src/org/gel/mauve/format/RichDelegatingSequence.java

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package org.gel.mauve.format;

import java.io.File;

import java.io.FileNotFoundException;
import java.util.Set;

import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.symbol.SymbolList;
import org.biojava.utils.ChangeVetoException;
import org.biojavax.Comment;
import org.biojavax.Namespace;
import org.biojavax.RankedCrossRef;
import org.biojavax.RankedDocRef;
import org.biojavax.RichAnnotation;
import org.biojavax.bio.BioEntryRelationship;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.taxa.NCBITaxon;
import org.gel.mauve.SupportedFormat;

public class RichDelegatingSequence extends DelegatingSequence implements
                RichSequence {
        
    public RichDelegatingSequence(Sequence s, SupportedFormat format, File source, int index) throws FileNotFoundException
    {
        super(s,format,source,index);
        richInit(s);
    }
    
    void richInit(Sequence s)
    {
        RichSequence rs = (RichSequence)s;
        featureSet = rs.getFeatureSet();
        seqVersion = rs.getSeqVersion();
        intSymList = rs.getInternalSymbolList();
        accession = rs.getAccession();
        comments = rs.getComments();
        description = rs.getDescription();
        division = rs.getDivision();
        identifier = rs.getIdentifier();
        bioname = rs.getName();
        ns = rs.getNamespace();
        rankedDocRefs = rs.getRankedDocRefs();
        relationships = rs.getRelationships();
        taxon = rs.getTaxon();
        bioVersion = rs.getVersion();
        noteSet = rs.getNoteSet();
        rankedCrossRefs = rs.getRankedCrossRefs();
        circular = rs.getCircular();
    }

    Set featureSet = null;
    Double seqVersion = null;
    SymbolList intSymList = null;
    
    //  RichSequence methods
        public Double getSeqVersion(){
                return seqVersion;
        }
        public void setSeqVersion(Double version) throws ChangeVetoException{
        throw new ChangeVetoException();
        }
        public Set getFeatureSet(){
                return featureSet;
        }
        public void setFeatureSet(Set s) throws ChangeVetoException{
        throw new ChangeVetoException();
        }
        public void setCircular(boolean circular) throws ChangeVetoException{
        throw new ChangeVetoException();
        }
        public boolean getCircular(){
                return circular;
        }
        public SymbolList getInternalSymbolList(){
                return intSymList;
        }
        

        // BioEntry methods
        public void addComment(Comment comment) throws ChangeVetoException {
        throw new ChangeVetoException();
        }
        public void addRankedDocRef(RankedDocRef docref) throws ChangeVetoException {        
                throw new ChangeVetoException();
        }
        public void addRelationship(BioEntryRelationship relation) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        String accession = null;
        Set comments = null;
        String description = null;
        String division = null;
        String identifier = null;
        String bioname = null;
        Namespace ns = null;
        Set rankedDocRefs = null;
        Set relationships = null;
        NCBITaxon taxon = null;
        int bioVersion = 0;

        public String getAccession(){return accession;}
        public Set getComments(){return comments;}
        public String getDescription(){return description;}
        public String getDivision(){return division;}
        public String getIdentifier(){return identifier;}
        public String getName(){return bioname;}
        public Namespace getNamespace(){return ns;}
        public Set getRankedDocRefs(){return rankedDocRefs;}
        public Set getRelationships(){return relationships;}
        public NCBITaxon getTaxon(){return taxon;}
        public int getVersion(){return bioVersion;}
        public void removeComment(Comment comment) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        public void removeRankedDocRef(RankedDocRef docref) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        public void removeRelationship(BioEntryRelationship relation) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        public void setDescription(String description) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        public void setDivision(String division) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        public void setIdentifier(String identifier) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        public void setTaxon(NCBITaxon taxon) throws ChangeVetoException {
                throw new ChangeVetoException();
        }

        // comparable methods
        public int compareTo(Object o){
                return -1;
        }
        
        // RichAnnotatable methods
        Set noteSet = null;
        public Set getNoteSet(){ return noteSet; }
        public void setNoteSet(Set notes) throws ChangeVetoException {
                throw new ChangeVetoException();
        }
        
        // RankedCrossRefable methods
        Set rankedCrossRefs = null;
        public Set getRankedCrossRefs()
    {
                return rankedCrossRefs;
    }
        public void setRankedCrossRefs(Set refs) throws ChangeVetoException
    {
                throw new ChangeVetoException();
    }
        public void addRankedCrossRef(RankedCrossRef crossref) throws ChangeVetoException
    {           
                throw new ChangeVetoException();
    }
        public void removeRankedCrossRef(RankedCrossRef crossref) throws ChangeVetoException
    {           
                throw new ChangeVetoException();
    }

        public RichAnnotation getRichAnnotation() {
                // TODO Auto-generated method stub
                return null;
        }
}

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