X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=338294b77bfab6ec444146bed2d39f3242c6e1a3;hb=d836fdf0564204d853e3ec844c8dbaec27d3cf23;hp=ac8f47a4f68e76ff1d75f43080272b03c00386ea;hpb=bb99b11825ccc8f9d7dd7b4b0dfcc2f64ebe0b75;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index ac8f47a..338294b 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -29,40 +29,30 @@ import java.util.*;
  */
 public class Alignment implements AlignmentI
 {
+    protected Alignment dataset;
     protected Vector sequences;
     protected Vector groups = new Vector();
     protected Vector superGroup = new Vector();
     protected char gapCharacter = '-';
-    protected boolean isNucleotide = true;
-
+    protected int type = NUCLEOTIDE;
+    public static final int PROTEIN = 0;
+    public static final int NUCLEOTIDE = 1;
 
     /** DOCUMENT ME!! */
     public AlignmentAnnotation[] annotations;
 
-    /** DOCUMENT ME!! */
-    public boolean featuresAdded = false;
-
     /** Make an alignment from an array of Sequences.
      *
      * @param sequences
      */
     public Alignment(SequenceI[] seqs)
     {
-        int i=0, iSize = seqs.length, j, jSize;
-        while(isNucleotide && i<iSize)
-        {
-            jSize = seqs[i].getLength();
-            for(j=0; j<jSize; j++)
-            {
-              if(!jalview.schemes.ResidueProperties.nucleotideHash.containsKey(seqs[i].getSequence(j, j+1))
-              && !jalview.util.Comparison.isGap(seqs[i].getSequence().charAt(j)))
-              {
-                isNucleotide = false;
-                break;
-              }
-            }
-            i++;
-        }
+        int i=0;
+
+        if( jalview.util.Comparison.isNucleotide(seqs))
+          type = NUCLEOTIDE;
+        else
+          type = PROTEIN;
 
         sequences = new Vector();
 
@@ -464,11 +454,9 @@ public class Alignment implements AlignmentI
 
         while (i < sequences.size())
         {
-            SequenceI s = getSequenceAt(i);
-
-            if (s.getName().equals(name))
+            if (getSequenceAt(i).getName().equals(name))
             {
-                return s;
+                return getSequenceAt(i);
             }
 
             i++;
@@ -477,25 +465,6 @@ public class Alignment implements AlignmentI
         return null;
     }
 
-    /**    */
-    public SequenceI findbyDisplayId(String name)
-    {
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI s = getSequenceAt(i);
-
-            if (s.getDisplayId().equals(name))
-            {
-                return s;
-            }
-
-            i++;
-        }
-
-        return null;
-    }
 
     /**    */
     public int findIndex(SequenceI s)
@@ -676,6 +645,7 @@ public class Alignment implements AlignmentI
             aSize = annotations.length + 1;
         }
 
+
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
         int i = 0;
 
@@ -704,11 +674,53 @@ public class Alignment implements AlignmentI
 
     public void setNucleotide(boolean b)
     {
-      isNucleotide = b;
+      if(b)
+        type = NUCLEOTIDE;
+      else
+        type = PROTEIN;
     }
 
     public boolean isNucleotide()
     {
-      return isNucleotide;
+      if(type==NUCLEOTIDE)
+        return true;
+      else
+        return false;
     }
+
+    public void setDataset(Alignment data)
+    {
+      if(dataset==null && data==null)
+      {
+        // 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()];
+        for (int i = 0; i < getHeight(); i++)
+        {
+
+          seqs[i] = new Sequence(getSequenceAt(i).getName(),
+                                 AlignSeq.extractGaps(
+                                     jalview.util.Comparison.GapChars,
+                                     getSequenceAt(i).getSequence()
+                                 ),
+                                 getSequenceAt(i).getStart(),
+                                 getSequenceAt(i).getEnd());
+
+          getSequenceAt(i).setDatasetSequence(seqs[i]);
+        }
+
+        dataset = new Alignment(seqs);
+      }
+      else if(dataset==null && data!=null)
+      {
+        dataset = data;
+      }
+    }
+
+    public Alignment getDataset()
+    {
+      return dataset;
+    }
+
 }