X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=65857ce0a4ff4d5ea504446f5dfbf46f49fdfe0e;hb=2b3edc77ed89937505a6c1297b4264cd8b820b8b;hp=39d68802880f437175960b6554fac32bf2bffc96;hpb=0ebbdf07a6afe841138a9c3473697e57349bf345;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 39d6880..65857ce 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
@@ -21,16 +21,18 @@ package jalview.datamodel;
 
 import java.util.*;
 
+import jalview.analysis.*;
 
 /**
- * DOCUMENT ME!
+ * 
+ * Implements the SequenceI interface for a char[] based sequence object.
  *
  * @author $author$
  * @version $Revision$
  */
-public class Sequence implements SequenceI
+public class Sequence
+    implements SequenceI
 {
-  
   SequenceI datasetSequence;
   String name;
   private char [] sequence;
@@ -45,21 +47,17 @@ public class Sequence implements SequenceI
    * positions are tied to the residues of this sequence */
   Vector annotation;
 
-  /** DOCUMENT ME!! */
+  /** array of seuqence features - may not be null for a valid sequence object */
   public SequenceFeature[] sequenceFeatures;
 
-  /** This array holds hidden sequences
-   * of which this sequence is the representitive member of a group
-   */
-  SequenceGroup hiddenSequences;
 
   /**
    * Creates a new Sequence object.
    *
-   * @param name DOCUMENT ME!
-   * @param sequence DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
+   * @param name display name string
+   * @param sequence string to form a possibly gapped sequence out of
+   * @param start first position of non-gap residue in the sequence
+   * @param end last position of ungapped residues (nearly always only used for display purposes)
    */
   public Sequence(String name, String sequence, int start, int end)
   {
@@ -88,6 +86,11 @@ public class Sequence implements SequenceI
 
   void parseId()
   {
+    if (name==null)
+    {
+      System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+      name = "";
+    }
     // Does sequence have the /start-end signiature?
     if (limitrx.search(name))
     {
@@ -133,20 +136,74 @@ 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)
   {
+    this(seq, seq.getAnnotation());
+  }
+  /**
+   * Create a new sequence object with new features, DBRefEntries, and PDBIds
+   * but inherits any existing dataset sequence reference, and duplicate of
+   * any annotation that is present in the given annotation array.
+   * @param seq the sequence to be copied
+   * @param alAnnotation an array of annotation including some associated with seq 
+   */
+  public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
+  {
     this(seq.getName(),
-         seq.getSequence(),
-         seq.getStart(),
-         seq.getEnd());
+            seq.getSequence(),
+            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++)
+      {
+        if (sqann[i]==null)
+        {
+          continue;
+        }
+        boolean found = (alAnnotation==null);
+        if (!found)
+        {
+          for (int apos = 0; !found && apos<alAnnotation.length; apos++)
+          {
+            found = (alAnnotation[apos] == sqann[i]);
+          }
+        }
+        if (found)
+        {
+          // only copy the given annotation
+          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()));
+      }
+    }
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -182,7 +239,9 @@ public class Sequence implements SequenceI
   public void deleteFeature(SequenceFeature sf)
   {
     if(sequenceFeatures==null)
+    {
       return;
+    }
 
     int index=0;
     for (index = 0; index < sequenceFeatures.length; index++)
@@ -195,7 +254,9 @@ public class Sequence implements SequenceI
 
 
     if(index==sequenceFeatures.length)
+    {
       return;
+    }
 
     int sfLength = sequenceFeatures.length;
     if(sfLength<2)
@@ -208,10 +269,12 @@ 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;
     }
@@ -230,7 +293,9 @@ public class Sequence implements SequenceI
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
+    {
       pdbIds = new Vector();
+    }
 
     pdbIds.addElement(entry);
   }
@@ -380,6 +445,8 @@ public class Sequence implements SequenceI
    */
   public char [] getSequence(int start, int end)
   {
+    if (start<0)
+      start=0;
     // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
     if (start >= sequence.length)
     {
@@ -407,19 +474,27 @@ 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;
   }
 
@@ -463,11 +538,11 @@ 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)
   {
@@ -546,14 +621,12 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
    */
   public void deleteChars(int i, int j)
   {
+    int newstart=start,newend=end;
     if (i >= sequence.length)
     {
       return;
@@ -572,10 +645,53 @@ public class Sequence implements SequenceI
       System.arraycopy(sequence,0,tmp,0,i);
       System.arraycopy(sequence,j,tmp,i,sequence.length-j);
     }
-
+    boolean createNewDs=false;
+    for (int s = i; s < j; s++)
+    {
+      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      {
+        if (createNewDs)
+        {
+          newend--;
+        } else {
+          int sindex = findIndex(start)-1;
+          if (sindex==s)
+        {
+          // delete characters including start of sequence
+          newstart = findPosition(j);
+          break; // don't need to search for any more residue characters.
+        } else {
+          // delete characters after start.
+          int eindex = findIndex(end)-1;
+          if (eindex<j)
+          {
+            // delete characters at end of sequence
+            newend = findPosition(i-1);
+            break; // don't need to search for any more residue characters.
+          } else {
+            createNewDs=true;
+            newend--; // decrease end position by one for the deleted residue and search further
+          }
+        }
+        }
+      }
+    }
+    // deletion occured in the middle of the sequence
+    if (createNewDs && this.datasetSequence != null)
+    {
+      // construct a new sequence
+      Sequence ds = new Sequence(datasetSequence);
+      // TODO: remove any non-inheritable properties ?
+      // TODO: create a sequence mapping (since there is a relation here ?)
+      ds.deleteChars(i, j);
+      datasetSequence = ds;
+    }
+    start = newstart;
+    end = newend;
     sequence = tmp;
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -641,17 +757,27 @@ 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].equalRef(entry))
       {
+        if (entry.getMap()!=null)
+        {
+          if (dbrefs[i].getMap()==null)
+          {
+            // overwrite with 'superior' entry that contains a mapping.
+            dbrefs[i] = entry;
+          }
+        }
         return;
       }
+    }
 
     DBRefEntry[] temp = new DBRefEntry[iSize + 1];
     System.arraycopy(dbrefs, 0, temp, 0, iSize);
@@ -673,11 +799,15 @@ 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;
   }
@@ -685,59 +815,146 @@ 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 SequenceGroup getHiddenSequences()
+  public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
   {
-    return hiddenSequences;
-  }
-
-  public void addHiddenSequence(SequenceI seq)
-  {
-    if (hiddenSequences == null)
+    if(this.annotation!=null)
     {
-      hiddenSequences = new SequenceGroup();
+      this.annotation.removeElement(annotation);
+      if(this.annotation.size()==0)
+        this.annotation = null;
     }
-    hiddenSequences.addSequence(seq, false);
   }
 
-  public void showHiddenSequence(SequenceI seq)
-  {
-    hiddenSequences.deleteSequence(seq, false);
-    if (hiddenSequences.getSize(false) < 1)
-    {
-      hiddenSequences = null;
-    }
-  }
+
   /**
    * test if this is a valid candidate for another
-   * sequence's dataset sequence. 
-   * 
+   * 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);
+        ds.setSequenceFeatures(getSequenceFeatures());
+        seq = this; // and return this sequence as the derived sequence.
+      }
+    }
+    return seq;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#createDatasetSequence()
+   */
+  public SequenceI createDatasetSequence()
+  {
+    if (datasetSequence==null)
+    {
+      datasetSequence = new Sequence(getName(),
+              AlignSeq.extractGaps(
+                jalview.util.Comparison.GapChars,
+                getSequenceAsString()),
+            getStart(),
+            getEnd());
+      datasetSequence.setSequenceFeatures(getSequenceFeatures());
+      datasetSequence.setDescription(getDescription());
+      setSequenceFeatures(null);
+      // move database references onto dataset sequence
+      datasetSequence.setDBRef(getDBRef());
+      setDBRef(null);
+    }
+    return datasetSequence;
+  }
+  /* (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]);
       }
-      return seq;
+    }
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
+   */
+  public AlignmentAnnotation[] getAnnotation(String label)
+  {
+    if (annotation==null || annotation.size()==0)
+    {
+      return null;
+    }
+    
+    Vector subset = new Vector();
+    Enumeration e = annotation.elements();
+    while (e.hasMoreElements())
+    {
+      AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+      if (ann.label!=null && ann.label.equals(label))
+      {
+        subset.addElement(ann);
+      }
+    }
+    if (subset.size()==0)
+    {
+      return null;
+    }
+    AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
+    int i=0;
+    e = subset.elements();
+    while (e.hasMoreElements())
+    {
+      anns[i++] = (AlignmentAnnotation) e.nextElement();
+    }
+    subset.removeAllElements();
+    return anns;
   }
 
 }