/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3
* of the License, or (at your option) any later version.
*
* Jalview 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 Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import java.util.HashMap;
import java.util.Map;
import com.stevesoft.pat.Regex;
/**
* A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
* sequence that is transcribed to RNA, but not necessarily translated to
* protein)
*
* @author gmcarstairs
*
*/
public class EnsemblCdna extends EnsemblSeqProxy
{
/*
* accepts ENST or ENSTG with 11 digits
* or ENSMUST or similar for other species
* or CCDSnnnnn.nn with at least 3 digits
*/
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
private static Map params = new HashMap();
static
{
params.put("object_type", "transcript");
}
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
*/
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
/**
* Default constructor (to use rest.ensembl.org)
*/
public EnsemblCdna()
{
super();
}
/**
* Constructor given the target domain to fetch data from
*
* @param d
*/
public EnsemblCdna(String d)
{
super(d);
}
@Override
public String getDbName()
{
return "ENSEMBL (CDNA)";
}
@Override
protected EnsemblSeqType getSourceEnsemblType()
{
return EnsemblSeqType.CDNA;
}
@Override
public Regex getAccessionValidator()
{
return ACCESSION_REGEX;
}
@Override
protected EnsemblFeatureType[] getFeaturesToFetch()
{
return FEATURES_TO_FETCH;
}
/**
* Answers true unless the feature type is 'transcript' (or a sub-type in the
* Sequence Ontology).
*/
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
if (isTranscript(sf.getType()))
{
return false;
}
return featureMayBelong(sf, accessionId);
}
/**
* Answers true if the sequence feature type is 'exon' (or a subtype of exon
* in the Sequence Ontology), and the Parent of the feature is the transcript
* we are retrieving
*/
@Override
protected boolean identifiesSequence(SequenceFeature sf, String accId)
{
if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
SequenceOntologyI.EXON))
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))
{
return true;
}
}
return false;
}
/**
* Parameter object_type=cdna added to ensure cdna and not peptide is returned
* (JAL-2529)
*/
@Override
protected Map getAdditionalParameters()
{
return params;
}
}