-    int i = 0;
+    groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
+    hiddenSequences = new HiddenSequences(this);
+    codonFrameList = new ArrayList<AlignedCodonFrame>();
 
-    if (jalview.util.Comparison.isNucleotide(seqs))
+    if (Comparison.isNucleotide(seqs))
     {
       type = NUCLEOTIDE;
     }
@@ -82,10 +83,9 @@ public class Alignment implements AlignmentI
       type = PROTEIN;
     }
 
-    sequences = java.util.Collections
-            .synchronizedList(new ArrayList<SequenceI>());
+    sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
 
-    for (i = 0; i < seqs.length; i++)
+    for (int i = 0; i < seqs.length; i++)
     {
       sequences.add(seqs[i]);
     }
@@ -104,13 +104,12 @@ public class Alignment implements AlignmentI
       seqs[i] = new Sequence(seqs[i]);
     }
 
+    initAlignment(seqs);
+
     /*
-     * Share the same dataset sequence mappings (if any). TODO: find a better
-     * place for these to live (alignment dataset?).
+     * Share the same dataset sequence mappings (if any). 
      */
     this.setCodonFrames(al.getCodonFrames());
-
-    initAlignment(seqs);
   }
 
   /**
@@ -1281,8 +1280,8 @@ public class Alignment implements AlignmentI
   @Override
   public void addCodonFrame(AlignedCodonFrame codons)
   {
-    Set<AlignedCodonFrame> acfs = getCodonFrames();
-    if (codons != null && acfs != null)
+    List<AlignedCodonFrame> acfs = getCodonFrames();
+    if (codons != null && acfs != null && !acfs.contains(codons))
     {
       acfs.add(codons);
     }
@@ -1319,7 +1318,7 @@ public class Alignment implements AlignmentI
    * @see jalview.datamodel.AlignmentI#setCodonFrames()
    */
   @Override
-  public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+  public void setCodonFrames(List<AlignedCodonFrame> acfs)
   {
     if (dataset != null)
     {
@@ -1339,7 +1338,7 @@ public class Alignment implements AlignmentI
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
   @Override
-  public Set<AlignedCodonFrame> getCodonFrames()
+  public List<AlignedCodonFrame> getCodonFrames()
   {
     return dataset != null ? dataset.getCodonFrames() : codonFrameList;
   }
@@ -1351,7 +1350,7 @@ public class Alignment implements AlignmentI
   @Override
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
-    Set<AlignedCodonFrame> acfs = getCodonFrames();
+    List<AlignedCodonFrame> acfs = getCodonFrames();
     if (codons == null || acfs == null)
     {
       return false;
@@ -1770,4 +1769,46 @@ public class Alignment implements AlignmentI
     }
     return hasValidSeq;
   }
+
+  /**
+   * Update any mappings to 'virtual' sequences to compatible real ones, if
+   * present in the added sequences. Returns a count of mappings updated.
+   * 
+   * @param seqs
+   * @return
+   */
+  @Override
+  public int realiseMappings(List<SequenceI> seqs)
+  {
+    int count = 0;
+    for (SequenceI seq : seqs)
+    {
+      for (AlignedCodonFrame mapping : getCodonFrames())
+      {
+        count += mapping.realiseWith(seq);
+      }
+    }
+    return count;
+  }
+
+  /**
+   * Returns the first AlignedCodonFrame that has a mapping between the given
+   * dataset sequences
+   * 
+   * @param mapFrom
+   * @param mapTo
+   * @return
+   */
+  @Override
+  public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
+  {
+    for (AlignedCodonFrame acf : getCodonFrames())
+    {
+      if (acf.getAaForDnaSeq(mapFrom) == mapTo)
+      {
+        return acf;
+      }
+    }
+    return null;
+  }
 }