X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=b4e2b3f45be44f4ef1db3623dbf085a6b4aee2cc;hb=4944c2f33bb34b4f262fd2f3ae40dcdc2a825557;hp=28849b608ea6fa87ff6d94cd29d3c84e74604f85;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 28849b6..b4e2b3f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -29,28 +29,46 @@ 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 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;
+
+        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]);
+
+            if(seqs[i].getDatasetSequence()!=null
+            && seqs[i].getDatasetSequence().getAnnotation()!=null)
+            {
+
+              for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)
+              {
+                       this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);
+              }
+            }
         }
 
         getWidth();
@@ -197,13 +215,23 @@ public class Alignment implements AlignmentI
      */
     public void trimLeft(int i)
     {
-        for (int j = 0; j < getHeight(); j++)
+        int j, jSize = getHeight();
+        for (j = 0; j < jSize; j++)
         {
             SequenceI s = getSequenceAt(j);
             int newstart = s.findPosition(i);
 
-            s.setStart(newstart);
-            s.setSequence(s.getSequence().substring(i));
+            if(i>s.getLength())
+            {
+              sequences.removeElement(s);
+              j--;
+              jSize--;
+            }
+            else
+            {
+              s.setStart(newstart);
+              s.setSequence(s.getSequence().substring(i));
+            }
         }
     }
 
@@ -220,7 +248,8 @@ public class Alignment implements AlignmentI
             int newend = s.findPosition(i);
 
             s.setEnd(newend);
-            s.setSequence(s.getSequence().substring(0, i + 1));
+            if(s.getLength()>i)
+              s.setSequence(s.getSequence().substring(0, i + 1));
         }
     }
 
@@ -334,9 +363,16 @@ 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))
             {
@@ -354,47 +390,7 @@ public class Alignment implements AlignmentI
         return ret;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void addSuperGroup(SuperGroup sg)
-    {
-        superGroup.addElement(sg);
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void removeSuperGroup(SuperGroup sg)
-    {
-        superGroup.removeElement(sg);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg)
-    {
-        for (int i = 0; i < this.superGroup.size(); i++)
-        {
-            SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
-
-            if (temp.sequenceGroups.contains(sg))
-            {
-                return temp;
-            }
-        }
-
-        return null;
-    }
 
     /**    */
     public void addGroup(SequenceGroup sg)
@@ -439,11 +435,9 @@ 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 +446,6 @@ 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)
@@ -638,6 +613,85 @@ public class Alignment implements AlignmentI
     }
 
     /**
+     *
+     * @param aa AlignmentAnnotation
+     * @param seqRef The sequence to associate this annotation with
+     * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added
+     */
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)
+    {
+      if(seqRef!=null)
+      {
+          //We can only add Annotations to the dataset sequences
+           if(seqRef.getDatasetSequence()==null)
+           {
+                  setDataset(null);
+            }
+
+        AlignmentAnnotation []  old = seqRef.getDatasetSequence().getAnnotation();
+
+        //First check if this is a new annotation or not. If it is new,
+        //we must add the annotation to the dataset
+        boolean newAnnotation = true;
+        if(seqRef.getDatasetSequence().getAnnotation()!=null)
+        {
+          for(int a=0; a<old.length; a++)
+          {
+            if(old[a] == aa)
+            {
+
+              newAnnotation = false;
+              break;
+            }
+          }
+        }
+
+        if(newAnnotation)
+         {
+           seqRef.getDatasetSequence().addAlignmentAnnotation(aa);
+         }
+
+          AlignmentAnnotation copy = null;
+          if (aa.graph > 0)
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations, aa.graphMin,
+                aa.graphMax, aa.graph
+                );
+          else
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations
+                );
+
+         copy.datasetAnnotation = aa;
+
+         addAnnotation(copy);
+
+         copy.sequenceRef = seqRef;
+
+         return copy;
+      }
+      else
+      {
+        addAnnotation(aa);
+        return aa;
+      }
+    }
+
+    public void adjustSequenceAnnotations()
+    {
+      if(annotations!=null)
+      {
+        for (int a = 0; a < annotations.length; a++)
+        {
+          if (annotations[a].sequenceRef != null)
+          {
+            annotations[a].adjustForAlignment();
+          }
+        }
+      }
+    }
+
+    /**
      * DOCUMENT ME!
      *
      * @param aa DOCUMENT ME!
@@ -645,24 +699,48 @@ public class Alignment implements AlignmentI
     public void addAnnotation(AlignmentAnnotation aa)
     {
         int aSize = 1;
-
         if (annotations != null)
         {
             aSize = annotations.length + 1;
         }
 
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+        temp[aSize-1] = aa;
+
         int i = 0;
 
         if (aSize > 1)
         {
-            for (i = 0; i < (aSize - 1); i++)
+            for (i = 0; i < (aSize-1); i++)
             {
                 temp[i] = annotations[i];
             }
         }
 
-        temp[i] = aa;
+        annotations = temp;
+    }
+
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+    {
+      if(aa==null || annotations==null || annotations.length-1<index)
+        return;
+
+      int aSize = annotations.length;
+      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+      temp[index] = aa;
+
+      for (int i = 0; i < aSize; i++)
+      {
+        if(i==index)
+          continue;
+
+        if(i<index)
+          temp[i] = annotations[i];
+        else
+          temp[i] = annotations[i-1];
+      }
 
         annotations = temp;
     }
@@ -676,4 +754,73 @@ 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).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;
+    }
+
+    public boolean padGaps() {
+      boolean modified=false;
+      int Width = getWidth();
+      SequenceI current;
+      for (int i = 0; i < sequences.size();
+           i++)
+      {
+        current = getSequenceAt(i);
+
+        if (current.getLength() < Width)
+        {
+          current.insertCharAt(Width - 1, gapCharacter);
+          modified=true;
+        }
+      }
+      return modified;
+    }
 }