X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=3a1b44a6ef095fba286bf110f71a41acc3f4b0dd;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=28849b608ea6fa87ff6d94cd29d3c84e74604f85;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 28849b6..3a1b44a 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -29,10 +29,15 @@ 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 Provenance provenance;
+    protected int type = NUCLEOTIDE;
+    public static final int PROTEIN = 0;
+    public static final int NUCLEOTIDE = 1;
 
     /** DOCUMENT ME!! */
     public AlignmentAnnotation[] annotations;
@@ -46,9 +51,16 @@ public class Alignment implements AlignmentI
      */
     public Alignment(SequenceI[] seqs)
     {
+        int i=0;
+
+        if( jalview.util.Comparison.isNucleotide(seqs))
+          type = NUCLEOTIDE;
+        else
+          type = PROTEIN;
+
         sequences = new Vector();
 
-        for (int i = 0; i < seqs.length; i++)
+        for (i = 0; i < seqs.length; i++)
         {
             sequences.addElement(seqs[i]);
         }
@@ -334,9 +346,16 @@ public class Alignment implements AlignmentI
     {
         Vector temp = new Vector();
 
-        for (int i = 0; i < this.groups.size(); i++)
+        int gSize = groups.size();
+        for (int i = 0; i < gSize; i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+            if(sg==null || sg.sequences==null)
+            {
+              this.deleteGroup(sg);
+              gSize--;
+              continue;
+            }
 
             if (sg.sequences.contains(s))
             {
@@ -439,11 +458,9 @@ 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++;
@@ -452,25 +469,6 @@ 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)
@@ -651,6 +649,7 @@ public class Alignment implements AlignmentI
             aSize = annotations.length + 1;
         }
 
+
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
         int i = 0;
 
@@ -676,4 +675,64 @@ public class Alignment implements AlignmentI
     {
         return annotations;
     }
+
+    public void setNucleotide(boolean b)
+    {
+      if(b)
+        type = NUCLEOTIDE;
+      else
+        type = PROTEIN;
+    }
+
+    public boolean 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).getDisplayId(true),
+                                 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;
+    }
+
+    public void setProvenance(Provenance prov)
+    {
+      provenance = prov;
+    }
+    public Provenance getProvenance()
+    {
+      return provenance;
+    }
 }