X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5f0bf6884fc9fabbb7acdec470c31a9e0c50bf10;hb=23d3cb8d0e4c227224587135f41132d436dc1178;hp=61735eeb1d763b0b8c78d8a32efe9b6f8deebca9;hpb=8c6e707d6d9b1b8ad6385eb7eeef0bc78cb46f6e;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 61735ee..5f0bf68 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,21 +24,23 @@ import jalview.util.*;
 
 import java.util.*;
 
-
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 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;
+    HiddenSequences hiddenSequences = new HiddenSequences(this);
+
 
     /** Make an alignment from an array of Sequences.
      *
@@ -46,14 +48,19 @@ 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]);
         }
-
-        getWidth();
     }
 
     /**
@@ -66,6 +73,16 @@ public class Alignment implements AlignmentI
         return sequences;
     }
 
+    public SequenceI [] getSequencesArray()
+    {
+      SequenceI [] reply = new SequenceI[sequences.size()];
+      for(int i=0; i<sequences.size(); i++)
+      {
+        reply[i] = (SequenceI)sequences.elementAt(i);
+      }
+      return reply;
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -89,22 +106,21 @@ public class Alignment implements AlignmentI
      */
     public void addSequence(SequenceI snew)
     {
-        sequences.addElement(snew);
-    }
+      if(dataset!=null)
+      {
+        Sequence ds = new Sequence(snew.getName(),
+                                   AlignSeq.extractGaps("-. ", snew.getSequence()),
+                                   snew.getStart(),
+                                   snew.getEnd());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void addSequence(SequenceI[] seq)
-    {
-        for (int i = 0; i < seq.length; i++)
-        {
-            addSequence(seq[i]);
-        }
+        snew.setDatasetSequence(ds);
+        getDataset().addSequence(ds);
+      }
+
+      sequences.addElement(snew);
     }
 
+
     /** Adds a sequence to the alignment.  Recalculates maxLength and size.
      *
      * @param snew
@@ -197,13 +213,23 @@ 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 +246,8 @@ 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));
         }
     }
 
@@ -250,62 +277,6 @@ public class Alignment implements AlignmentI
         sequences.removeElementAt(i);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param threshold DOCUMENT ME!
-     * @param sel DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector removeRedundancy(float threshold, Vector sel)
-    {
-        Vector del = new Vector();
-
-        for (int i = 1; i < sel.size(); i++)
-        {
-            for (int j = 0; j < i; j++)
-            {
-                // Only do the comparison if either have not been deleted
-                if (!del.contains((SequenceI) sel.elementAt(i)) ||
-                        !del.contains((SequenceI) sel.elementAt(j)))
-                {
-                    // use PID instead of Comparison (which is really not pleasant)
-                    float pid = Comparison.PID((SequenceI) sel.elementAt(j),
-                            (SequenceI) sel.elementAt(i));
-
-                    if (pid >= threshold)
-                    {
-                        // Delete the shortest one
-                        if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
-                                                                                         .elementAt(
-                                    i)).getSequence().length())
-                        {
-                            del.addElement(sel.elementAt(i));
-                        }
-                        else
-                        {
-                            del.addElement(sel.elementAt(i));
-                        }
-                    }
-                }
-            }
-        }
-
-        // Now delete the sequences
-        for (int i = 0; i < del.size(); i++)
-        {
-            deleteSequence((SequenceI) del.elementAt(i));
-        }
-
-        return del;
-    }
-
-    /**    */
-    public SequenceGroup findGroup(int i)
-    {
-        return findGroup(getSequenceAt(i));
-    }
 
     /**    */
     public SequenceGroup findGroup(SequenceI s)
@@ -314,7 +285,7 @@ public class Alignment implements AlignmentI
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-            if (sg.sequences.contains(s))
+            if (sg.getSequences(false).contains(s))
             {
                 return sg;
             }
@@ -338,14 +309,14 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < gSize; i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.sequences==null)
+            if(sg==null || sg.getSequences(false)==null)
             {
               this.deleteGroup(sg);
               gSize--;
               continue;
             }
 
-            if (sg.sequences.contains(s))
+            if (sg.getSequences(false).contains(s))
             {
                 temp.addElement(sg);
             }
@@ -361,47 +332,7 @@ 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)
@@ -418,7 +349,6 @@ public class Alignment implements AlignmentI
     public void deleteAllGroups()
     {
         groups.removeAllElements();
-        superGroup.removeAllElements();
 
         int i = 0;
 
@@ -446,11 +376,9 @@ 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++;
@@ -459,25 +387,6 @@ 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)
@@ -566,9 +475,9 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < sequences.size(); i++)
         {
             Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.sequence = seq.sequence.replace('.', gc);
-            seq.sequence = seq.sequence.replace('-', gc);
-            seq.sequence = seq.sequence.replace(' ', gc);
+            seq.setSequence( seq.getSequence().replace('.', gc) );
+            seq.setSequence( seq.getSequence().replace('-', gc) );
+            seq.setSequence( seq.getSequence().replace(' ', gc) );
         }
     }
 
@@ -644,6 +553,21 @@ public class Alignment implements AlignmentI
         annotations = temp;
     }
 
+
+    public void adjustSequenceAnnotations()
+    {
+      if(annotations!=null)
+      {
+        for (int a = 0; a < annotations.length; a++)
+        {
+          if (annotations[a].sequenceRef != null)
+          {
+            annotations[a].adjustForAlignment();
+          }
+        }
+      }
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -652,24 +576,48 @@ 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;
     }
@@ -683,4 +631,102 @@ 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;
+
+      //Remove excess gaps from the end of alignment
+      int maxLength = -1;
+
+      SequenceI current;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        current = getSequenceAt(i);
+        for (int j = current.getLength(); j > maxLength; j--)
+        {
+          if (j > maxLength && !jalview.util.Comparison.isGap(
+              current.getCharAt(j)))
+          {
+            maxLength = j;
+            break;
+          }
+        }
+      }
+
+      maxLength++;
+
+      for (int i = 0; i < sequences.size();
+           i++)
+      {
+        current = getSequenceAt(i);
+
+        if (current.getLength() < maxLength)
+        {
+          current.insertCharAt(maxLength - 1, gapCharacter);
+          modified=true;
+        }
+        else if(current.getLength() > maxLength)
+        {
+          current.deleteChars(maxLength, current.getLength());
+        }
+      }
+      return modified;
+    }
+
+    public HiddenSequences getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
 }