GFFDocumentEntry.java

/* GFFDocumentEntry.java
 *
 * created: Tue Sep 14 1999
 *
 * This file is part of Artemis
 *
 * Copyright (C) 1999-2005  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.37 2007-02-09 15:15:20 tjc Exp $
 */

package uk.ac.sanger.artemis.io;

import uk.ac.sanger.artemis.util.*;

import java.io.IOException;
import java.util.Hashtable;
import java.util.Enumeration;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.Vector;
import java.sql.Timestamp;

/**
 *  A DocumentEntry that can read an GFF entry from a Document.
 *
 *  @author Kim Rutherford
 *  @version $Id: GFFDocumentEntry.java,v 1.37 2007-02-09 15:15:20 tjc Exp $
 **/

public class GFFDocumentEntry extends SimpleDocumentEntry
    implements DocumentEntry 
{
  private boolean finished_constructor = false;
  
  /**
   *  Create a new GFFDocumentEntry object associated with the given
   *  Document.
   *  @param document This is the file that we will read from.  This is also
   *    used for saving the entry back to the file it came from and to give
   *    the new object a name.
   *  @param listener The object that will listen for ReadEvents.
   *  @exception IOException thrown if there is a problem reading the entry -
   *    most likely ReadFormatException.
   **/
  GFFDocumentEntry(final Document document, final ReadListener listener)
      throws IOException, EntryInformationException 
  {
    super(new GFFEntryInformation(), document, listener);

    // join the separate exons into one feature (if appropriate)
    //combineFeatures();
    combineGeneFeatures();
    finished_constructor = true;
  }

  /**
   *  Create a new GFFDocumentEntry that will be a copy of the given Entry and
   *  has no Document associated with it.  The new GFFDocumentEntry cannot be
   *  saved to a file with save() unless save(Document) has been called
   *  first.  Some qualifier and location information will be lost.
   *  @param force If true then invalid qualifiers and any features with
   *    invalid keys in the new Entry will be quietly thrown away.  "Invalid"
   *    means that the key/qualifier is not allowed to occur in an Entry of
   *    this type (probably determined by the EntryInformation object of this
   *    Entry).  If false an EntryInformationException will be thrown for
   *    invalid keys or qualifiers.
   **/
  public GFFDocumentEntry(final Entry new_entry, final boolean force)
      throws EntryInformationException 
  {
    super(new GFFEntryInformation(), new_entry, force);
    finished_constructor = true;
  }

  /**
   *  Create a new empty GFFDocumentEntry object that has no Document
   *  associated with it.  The new GFFDocumentEntry cannot be saved to a
   *  file with save() unless save(Document) has been called first.  The
   *  save(Document) method will assign a Document.
   **/
  public GFFDocumentEntry(final EntryInformation entry_information) 
  {
    super(new GFFEntryInformation());
    finished_constructor = true;
  }

  /**
   *  Returns true if and only if this entry is read only.  For now this
   *  always returns true - GFFDocumentEntry objects can't be changed.
   **/
  public boolean isReadOnly() 
  {
//  return finished_constructor;
    return false;
  }

  /**
   *  If the given feature can be added directly to this Entry, then return
   *  it, otherwise create and return a new feature of the appropriate type.
   *  @param copy if true then always new a new copy of the Feature.
   **/
  protected SimpleDocumentFeature makeNativeFeature(final Feature feature,
                                                    final boolean copy) 
  {
    if(!copy && feature instanceof GFFStreamFeature) 
      return (GFFStreamFeature)feature;
    else 
      return new GFFStreamFeature(feature);
  }

  /**
   *  If the given Sequence can be added directly to this Entry, then return a
   *  copy of it, otherwise create and return a new feature of the appropriate
   *  type for this Entry.
   **/
  protected StreamSequence makeNativeSequence(final Sequence sequence)
  {
    return new FastaStreamSequence(sequence);
  }

  private void combineGeneFeatures()
  {
    final FeatureVector original_features = getAllFeatures();
    
    Feature this_feature;
    Hashtable chado_gene = new Hashtable();
    try
    {
      // find the genes
      for(int i = 0 ; i < original_features.size() ; ++i) 
      {
        this_feature = original_features.featureAt(i);
        String key = this_feature.getKey().getKeyString();
        
        if(key.equals("gene"))
        {
          String id = (String)this_feature.getQualifierByName("ID").getValues().get(0);
          ChadoCanonicalGene gene = new ChadoCanonicalGene();
          gene.setGene(this_feature);
          chado_gene.put(id, gene);
          ((GFFStreamFeature)this_feature).setChadoGene(gene);
        }
      }

      // find the transcripts
      Hashtable transcripts_lookup = new Hashtable();
      for(int i = 0 ; i < original_features.size() ; ++i) 
      {
        this_feature = original_features.featureAt(i);
        
        // transcript 
        Qualifier parent_qualifier = this_feature.getQualifierByName("Parent");
        
        if(parent_qualifier == null)
          continue;

        StringVector parents = parent_qualifier.getValues();
        for(int j=0; j<parents.size(); j++)
        {
          String parent = (String)parents.get(j);
          
          if(chado_gene.containsKey(parent))
          {
            // store transcript
            ChadoCanonicalGene gene = (ChadoCanonicalGene)chado_gene.get(parent);
            gene.addTranscript(this_feature);
            
            // store the transcript ID with its ChadoCanonicalGene object
            transcripts_lookup.put((String)this_feature.getQualifierByName("ID").getValues().get(0),
                                   gene);
            continue;
          }
        }
      }
      
      
      // find exons & protein
      String key;
      for(int i = 0 ; i < original_features.size() ; ++i) 
      {
        this_feature = original_features.featureAt(i);
        // exons
        key = this_feature.getKey().getKeyString();
        //if(!key.equals("exon") && !key.equals("polypeptide") &&
        //   !key.endsWith("prime_UTR"))
        //  continue;
        
        Qualifier parent_qualifier  = this_feature.getQualifierByName("Parent");
        Qualifier derives_qualifier = this_feature.getQualifierByName("Derives_from");
        if(parent_qualifier == null && derives_qualifier == null)
          continue;    
          
        Qualifier featureRelationship = 
          this_feature.getQualifierByName("feature_relationship_rank");
        // compare this features parent_id's to transcript id's in the 
        // chado gene hash to decide if it is part of it
        final StringVector parent_id;
        
        if(parent_qualifier != null)
          parent_id = parent_qualifier.getValues();
        else
          parent_id = derives_qualifier.getValues();
        
        for(int j=0; j<parent_id.size(); j++)
        {
          String parent = (String)parent_id.get(j);
         
          if(transcripts_lookup.containsKey(parent))
          {
            ChadoCanonicalGene gene = (ChadoCanonicalGene)transcripts_lookup.get(parent);
             
            if(parent_qualifier == null)
              gene.addProtein(parent, this_feature);
            else if(key.equals("three_prime_UTR"))
              gene.add3PrimeUtr(parent, this_feature);
            else if(key.equals("five_prime_UTR"))
              gene.add5PrimeUtr(parent, this_feature);
            else if(key.equals("exon") || featureRelationship != null)
              gene.addSplicedFeatures(parent, this_feature);
            else
              gene.addOtherFeatures(parent, this_feature);
          }
        } 
          
        /*
        Enumeration enum_genes = chado_gene.elements();
        while(enum_genes.hasMoreElements())
        {
          ChadoCanonicalGene gene = (ChadoCanonicalGene)enum_genes.nextElement();
          Feature transcript = (Feature)gene.containsTranscript(parent_id);
          
          if(transcript != null)
          {
            if(parent_qualifier == null)
              gene.addProtein((String)transcript.getQualifierByName("ID").getValues().get(0), 
                              this_feature);
            else
              gene.addExon((String)transcript.getQualifierByName("ID").getValues().get(0),
                           this_feature);
          }
          
        }
        */
      }

      // now join exons
      //combineFeatures();
      Enumeration enum_genes = chado_gene.elements();
      while(enum_genes.hasMoreElements())
      {
        ChadoCanonicalGene gene = (ChadoCanonicalGene)enum_genes.nextElement();
        combineChadoExons(gene);
      }
    }
    catch(InvalidRelationException e)
    {
      e.printStackTrace();
    }
  }
  
  /**
   *  Join the separate exons into one feature (if appropriate).
   **/
  /*private void combineFeatures()
  {
    final FeatureVector original_features = getAllFeatures();

    // the key of these hashes will be the group name and the value is a
    // FeatureVector containing the feature that are in that group
    final Hashtable forward_feature_groups = new Hashtable();
    final Hashtable reverse_feature_groups = new Hashtable();

    Feature this_feature;
    Hashtable this_strand_feature_groups;
    String group_name = null;

    for(int i = 0 ; i < original_features.size() ; ++i) 
    {
      this_feature = original_features.featureAt(i);

      if(this_feature.getLocation().isComplement()) 
        this_strand_feature_groups = reverse_feature_groups;
      else
        this_strand_feature_groups = forward_feature_groups;

      try 
      {
        String key = this_feature.getKey().getKeyString();
        if(key.equals("CDS") || key.equals("polypeptide_domain") || 
           key.equals("polypeptide") || key.equals("exon"))
        {
          if(this_feature.getQualifierByName("Parent") != null)
          {
            StringVector values =
              this_feature.getQualifierByName("Parent").getValues();
            group_name = (String)values.elementAt(0);

            if(this_feature.getQualifierByName("ID") != null &&
               !key.equals("exon"))
            {
              values =
                  this_feature.getQualifierByName("ID").getValues();
              group_name = group_name+values.elementAt(0);
            }
          }
          else
            continue; 
        }
        else
          continue;

        final FeatureVector other_features =
          (FeatureVector) this_strand_feature_groups.get(group_name);

        if(other_features == null)
        {
          final FeatureVector new_feature_vector = new FeatureVector();
          new_feature_vector.add(this_feature);
          this_strand_feature_groups.put(group_name, new_feature_vector);
        }
        else
          other_features.add(this_feature);

      }
      catch(InvalidRelationException e) 
      {
        throw new Error("internal error - unexpected exception: " + e);
      }

    }

    combineFeaturesFromHash(forward_feature_groups);
    combineFeaturesFromHash(reverse_feature_groups);
  }*/

  /**
   *  Combine the features (which are exons) and delete the orignals from this
   *  Entry.  The key of this hash will be the group name and the value is a
   *  FeatureVector containing the feature that are in that group.  Groups
   *  that have more than one member will be combined.
   **/
  public void combineChadoExons(ChadoCanonicalGene gene) 
  {
    Vector transcripts = (Vector)gene.getTranscripts();
    gene.correctSpliceSiteAssignments();
    
    for(int i=0; i<transcripts.size(); i++)
    {
      GFFStreamFeature transcript = (GFFStreamFeature)transcripts.get(i);
      String transcript_id = null;
      transcript_id = (String)(transcript.getQualifierByName("ID").getValues().get(0));
      
      Set splicedSiteTypes = gene.getSpliceTypes(transcript_id);
      if(splicedSiteTypes == null)
        continue;
      
      Iterator it = splicedSiteTypes.iterator();
      Vector new_set = new Vector();
      while(it.hasNext())
      {
        String type = (String)it.next();
        List splicedSites = gene.getSpliceSitesOfTranscript(transcript_id, type);
           
        if(splicedSites == null)
          continue;
      
        mergeFeatures(splicedSites, new_set, 
                      (String)(transcript.getQualifierByName("ID").getValues().get(0)));
      }
      
      for(int j=0; j<new_set.size(); j++)
      {
        try
        {
          if(j == 0)
            gene.addSplicedFeatures(transcript_id, 
                (Feature)new_set.get(j), true );
          else
            gene.addSplicedFeatures(transcript_id, 
                (Feature)new_set.get(j));
        }
        catch(InvalidRelationException e)
        {
          // TODO Auto-generated catch block
          e.printStackTrace();
        }
      }
      
    }   
    
    // now merge the exons in the ChadoCanonicalGene feature
    /*Enumeration enum_exon_set = new_exon_set.keys();
    int num = 0;
    while(enum_exon_set.hasMoreElements())
    {
      String transcript_id = (String)enum_exon_set.nextElement();
      try
      {
        if(num == 0)
          gene.addSplicedFeatures(transcript_id, 
                       (Feature)new_exon_set.get(transcript_id), true );
        else
          gene.addSplicedFeatures(transcript_id, 
                       (Feature)new_exon_set.get(transcript_id));
        num++;
      }
      catch(InvalidRelationException e)
      {
        // TODO Auto-generated catch block
        e.printStackTrace();
      }
    }*/
  }
  
  
  private void mergeFeatures(final List gffFeatures,
                             final List new_set, 
                             final String transcript_id)
  {
    Hashtable feature_relationship_rank_store = new Hashtable();
    Hashtable id_range_store = new Hashtable();
    RangeVector new_range_vector = new RangeVector();
    QualifierVector qualifier_vector = new QualifierVector();
    Timestamp lasttimemodified = null;

    for(int j = 0; j < gffFeatures.size(); j++)
    {
      final GFFStreamFeature this_feature = (GFFStreamFeature)gffFeatures.get(j);
      
      Integer rank;
      Qualifier rankQualifier = this_feature
          .getQualifierByName("feature_relationship_rank");
      if(rankQualifier == null)
        rank = new Integer(0);
      else
      {
        rank = new Integer((String) (rankQualifier.getValues().get(0)));
        this_feature.getQualifiers().removeQualifierByName("feature_relationship_rank");
      }
      
      // use the most current lastmodified datestamp
      if(this_feature.getLastModified() != null
          && (lasttimemodified == null || this_feature.getLastModified()
              .compareTo(lasttimemodified) > 0))
        lasttimemodified = this_feature.getLastModified();

      final Location this_feature_location = this_feature.getLocation();

      if(this_feature_location.getRanges().size() > 1)
      {
        throw new Error("internal error - new location should have "
            + "exactly one range");
      }

      final Range new_range = (Range) this_feature_location.getRanges()
          .elementAt(0);

      Qualifier id_qualifier = this_feature.getQualifierByName("ID");
      if(id_qualifier != null)
      {
        String id = (String) (id_qualifier.getValues()).elementAt(0);
        id_range_store.put(id, new_range);
        feature_relationship_rank_store.put(id, rank);
      }

      if(this_feature_location.isComplement())
        new_range_vector.insertElementAt(new_range, 0);
      else
        new_range_vector.add(new_range);

      removeInternal(this_feature);
      qualifier_vector.addAll(this_feature.getQualifiers());
    }

    final Feature first_old_feature = (Feature)gffFeatures.get(0);

    final Location new_location = new Location(new_range_vector,
        first_old_feature.getLocation().isComplement());

    qualifier_vector = mergeQualifiers(qualifier_vector, first_old_feature
        .getLocation().isComplement());

    final GFFStreamFeature new_feature = new GFFStreamFeature(first_old_feature
        .getKey(), new_location, qualifier_vector);

    if(lasttimemodified != null)
      new_feature.setLastModified(lasttimemodified);
    new_feature.setSegmentRangeStore(id_range_store);
    new_feature
        .setFeature_relationship_rank_store(feature_relationship_rank_store);

    // set the ID
    String ID = new_feature.getSegmentID(new_feature.getLocation().getRanges());

    Qualifier id_qualifier = new_feature.getQualifierByName("ID");
    id_qualifier.removeValue((String) (id_qualifier.getValues()).elementAt(0));
    id_qualifier.addValue(ID);

    try
    {
      new_feature.setLocation(new_location);

      final Qualifier gene_qualifier = new_feature.getQualifierByName("gene");

      if(gene_qualifier != null
          && gene_qualifier.getValues().size() > 0
          && ((String) (gene_qualifier.getValues()).elementAt(0))
              .startsWith("Phat"))
      {
        // special case to handle incorrect output of the Phat gene
        // prediction tool
        new_feature.removeQualifierByName("codon_start");
      }
      else
      {
        final Qualifier old_codon_start_qualifier = first_old_feature
            .getQualifierByName("codon_start");

        if(old_codon_start_qualifier != null)
          new_feature.setQualifier(old_codon_start_qualifier);
      }
      forcedAdd(new_feature);
      //gene.addExon(transcript_id, new_feature, true );
      new_set.add(new_feature);

    }
    catch(ReadOnlyException e)
    {
      throw new Error("internal error - unexpected exception: " + e);
    }
    catch(OutOfRangeException e)
    {
      throw new Error("internal error - unexpected exception: " + e);
    }
    catch(EntryInformationException e)
    {
      throw new Error("internal error - unexpected exception: " + e);
    }
  }
  
  /**
   *  Combine the features (which are exons) and delete the orignals from this
   *  Entry.  The key of this hash will be the group name and the value is a
   *  FeatureVector containing the feature that are in that group.  Groups
   *  that have more than one member will be combined.
   **/
  /*private void combineFeaturesFromHash(final Hashtable feature_groups) 
  {
    final Enumeration enumFeat = feature_groups.keys();
    String name;
    FeatureVector feature_group;

    while(enumFeat.hasMoreElements()) 
    {
      name = (String)enumFeat.nextElement();

      feature_group = (FeatureVector)feature_groups.get(name);

      if(feature_group.size() > 1) 
      {
        // combine the features (exons) and delete the orignals

        final RangeVector new_range_vector = new RangeVector();
        QualifierVector qualifier_vector = new QualifierVector();
        Hashtable id_range_store = new Hashtable();
        Timestamp lasttimemodified = null;
        
        for (int i = 0 ; i < feature_group.size() ; ++i) 
        {
          final GFFStreamFeature this_feature =
            (GFFStreamFeature)feature_group.elementAt(i);
          lasttimemodified = this_feature.getLastModified();
          
          final Location this_feature_location = this_feature.getLocation();

          if(this_feature_location.getRanges().size() > 1)
          {
            throw new Error("internal error - new location should have " +
                             "exactly one range");
          }

          final Range new_range =
            (Range)this_feature_location.getRanges().elementAt(0);

          Qualifier id_qualifier = this_feature.getQualifierByName("ID");
          if(id_qualifier != null)
          {
            String id = (String)(id_qualifier.getValues()).elementAt(0);
            id_range_store.put(new_range, id);
          }


          if(this_feature_location.isComplement()) 
            new_range_vector.insertElementAt(new_range, 0);
          else 
            new_range_vector.add(new_range);

          removeInternal(this_feature);
          qualifier_vector.addAll(this_feature.getQualifiers());
        }

        final Feature first_old_feature = feature_group.featureAt(0);

        final Location new_location = new Location(new_range_vector,
                    first_old_feature.getLocation().isComplement());

        qualifier_vector = mergeQualifiers(qualifier_vector,
                                           first_old_feature.getLocation().isComplement());

        final GFFStreamFeature new_feature = new GFFStreamFeature(first_old_feature.getKey(),
                                                             new_location, qualifier_vector);
        
        if(lasttimemodified != null)
          new_feature.setLastModified(lasttimemodified);
        new_feature.setSegmentRangeStore(id_range_store);

        try 
        {
          new_feature.setLocation(new_location);

          final Qualifier gene_qualifier =
            new_feature.getQualifierByName("gene");

          if(gene_qualifier != null &&
             gene_qualifier.getValues().size() > 0 &&
             ((String)(gene_qualifier.getValues()).elementAt(0)).startsWith("Phat"))
          {
            // special case to handle incorrect output of the Phat gene
            // prediction tool
            new_feature.removeQualifierByName("codon_start");
          } 
          else
          {
            final Qualifier old_codon_start_qualifier =
              first_old_feature.getQualifierByName("codon_start");

            if(old_codon_start_qualifier != null)
              new_feature.setQualifier(old_codon_start_qualifier);
          }

          forcedAdd(new_feature);
        } 
        catch(ReadOnlyException e) 
        {
          throw new Error("internal error - unexpected exception: " + e);
        }
        catch(OutOfRangeException e) 
        {
          throw new Error("internal error - unexpected exception: " + e);
        }
        catch(EntryInformationException e) 
        {
          throw new Error("internal error - unexpected exception: " + e);
        }
      }
    }
  }*/

  private QualifierVector mergeQualifiers(QualifierVector qualifier_vector,
                                          boolean complement)
  {
    QualifierVector merge_qualifier_vector = new QualifierVector();
    boolean seen = false;

    for(int i = 0 ; i < qualifier_vector.size() ; ++i)
    {
      Qualifier qual = (Qualifier)qualifier_vector.elementAt(i);
 
      if(qual.getName().equals("codon_start"))
      {
        if(!complement && !seen)
        {
          merge_qualifier_vector.addElement(qual);
          seen = true;
        }
        else if(complement)
          merge_qualifier_vector.setQualifier(qual);
      }
      else if(qual.getName().equals("Alias"))
      { 
        final Qualifier id_qualifier = 
          merge_qualifier_vector.getQualifierByName("Alias");

        if(id_qualifier == null)
          merge_qualifier_vector.addElement(qual);
        else
        {
          String id1 = (String)(id_qualifier.getValues()).elementAt(0);
          String id2 = (String)(qual.getValues()).elementAt(0);
          id_qualifier.removeValue(id1);
          id_qualifier.addValue(id1+","+id2);
        }
      }
      else if(!qual.getName().equals("ID") &&
              !qual.getName().equals("feature_id"))
        merge_qualifier_vector.setQualifier(qual);
    }
    return merge_qualifier_vector;
  }

}