package jalview.datamodel.xdb.embl;
import jalview.analysis.SequenceIdMatcher;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.FeatureProperties;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
+import jalview.util.DnaUtils;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.StringUtils;
+import java.text.ParseException;
import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
* Castor binding file
*
* For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
+ * http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
*
* @see embl_mapping.xml
*/
String accession;
- String version;
+ String entryVersion;
- String taxDivision;
+ String sequenceVersion;
- String desc;
+ String dataClass;
- String rCreated;
+ String moleculeType;
- String rLastUpdated;
+ String topology;
- String lastUpdated;
+ String sequenceLength;
+
+ String taxonomicDivision;
+
+ String description;
+
+ String firstPublicDate;
+
+ String firstPublicRelease;
+
+ String lastUpdatedDate;
+
+ String lastUpdatedRelease;
Vector<String> keywords;
}
/**
- * @return the desc
- */
- public String getDesc()
- {
- return desc;
- }
-
- /**
- * @param desc
- * the desc to set
- */
- public void setDesc(String desc)
- {
- this.desc = desc;
- }
-
- /**
* @return the features
*/
public Vector<EmblFeature> getFeatures()
}
/**
- * @return the lastUpdated
- */
- public String getLastUpdated()
- {
- return lastUpdated;
- }
-
- /**
- * @param lastUpdated
- * the lastUpdated to set
- */
- public void setLastUpdated(String lastUpdated)
- {
- this.lastUpdated = lastUpdated;
- }
-
- /**
- * @return the releaseCreated
- */
- public String getRCreated()
- {
- return rCreated;
- }
-
- /**
- * @param releaseCreated
- * the releaseCreated to set
- */
- public void setRCreated(String releaseCreated)
- {
- this.rCreated = releaseCreated;
- }
-
- /**
- * @return the releaseLastUpdated
- */
- public String getRLastUpdated()
- {
- return rLastUpdated;
- }
-
- /**
- * @param releaseLastUpdated
- * the releaseLastUpdated to set
- */
- public void setRLastUpdated(String releaseLastUpdated)
- {
- this.rLastUpdated = releaseLastUpdated;
- }
-
- /**
* @return the sequence
*/
public EmblSequence getSequence()
}
/**
- * @return the taxDivision
- */
- public String getTaxDivision()
- {
- return taxDivision;
- }
-
- /**
- * @param taxDivision
- * the taxDivision to set
- */
- public void setTaxDivision(String taxDivision)
- {
- this.taxDivision = taxDivision;
- }
-
- /**
- * @return the version
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- */
- public void setVersion(String version)
- {
- this.version = version;
- }
-
- /**
* Recover annotated sequences from EMBL file
*
* @param sourceDb
*/
public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
{
- SequenceI dna = new Sequence(sourceDb + "|" + accession,
- sequence.getSequence());
- dna.setDescription(desc);
- DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession);
+ SequenceI dna = makeSequence(sourceDb);
+ if (dna == null)
+ {
+ return null;
+ }
+ dna.setDescription(description);
+ DBRefEntry retrievedref = new DBRefEntry(sourceDb,
+ getSequenceVersion(), 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
+
+
+ /*
+ * transform EMBL Database refs to canonical form
+ */
if (dbRefs != null)
{
for (DBRefEntry dbref : dbRefs)
{
+ dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
dna.addDBRef(dbref);
}
}
+ SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
try
{
for (EmblFeature feature : features)
{
- if (feature.dbRefs != null)
- {
- for (DBRefEntry dbref : feature.dbRefs)
- {
- dna.addDBRef(dbref);
- }
- }
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
- parseCodingFeature(feature, sourceDb, dna, peptides);
+ parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
}
}
} catch (Exception e)
}
/**
+ * @param sourceDb
+ * @return
+ */
+ SequenceI makeSequence(String sourceDb)
+ {
+ if (sequence == null)
+ {
+ System.err.println("No sequence was returned for ENA accession "
+ + accession);
+ return null;
+ }
+ SequenceI dna = new Sequence(sourceDb + "|" + accession,
+ sequence.getSequence());
+ return dna;
+ }
+
+ /**
* Extracts coding region and product from a CDS feature and properly decorate
* it with annotations.
*
* parent dna sequence for this record
* @param peptides
* list of protein product sequences for Embl entry
+ * @param matcher
+ * helper to match xrefs in already retrieved sequences
*/
void parseCodingFeature(EmblFeature feature, String sourceDb,
- SequenceI dna, List<SequenceI> peptides)
+ SequenceI dna, List<SequenceI> peptides, SequenceIdMatcher matcher)
{
boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
- int[] exon = getCdsRanges(feature);
+ int[] exons = getCdsRanges(feature);
- String prseq = null;
- String prname = "";
- String prid = null;
+ String translation = null;
+ String proteinName = "";
+ String proteinId = null;
Map<String, String> vals = new Hashtable<String, String>();
- SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
/*
* codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
if (qname.equals("translation"))
{
// remove all spaces (precompiled String.replaceAll(" ", ""))
- prseq = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll("");
+ translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll("");
}
else if (qname.equals("protein_id"))
{
- prid = q.getValues()[0];
+ proteinId = q.getValues()[0].trim();
}
else if (qname.equals("codon_start"))
{
try
{
- codonStart = Integer.parseInt(q.getValues()[0]);
+ codonStart = Integer.parseInt(q.getValues()[0].trim());
} catch (NumberFormatException e)
{
System.err.println("Invalid codon_start in XML for "
else if (qname.equals("product"))
{
// sometimes name is returned e.g. for V00488
- prname = q.getValues()[0];
+ proteinName = q.getValues()[0].trim();
}
else
{
}
}
- DBRefEntry protEMBLCDS = null;
- exon = MappingUtils.removeStartPositions(codonStart - 1, exon);
- boolean noProteinDbref = true;
+ DBRefEntry proteinToEmblProteinRef = null;
+ exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
SequenceI product = null;
- Mapping map = null;
- if (prseq != null && prname != null && prid != null)
+ Mapping dnaToProteinMapping = null;
+ if (translation != null && proteinName != null && proteinId != null)
{
+ int translationLength = translation.length();
+
/*
* look for product in peptides list, if not found, add it
*/
- product = matcher.findIdMatch(prid);
+ product = matcher.findIdMatch(proteinId);
if (product == null)
{
- product = new Sequence(prid, prseq, 1, prseq.length());
- product.setDescription(((prname.length() == 0) ? "Protein Product from "
+ product = new Sequence(proteinId, translation, 1, translationLength);
+ product.setDescription(((proteinName.length() == 0) ? "Protein Product from "
+ sourceDb
- : prname));
+ : proteinName));
peptides.add(product);
matcher.add(product);
}
// we have everything - create the mapping and perhaps the protein
// sequence
- if (exon == null || exon.length == 0)
+ if (exons == null || exons.length == 0)
{
+ /*
+ * workaround until we handle dna location for CDS sequence
+ * e.g. location="X53828.1:60..1058" correctly
+ */
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 == (1 - codonStart + dna.getSequence().length))
+ if (translationLength * 3 == (1 - codonStart + 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() + (codonStart - 1),
+ // this might occur for CDS sequences where no features are marked
+ exons = new int[] { dna.getStart() + (codonStart - 1),
dna.getEnd() };
- map = new Mapping(product, exon, new int[] { 1, prseq.length() },
- 3, 1);
+ dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
+ translationLength }, 3, 1);
}
- if ((prseq.length() + 1) * 3 == (1 - codonStart + dna.getSequence().length))
+ if ((translationLength + 1) * 3 == (1 - codonStart + 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() + (codonStart - 1),
+ exons = new int[] { dna.getStart() + (codonStart - 1),
dna.getEnd() - 3 };
- map = new Mapping(product, exon, new int[] { 1, prseq.length() },
- 3, 1);
+ dnaToProteinMapping = new Mapping(product, exons, new int[] { 1,
+ translationLength }, 3, 1);
}
}
else
else
{
// final product length truncation check
- // TODO should from range include stop codon even if not in protein
- // in order to include stop codon in CDS sequence (as done for
- // Ensembl)?
- int[] cdsRanges = adjustForProteinLength(prseq.length(), exon);
- map = new Mapping(product, cdsRanges, new int[] { 1,
- prseq.length() }, 3, 1);
- // reconstruct the EMBLCDS entry
- // TODO: this is only necessary when there codon annotation is
- // complete (I think JBPNote)
- DBRefEntry pcdnaref = new DBRefEntry();
- pcdnaref.setAccessionId(prid);
- pcdnaref.setSource(DBRefSource.EMBLCDS);
- pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
- MapList mp = new MapList(new int[] { 1, prseq.length() },
- new int[] { 1 + (codonStart - 1),
- (codonStart - 1) + 3 * prseq.length() }, 1, 3);
- pcdnaref.setMap(new Mapping(mp));
+ int[] cdsRanges = adjustForProteinLength(translationLength, exons);
+ dnaToProteinMapping = new Mapping(product, cdsRanges, new int[] {
+ 1, translationLength }, 3, 1);
if (product != null)
{
- product.addDBRef(pcdnaref);
- protEMBLCDS = new DBRefEntry(pcdnaref);
- protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
- product.addDBRef(protEMBLCDS);
+ /*
+ * make xref with mapping from protein to EMBL dna
+ */
+ DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
+ getSequenceVersion(), proteinId, new Mapping(
+ dnaToProteinMapping.getMap().getInverse()));
+ product.addDBRef(proteinToEmblRef);
+
+ /*
+ * make xref from protein to EMBLCDS; we assume here that the
+ * CDS sequence version is same as dna sequence (?!)
+ */
+ MapList proteinToCdsMapList = new MapList(new int[] { 1,
+ translationLength }, new int[] { 1 + (codonStart - 1),
+ (codonStart - 1) + 3 * translationLength }, 1, 3);
+ DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
+ DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
+ new Mapping(proteinToCdsMapList));
+ product.addDBRef(proteinToEmblCdsRef);
+
+ /*
+ * make 'direct' xref from protein to EMBLCDSPROTEIN
+ */
+ proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
+ proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
+ proteinToEmblProteinRef.setMap(null);
+ product.addDBRef(proteinToEmblProteinRef);
}
}
}
- // add cds feature to dna seq - this may include the stop codon
- for (int xint = 0; exon != null && xint < exon.length; xint += 2)
+
+ /*
+ * add cds features to dna sequence
+ */
+ for (int xint = 0; exons != null && xint < exons.length; xint += 2)
{
- SequenceFeature sf = makeCdsFeature(exon, xint, prname, prid, vals,
- codonStart);
+ SequenceFeature sf = makeCdsFeature(exons, xint, proteinName,
+ proteinId, vals, codonStart);
sf.setType(feature.getName()); // "CDS"
+ sf.setEnaLocation(feature.getLocation());
sf.setFeatureGroup(sourceDb);
dna.addSequenceFeature(sf);
}
}
/*
- * add dbRefs to sequence, and mappings for Uniprot xrefs
+ * add feature dbRefs to sequence, and mappings for Uniprot xrefs
*/
+ boolean hasUniprotDbref = false;
if (feature.dbRefs != null)
{
boolean mappingUsed = false;
for (DBRefEntry ref : feature.dbRefs)
{
- ref.setSource(DBRefUtils.getCanonicalName(ref.getSource()));
- if (ref.getSource().equals(DBRefSource.UNIPROT))
+ /*
+ * ensure UniProtKB/Swiss-Prot converted to UNIPROT
+ */
+ String source = DBRefUtils.getCanonicalName(ref.getSource());
+ ref.setSource(source);
+ DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(), ref.getVersion(), ref
+ .getAccessionId());
+ if (source.equals(DBRefSource.UNIPROT))
{
String proteinSeqName = DBRefSource.UNIPROT + "|"
+ ref.getAccessionId();
- if (map != null && map.getTo() != null)
+ if (dnaToProteinMapping != null && dnaToProteinMapping.getTo() != null)
{
if (mappingUsed)
{
* two or more Uniprot xrefs for the same CDS -
* each needs a distinct Mapping (as to a different sequence)
*/
- map = new Mapping(map);
+ dnaToProteinMapping = new Mapping(dnaToProteinMapping);
}
mappingUsed = true;
/*
* try to locate the protein mapped to (possibly by a
- * previous CDS feature)
+ * previous CDS feature); if not found, construct it from
+ * the EMBL translation
*/
SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
if (proteinSeq == null)
matcher.add(proteinSeq);
peptides.add(proteinSeq);
}
- map.setTo(proteinSeq);
- map.getTo().addDBRef(
- new DBRefEntry(ref.getSource(), ref.getVersion(), ref
- .getAccessionId()));
- ref.setMap(map);
+ dnaToProteinMapping.setTo(proteinSeq);
+ dnaToProteinMapping.setMappedFromId(proteinId);
+ proteinSeq.addDBRef(proteinDbRef);
+ ref.setMap(dnaToProteinMapping);
}
- noProteinDbref = false;
+ hasUniprotDbref = true;
}
if (product != null)
{
- DBRefEntry pref = new DBRefEntry(ref.getSource(),
- ref.getVersion(), ref.getAccessionId());
+ /*
+ * copy feature dbref to our protein product
+ */
+ DBRefEntry pref = proteinDbRef;
pref.setMap(null); // reference is direct
product.addDBRef(pref);
// Add converse mapping reference
- if (map != null)
+ if (dnaToProteinMapping != null)
{
- Mapping pmap = new Mapping(dna, map.getMap().getInverse());
- pref = new DBRefEntry(sourceDb, getVersion(),
+ Mapping pmap = new Mapping(dna, dnaToProteinMapping.getMap()
+ .getInverse());
+ pref = new DBRefEntry(sourceDb, getSequenceVersion(),
this.getAccession());
pref.setMap(pmap);
- if (map.getTo() != null)
+ if (dnaToProteinMapping.getTo() != null)
{
- map.getTo().addDBRef(pref);
+ dnaToProteinMapping.getTo().addDBRef(pref);
}
}
}
dna.addDBRef(ref);
}
- if (noProteinDbref && product != null)
+ }
+
+ /*
+ * if we have a product (translation) but no explicit Uniprot dbref
+ * (example: EMBL AAFI02000057 protein_id EAL65544.1)
+ * then construct mappings to an assumed EMBLCDSPROTEIN accession
+ */
+ if (!hasUniprotDbref && product != null)
+ {
+ if (proteinToEmblProteinRef == null)
{
- // add protein coding reference to dna sequence so xref matches
- if (protEMBLCDS == null)
- {
- protEMBLCDS = new DBRefEntry();
- protEMBLCDS.setAccessionId(prid);
- protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
- protEMBLCDS.setVersion(getVersion());
- protEMBLCDS
- .setMap(new Mapping(product, map.getMap().getInverse()));
- }
- product.addDBRef(protEMBLCDS);
+ // assuming CDSPROTEIN sequence version = dna version (?!)
+ proteinToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
+ }
+ product.addDBRef(proteinToEmblProteinRef);
- // Add converse mapping reference
- if (map != null)
- {
- Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
- .getInverse());
- DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
- ncMap.setMap(pmap);
- if (map.getTo() != null)
- {
- dna.addDBRef(ncMap);
- }
- }
+ if (dnaToProteinMapping != null
+ && dnaToProteinMapping.getTo() != null)
+ {
+ DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
+ DBRefSource.EMBLCDSProduct, getSequenceVersion(), proteinId);
+ dnaToEmblProteinRef.setMap(dnaToProteinMapping);
+ dnaToProteinMapping.setMappedFromId(proteinId);
+ dna.addDBRef(dnaToEmblProteinRef);
}
}
}
}
/**
- * Returns the CDS positions as a list of [start, end, start, end...]
+ * Returns the CDS positions as a single array of [start, end, start, end...]
* positions. If on the reverse strand, these will be in descending order.
*
* @param feature
*/
protected int[] getCdsRanges(EmblFeature feature)
{
- if (feature.locations == null)
+ if (feature.location == null)
{
return new int[] {};
}
- int cdsBoundaryCount = 0; // count of all start/stop locations
- int[][] cdsLocations = new int[feature.locations.size()][];
- int locationNumber = 0;
- for (EmblFeatureLocations loc : feature.locations)
+
+ try
{
- int[] locationRanges = loc.getElementRanges(accession);
- cdsLocations[locationNumber++] = locationRanges;
- cdsBoundaryCount += locationRanges.length;
- }
- int[] cdsRanges = new int[cdsBoundaryCount];
- int copyTo = 0;
- for (int[] ranges : cdsLocations)
+ List<int[]> ranges = DnaUtils.parseLocation(feature.location);
+ return listToArray(ranges);
+ } catch (ParseException e)
{
- System.arraycopy(ranges, 0, cdsRanges, copyTo, ranges.length);
- copyTo += ranges.length;
+ Cache.log.warn(String.format(
+ "Not parsing inexact CDS location %s in ENA %s",
+ feature.location, this.accession));
+ return new int[] {};
}
- return cdsRanges;
+ }
+ /**
+ * Converts a list of [start, end] ranges to a single array of [start, end,
+ * start, end ...]
+ *
+ * @param ranges
+ * @return
+ */
+ int[] listToArray(List<int[]> ranges)
+ {
+ int[] result = new int[ranges.size() * 2];
+ int i = 0;
+ for (int[] range : ranges)
+ {
+ result[i++] = range[0];
+ result[i++] = range[1];
+ }
+ return result;
}
/**
- * truncate the last exon interval to the prlength'th codon
+ * Truncates (if necessary) the exon intervals to match 3 times the length of
+ * the protein; also accepts 3 bases longer (for stop codon not included in
+ * protein)
*
- * @param prlength
+ * @param proteinLength
* @param exon
- * @return new exon
+ * an array of [start, end, start, end...] intervals
+ * @return the same array (if unchanged) or a truncated copy
*/
- static int[] adjustForProteinLength(int prlength, int[] exon)
+ static int[] adjustForProteinLength(int proteinLength, int[] exon)
{
- if (prlength <= 0 || exon == null)
+ if (proteinLength <= 0 || exon == null)
{
return exon;
}
- int desiredCdsLength = prlength * 3;
+ int expectedCdsLength = proteinLength * 3;
int exonLength = MappingUtils.getLength(Arrays.asList(exon));
/*
- * assuming here exon might include stop codon in addition to protein codons
+ * if exon length matches protein, or is shorter, or longer by the
+ * length of a stop codon (3 bases), then leave it unchanged
*/
- if (desiredCdsLength == exonLength
- || desiredCdsLength == exonLength - 3)
+ if (expectedCdsLength >= exonLength
+ || expectedCdsLength == exonLength - 3)
{
return exon;
}
for (int x = 0; x < exon.length; x += 2)
{
cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
- if (desiredCdsLength <= cdspos)
+ if (expectedCdsLength <= cdspos)
{
// advanced beyond last codon.
sxpos = x;
- if (desiredCdsLength != cdspos)
+ if (expectedCdsLength != cdspos)
{
// System.err
// .println("Truncating final exon interval on region by "
*/
if (exon[x + 1] >= exon[x])
{
- endxon = exon[x + 1] - cdspos + desiredCdsLength;
+ endxon = exon[x + 1] - cdspos + expectedCdsLength;
}
else
{
- endxon = exon[x + 1] + cdspos - desiredCdsLength;
+ endxon = exon[x + 1] + cdspos - expectedCdsLength;
}
break;
}
}
return exon;
}
+
+ public String getSequenceVersion()
+ {
+ return sequenceVersion;
+ }
+
+ public void setSequenceVersion(String sequenceVersion)
+ {
+ this.sequenceVersion = sequenceVersion;
+ }
+
+ public String getSequenceLength()
+ {
+ return sequenceLength;
+ }
+
+ public void setSequenceLength(String sequenceLength)
+ {
+ this.sequenceLength = sequenceLength;
+ }
+
+ public String getEntryVersion()
+ {
+ return entryVersion;
+ }
+
+ public void setEntryVersion(String entryVersion)
+ {
+ this.entryVersion = entryVersion;
+ }
+
+ public String getMoleculeType()
+ {
+ return moleculeType;
+ }
+
+ public void setMoleculeType(String moleculeType)
+ {
+ this.moleculeType = moleculeType;
+ }
+
+ public String getTopology()
+ {
+ return topology;
+ }
+
+ public void setTopology(String topology)
+ {
+ this.topology = topology;
+ }
+
+ public String getTaxonomicDivision()
+ {
+ return taxonomicDivision;
+ }
+
+ public void setTaxonomicDivision(String taxonomicDivision)
+ {
+ this.taxonomicDivision = taxonomicDivision;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ public String getFirstPublicDate()
+ {
+ return firstPublicDate;
+ }
+
+ public void setFirstPublicDate(String firstPublicDate)
+ {
+ this.firstPublicDate = firstPublicDate;
+ }
+
+ public String getFirstPublicRelease()
+ {
+ return firstPublicRelease;
+ }
+
+ public void setFirstPublicRelease(String firstPublicRelease)
+ {
+ this.firstPublicRelease = firstPublicRelease;
+ }
+
+ public String getLastUpdatedDate()
+ {
+ return lastUpdatedDate;
+ }
+
+ public void setLastUpdatedDate(String lastUpdatedDate)
+ {
+ this.lastUpdatedDate = lastUpdatedDate;
+ }
+
+ public String getLastUpdatedRelease()
+ {
+ return lastUpdatedRelease;
+ }
+
+ public void setLastUpdatedRelease(String lastUpdatedRelease)
+ {
+ this.lastUpdatedRelease = lastUpdatedRelease;
+ }
+
+ public String getDataClass()
+ {
+ return dataClass;
+ }
+
+ public void setDataClass(String dataClass)
+ {
+ this.dataClass = dataClass;
+ }
}
git://source.jalview.org / jalview.git / blobdiff