/**
* @param accession
- * the accession to set
+ * the accession to set
*/
public void setAccession(String accession)
{
/**
* @param dbRefs
- * the dbRefs to set
+ * the dbRefs to set
*/
public void setDbRefs(Vector dbRefs)
{
/**
* @param desc
- * the desc to set
+ * the desc to set
*/
public void setDesc(String desc)
{
/**
* @param features
- * the features to set
+ * the features to set
*/
public void setFeatures(Vector features)
{
/**
* @param keywords
- * the keywords to set
+ * the keywords to set
*/
public void setKeywords(Vector keywords)
{
/**
* @param lastUpdated
- * the lastUpdated to set
+ * the lastUpdated to set
*/
public void setLastUpdated(String lastUpdated)
{
/**
* @param refs
- * the refs to set
+ * the refs to set
*/
public void setRefs(Vector refs)
{
/**
* @param releaseCreated
- * the releaseCreated to set
+ * the releaseCreated to set
*/
public void setRcreated(String releaseCreated)
{
/**
* @param releaseLastUpdated
- * the releaseLastUpdated to set
+ * the releaseLastUpdated to set
*/
public void setRLastUpdated(String releaseLastUpdated)
{
/**
* @param sequence
- * the sequence to set
+ * the sequence to set
*/
public void setSequence(EmblSequence sequence)
{
/**
* @param taxDivision
- * the taxDivision to set
+ * the taxDivision to set
*/
public void setTaxDivision(String taxDivision)
{
/**
* @param version
- * the version to set
+ * the version to set
*/
public void setVersion(String version)
{
* EMBL Feature support is limited. The text below is included for the benefit
* of any developer working on improving EMBL feature import in Jalview.
* Extract from EMBL feature specification see
- * http://www.embl-ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
- * 3.5 Location 3.5.1 Purpose
+ * http://www.embl-ebi.ac.uk/embl/Documentation
+ * /FT_definitions/feature_table.html 3.5 Location 3.5.1 Purpose
*
* The location indicates the region of the presented sequence which
* corresponds to a feature.
*
* join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
* with the region 100..202 of remote entry J00194
- *
*/
/**
* Recover annotated sequences from EMBL file
*
* @param noNa
- * don't return nucleic acid sequences
+ * don't return nucleic acid sequences
* @param sourceDb
- * TODO
+ * TODO
* @param noProtein
- * don't return any translated protein sequences marked in
- * features
+ * don't return any translated protein sequences marked in features
* @return dataset sequences with DBRefs and features - DNA always comes first
*/
public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
// pointer exception
dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
dna.setDescription(desc);
- dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
- // TODO: add mapping for parentAccession attribute
+ DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
+ dna.addDBRef(retrievedref);
+ // add map to indicate the sequence is a valid coordinate frame for the
+ // dbref
+ retrievedref.setMap(new Mapping(null, new int[]
+ { 1, dna.getLength() }, new int[]
+ { 1, dna.getLength() }, 1, 1));
// TODO: transform EMBL Database refs to canonical form
if (dbRefs != null)
for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
* decorate it with annotations.
*
* @param feature
- * coding feature
+ * coding feature
* @param sourceDb
- * source database for the EMBLXML
+ * source database for the EMBLXML
* @param seqs
- * place where sequences go
+ * place where sequences go
* @param dna
- * parent dna sequence for this record
+ * parent dna sequence for this record
* @param noPeptide
- * flag for generation of Peptide sequence objects
+ * flag for generation of Peptide sequence objects
*/
private void parseCodingFeature(EmblFeature feature, String sourceDb,
Vector seqs, Sequence dna, boolean noPeptide)
}
}
Sequence product = null;
+ int origxon[], sxpos = -1, sxstart, sxstop;
+ // first adjust range for codon start attribute
+ if (prstart > 1)
+ {
+ origxon = new int[exon.length];
+ System.arraycopy(exon, 0, origxon, 0, exon.length);
+ int cdspos = 0;
+ for (int x = 0; x < exon.length && sxpos == -1; x += 2)
+ {
+ cdspos += exon[x + 1] - exon[x] + 1;
+ if (prstart <= cdspos)
+ {
+ sxpos = x;
+ sxstart = exon[x];
+ sxstop = exon[x + 1];
+ // and adjust start boundary of first exon.
+ exon[x] = exon[x + 1] - cdspos + prstart;
+ break;
+ }
+ }
+
+ if (sxpos > 0)
+ {
+ int[] nxon = new int[exon.length - sxpos];
+ System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos);
+ exon = nxon;
+ }
+ }
+
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
- product = new Sequence(prid, prseq, prstart, prstart + prseq.length()
- - 1);
+ product = new Sequence(prid, prseq, 1, prseq.length());
product
.setDescription(((prname.length() == 0) ? "Protein Product from "
+ sourceDb
System.err
.println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
+ sourceDb + ":" + getAccession() + ")");
- if (prseq.length() * 3 == dna.getSequence().length)
+ if (prseq.length() * 3 == (1-prstart + dna.getSequence().length))
{
+ System.err
+ .println("Not allowing for additional stop codon at end of cDNA fragment... !");
// this might occur for CDS sequences where no features are
// marked.
exon = new int[]
- { dna.getStart(), dna.getEnd() };
+ { dna.getStart() + (prstart - 1), dna.getEnd() };
map = new jalview.datamodel.Mapping(product, exon, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ { 1, prseq.length() }, 3, 1);
}
- if ((prseq.length() + 1) * 3 == dna.getSequence().length)
+ if ((prseq.length() + 1) * 3 == (1-prstart + dna.getSequence().length))
{
+ System.err
+ .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
exon = new int[]
- { dna.getStart(), dna.getEnd() - 3 };
+ { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
map = new jalview.datamodel.Mapping(product, exon, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ { 1, prseq.length() }, 3, 1);
}
}
else
else
{
map = new jalview.datamodel.Mapping(product, exon, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ { 1, prseq.length() }, 3, 1);
// reconstruct the EMBLCDS entry
DBRefEntry pcdnaref = new DBRefEntry();
pcdnaref.setAccessionId(prid);
pcdnaref.setSource(DBRefSource.EMBLCDS);
pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
jalview.util.MapList mp = new jalview.util.MapList(new int[]
- { 1 + (prstart - 1) * 3,
- 1 + (prstart - 1) * 3 + (prseq.length() - 1) * 3 }, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ { 1, prseq.length() },
+ new int[]
+ { 1 + (prstart - 1),
+ (prstart - 1) + 3 * prseq.length() }, 1, 3);
+ // { 1 + (prstart - 1) * 3,
+ // 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
+ // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);
pcdnaref.setMap(new Mapping(mp));
if (product != null)
product.addDBRef(pcdnaref);