X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=81a0f408da1d0274e337597e49d17fa3cf073bed;hb=855f7a4bb3e8d5fcfa9059df64262fc73f0164be;hp=02fc54345bf53e3c4473ca36b45b38fe01943120;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 02fc543..81a0f40 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -21,6 +21,7 @@ package jalview.datamodel;
 
 import java.util.*;
 
+import jalview.analysis.*;
 
 /**
  * DOCUMENT ME!
@@ -28,7 +29,8 @@ import java.util.*;
  * @author $author$
  * @version $Revision$
  */
-public class Sequence implements SequenceI
+public class Sequence
+    implements SequenceI
 {
   SequenceI datasetSequence;
   String name;
@@ -128,8 +130,8 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * Creates a new Sequence object.
-   *
+   * Creates a new Sequence object with new features, DBRefEntries, AlignmentAnnotations, and PDBIds
+   * but inherits any existing dataset sequence reference.
    * @param seq DOCUMENT ME!
    */
   public Sequence(SequenceI seq)
@@ -139,6 +141,34 @@ public class Sequence implements SequenceI
          seq.getStart(),
          seq.getEnd());
     description = seq.getDescription();
+    if (seq.getSequenceFeatures()!=null) {
+      SequenceFeature[] sf = seq.getSequenceFeatures();
+      for (int i=0; i<sf.length; i++) {
+        addSequenceFeature(new SequenceFeature(sf[i]));
+      }
+    }
+    if (seq.getDBRef()!=null) {
+      DBRefEntry[] dbr = seq.getDBRef();
+      for (int i=0; i<dbr.length; i++) {
+        addDBRef(new DBRefEntry(dbr[i]));
+      }
+    }
+    setDatasetSequence(seq.getDatasetSequence());
+    if (seq.getAnnotation()!=null) {
+      AlignmentAnnotation[] sqann = seq.getAnnotation();
+      for (int i=0;i<sqann.length; i++)
+      {
+        AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
+        addAlignmentAnnotation(newann);
+      }
+    }
+    if (seq.getPDBId()!=null) {
+      Vector ids = seq.getPDBId();
+      Enumeration e = ids.elements();
+      while (e.hasMoreElements()) {
+        this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+      }
+    }
   }
 
 
@@ -177,7 +207,9 @@ public class Sequence implements SequenceI
   public void deleteFeature(SequenceFeature sf)
   {
     if(sequenceFeatures==null)
+    {
       return;
+    }
 
     int index=0;
     for (index = 0; index < sequenceFeatures.length; index++)
@@ -190,7 +222,9 @@ public class Sequence implements SequenceI
 
 
     if(index==sequenceFeatures.length)
+    {
       return;
+    }
 
     int sfLength = sequenceFeatures.length;
     if(sfLength<2)
@@ -203,10 +237,12 @@ public class Sequence implements SequenceI
       System.arraycopy(sequenceFeatures, 0, temp, 0, index);
 
       if(index<sfLength)
+      {
         System.arraycopy(sequenceFeatures,
                          index + 1,
                          temp,
                          index, sequenceFeatures.length - index -1);
+      }
 
       sequenceFeatures = temp;
     }
@@ -225,7 +261,9 @@ public class Sequence implements SequenceI
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
+    {
       pdbIds = new Vector();
+    }
 
     pdbIds.addElement(entry);
   }
@@ -402,19 +440,27 @@ public class Sequence implements SequenceI
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
+    }
     char [] seq = getSequence(start, end);
     if (seq.length == 0)
+    {
       return null;
+    }
     int nstart = findPosition(start);
     int nend = findPosition(end) - 1;
     // JBPNote - this is an incomplete copy.
     SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
     nseq.setDescription(description);
     if (datasetSequence!=null)
+    {
         nseq.setDatasetSequence(datasetSequence);
+    }
     else
+    {
         nseq.setDatasetSequence(this);
+    }
     return nseq;
   }
 
@@ -458,11 +504,11 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Return the alignment position for a sequence position
    *
-   * @param pos DOCUMENT ME!
+   * @param pos lying from start to end
    *
-   * @return DOCUMENT ME!
+   * @return aligned position of residue pos
    */
   public int findIndex(int pos)
   {
@@ -568,9 +614,31 @@ public class Sequence implements SequenceI
       System.arraycopy(sequence,j,tmp,i,sequence.length-j);
     }
 
+    if (this.datasetSequence != null)
+    {
+      for (int s = i; s < j; s++)
+      {
+        if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+        {
+
+          Sequence ds = new Sequence(name,
+                                     AlignSeq.extractGaps(
+                                         jalview.util.Comparison.GapChars,
+                                         this.getSequenceAsString()
+                                     ),
+                                     start,
+                                     end);
+          ds.setDescription(description);
+        }
+        break;
+      }
+    }
+
     sequence = tmp;
+
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -636,17 +704,19 @@ public class Sequence implements SequenceI
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
+    {
       dbrefs = new DBRefEntry[0];
+    }
 
     int i, iSize = dbrefs.length;
 
     for(i=0; i<iSize; i++)
-      if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
-      && dbrefs[i].getSource().equals(entry.getSource())
-      && dbrefs[i].getVersion().equals(entry.getVersion()))
+    {
+      if(dbrefs[i].equals(entry))
       {
         return;
       }
+    }
 
     DBRefEntry[] temp = new DBRefEntry[iSize + 1];
     System.arraycopy(dbrefs, 0, temp, 0, iSize);
@@ -668,11 +738,15 @@ public class Sequence implements SequenceI
   public AlignmentAnnotation[] getAnnotation()
   {
     if (annotation == null)
+    {
       return null;
+    }
 
     AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
     for (int r = 0; r < ret.length; r++)
+    {
       ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+    }
 
     return ret;
   }
@@ -680,9 +754,22 @@ public class Sequence implements SequenceI
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
+    {
       this.annotation = new Vector();
+    }
 
     this.annotation.addElement(annotation);
+    annotation.setSequenceRef(this);
+  }
+
+  public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    if(this.annotation!=null)
+    {
+      this.annotation.removeElement(annotation);
+      if(this.annotation.size()==0)
+        this.annotation = null;
+    }
   }
 
 
@@ -691,27 +778,63 @@ public class Sequence implements SequenceI
    * sequence's dataset sequence.
    *
    */
-  private boolean isValidDatasetSequence() {
-      if (datasetSequence!=null)
+  private boolean isValidDatasetSequence()
+  {
+    if (datasetSequence!=null)
+    {
           return false;
+    }
       for (int i=0;i<sequence.length; i++)
+    {
           if (jalview.util.Comparison.isGap(sequence[i]))
+      {
               return false;
+      }
+    }
       return true;
   }
   /* (non-Javadoc)
    * @see jalview.datamodel.SequenceI#deriveSequence()
    */
-  public SequenceI deriveSequence() {
-      SequenceI seq = new Sequence(name, sequence, start, end);
-      seq.setDescription(description);
-      if (datasetSequence!=null) {
-          seq.setDatasetSequence(datasetSequence);
+  public SequenceI deriveSequence()
+  {
+    SequenceI seq=new Sequence(this);
+    if (datasetSequence != null)
+    {
+      // duplicate current sequence with same dataset
+      seq.setDatasetSequence(datasetSequence);
+    }
+    else
+    {
+      if (isValidDatasetSequence())
+      {
+        // Use this as dataset sequence
+        seq.setDatasetSequence(this);
       } else {
-          if (isValidDatasetSequence())
-              seq.setDatasetSequence(this);
+        // Create a new, valid dataset sequence
+        SequenceI ds = seq;
+        ds.setSequence(AlignSeq.extractGaps(jalview.util.Comparison.GapChars, new String(sequence)));
+        setDatasetSequence(ds);
+        seq = this; // and return this sequence as the derived sequence.
       }
-      return seq;
+    }
+    return seq;
+  }
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] annotations)
+   */
+  public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
+  {
+    if (annotation!=null) {
+      annotation.removeAllElements();
+    }
+    if (annotations!=null) {
+      for (int i=0; i<annotations.length; i++)
+      {
+        if (annotations[i]!=null)
+          addAlignmentAnnotation(annotations[i]);
+      }
+    }
   }
 
 }