/**
* @return return/create item of class seqClsName for given identifier
* @throws ObjectStoreException if the Item can't be stored
*/
private Item getSeq(String id) throws ObjectStoreException {
// the seqHandler may have changed the id used, e.g. if using an IdResolver
String identifier = sequenceHandler.getSeqIdentifier(id);
if (identifier == null) {
return null;
}
// if (identifier.startsWith("chr")) {
// identifier = identifier.substring(3);
// }
Item seq = seqs.get(identifier);
if (seq == null) {
seq = sequenceHandler.makeSequenceItem(this, identifier);
// sequence handler may choose not to create sequence
if (seq != null) {
seq.addReference(getOrgRef());
store(seq);
seqs.put(identifier, seq);
}
}
handler.setSequence(seq);
return seq;
}
/**
* process GFF3 record and give a xml presentation
*
* @param record GFF3Record
* @throws ObjectStoreException if an error occurs storing items
*/
public void process(GFF3Record record) throws ObjectStoreException {
String identifier = record.getId();
String refId = identifierMap.get(identifier);
// get rid of previous record Items from handler
handler.clear();
List<?> names = record.getNames();
Item seq = getSeq(record.getSequenceID());
String term = record.getType();
String className = TypeUtil.javaiseClassName(term);
String fullClassName = tgtModel.getPackageName() + "." + className;
ClassDescriptor cd = tgtModel.getClassDescriptorByName(fullClassName);
if (cd == null) {
throw new IllegalArgumentException(
"no class found in model for: "
+ className
+ " (original GFF record type: "
+ term
+ ") for "
+ "record: "
+ record);
}
Set<Item> synonymsToAdd = new HashSet<Item>();
Item feature = null;
// new feature
if (refId == null) {
feature = createItem(className);
refId = feature.getIdentifier();
}
if (!"chromosome".equals(record.getType()) && seq != null) {
boolean makeLocation =
record.getStart() >= 1
&& record.getEnd() >= 1
&& !dontCreateLocations
&& handler.createLocations(record);
if (makeLocation) {
Item location = getLocation(record, refId, seq, cd);
if (feature == null) {
// this feature has already been created and stored
// we only wanted the location, we're done here.
store(location);
return;
}
int length = getLength(record);
feature.setAttribute("length", String.valueOf(length));
handler.setLocation(location);
if ("Chromosome".equals(seqClsName)
&& (cd.getFieldDescriptorByName("chromosome") != null)) {
feature.setReference("chromosome", seq.getIdentifier());
feature.setReference("chromosomeLocation", location);
}
}
}
if (feature == null) {
// this feature has already been created and stored
// feature with discontinous location, this location wasn't valid for some reason
return;
}
if (identifier != null) {
feature.setAttribute("primaryIdentifier", identifier);
}
handler.setFeature(feature);
identifierMap.put(identifier, feature.getIdentifier());
if (names != null) {
setNames(names, synonymsToAdd, record.getId(), feature, cd);
}
List<String> parents = record.getParents();
if (parents != null && !parents.isEmpty()) {
setRefsAndCollections(parents, feature);
}
feature.addReference(getOrgRef());
feature.addToCollection("dataSets", dataSet);
handler.addDataSet(dataSet);
Double score = record.getScore();
if (score != null && !"".equals(String.valueOf(score))) {
feature.setAttribute("score", String.valueOf(score));
feature.setAttribute("scoreType", record.getSource());
}
for (Item synonym : synonymsToAdd) {
handler.addItem(synonym);
}
handler.process(record);
if (handler.getDataSetReferenceList().getRefIds().size() > 0) {
feature.addCollection(handler.getDataSetReferenceList());
}
handler.clearDataSetReferenceList();
if (handler.getPublicationReferenceList().getRefIds().size() > 0) {
feature.addCollection(handler.getPublicationReferenceList());
}
handler.clearPublicationReferenceList();
try {
Iterator<Item> iter = handler.getItems().iterator();
while (iter.hasNext()) {
store(iter.next());
}
} catch (ObjectStoreException e) {
LOG.error("Problem writing item to the itemwriter");
throw e;
}
}
/**
* process GFF3 record and give a xml presentation
*
* @param record GFF3Record
* @throws ObjectStoreException if an error occurs storing items
* @throws IOException
*/
public void process(GFF3Record record) throws ObjectStoreException {
String term = record.getType();
if (config_exclude != null
&& !config_exclude.isEmpty()) { // don't process terms in the exclude list
if (config_exclude.containsKey(this.orgTaxonId)) {
if (config_exclude.get(this.orgTaxonId).contains(term)) {
return;
}
}
}
if (config_term != null && !config_term.isEmpty()) { // otherwise all terms are processed
if (config_term.containsKey(this.orgTaxonId)) {
if (!config_term.get(this.orgTaxonId).contains(term)) {
return;
}
}
}
// By default, use ID field in attributes
String primaryIdentifier = record.getId();
// If pid set in gff_config.propeties, look for the attribute field, e.g. locus_tag
if (config_attr.containsKey(this.orgTaxonId)) {
if (config_attr.get(this.orgTaxonId).containsKey("primaryIdentifier")) {
String cls = config_attr_class.get(this.orgTaxonId).get("primaryIdentifier");
if ("all".equals(cls) || term.equals(cls)) {
String pidAttr = config_attr.get(this.orgTaxonId).get("primaryIdentifier");
if (pidAttr.contains("Dbxref") && record.getDbxrefs() != null) {
String pidAttrPrefix = pidAttr.split("\\.")[1];
for (Iterator<?> i = record.getDbxrefs().iterator(); i.hasNext(); ) {
String xref = (String) i.next();
if (xref.contains(pidAttrPrefix)) {
primaryIdentifier = xref.split(":")[1];
break;
}
}
} else {
if (record.getAttributes().get(pidAttr) != null) {
primaryIdentifier = record.getAttributes().get(pidAttr).get(0);
}
}
}
}
}
String refId = identifierMap.get(primaryIdentifier);
// get rid of previous record Items from handler
handler.clear();
Item seq = getSeq(record.getSequenceID());
String className = TypeUtil.javaiseClassName(term);
String fullClassName = tgtModel.getPackageName() + "." + className;
ClassDescriptor cd = tgtModel.getClassDescriptorByName(fullClassName);
if (cd == null) {
throw new IllegalArgumentException(
"no class found in model for: "
+ className
+ " (original GFF record type: "
+ term
+ ") for "
+ "record: "
+ record);
}
Set<Item> synonymsToAdd = new HashSet<Item>();
Item feature = null;
// new feature
if (refId == null) {
feature = createItem(className);
refId = feature.getIdentifier();
}
if (!"chromosome".equals(term) && seq != null) {
boolean makeLocation =
record.getStart() >= 1
&& record.getEnd() >= 1
&& !dontCreateLocations
&& handler.createLocations(record);
if (makeLocation) {
Item location = getLocation(record, refId, seq, cd);
if (feature == null) {
// this feature has already been created and stored
// we only wanted the location, we're done here.
store(location);
return;
}
int length = getLength(record);
feature.setAttribute("length", String.valueOf(length));
handler.setLocation(location);
if ("Chromosome".equals(seqClsName)
&& (cd.getFieldDescriptorByName("chromosome") != null)) {
feature.setReference("chromosome", seq.getIdentifier());
feature.setReference("chromosomeLocation", location);
}
}
}
if (feature == null) {
// this feature has already been created and stored
// feature with discontinous location, this location wasn't valid for some reason
return;
}
if (primaryIdentifier != null) {
feature.setAttribute("primaryIdentifier", primaryIdentifier);
}
handler.setFeature(feature);
identifierMap.put(primaryIdentifier, feature.getIdentifier());
List<?> names = record.getNames();
String symbol = null;
List<String> synonyms = new ArrayList<String>();
// get the attribute set for symbol
if (config_attr.containsKey(this.orgTaxonId)) {
if (config_attr.get(this.orgTaxonId).containsKey("symbol")) {
String cls = config_attr_class.get(this.orgTaxonId).get("symbol");
if ("all".equals(cls) || term.equals(cls)) {
String symbolAttr = config_attr.get(this.orgTaxonId).get("symbol");
if (symbolAttr.contains("Dbxref") && record.getDbxrefs() != null) {
String symbolAttrPrefix = symbolAttr.split("\\.")[1];
for (Iterator<?> i = record.getDbxrefs().iterator(); i.hasNext(); ) {
String xref = (String) i.next();
if (xref.contains(symbolAttrPrefix)) {
symbol = xref.split(":")[1];
break;
}
}
} else {
if (record.getAttributes().get(symbolAttr) != null) {
symbol = record.getAttributes().get(symbolAttr).get(0);
}
}
}
}
}
// get the attribute set for synonym
if (config_attr.containsKey(this.orgTaxonId)) {
if (config_attr.get(this.orgTaxonId).containsKey("synonym")) {
String cls = config_attr_class.get(this.orgTaxonId).get("synonym");
if ("all".equals(cls) || term.equals(cls)) {
String synonymAttr = config_attr.get(this.orgTaxonId).get("synonym");
if (synonymAttr.contains("Dbxref") && record.getDbxrefs() != null) {
String synonymAttrPrefix = synonymAttr.split("\\.")[1];
Set<String> synSet = new HashSet<String>();
for (Iterator<?> i = record.getDbxrefs().iterator(); i.hasNext(); ) {
String xref = (String) i.next();
if (xref.contains(synonymAttrPrefix)) {
synSet.add(xref.split(":")[1]);
}
}
synonyms.addAll(synSet);
} else {
synonyms = record.getAttributes().get(synonymAttr);
}
// synonyms.removeAll(Collections.singleton(null));
}
}
}
if (names != null) {
setNames(names, symbol, synonyms, synonymsToAdd, primaryIdentifier, feature, cd);
}
// Other attributes
List<String> primeAttrList = Arrays.asList("primaryIdentifier", "symbol", "synonym");
if (config_attr.containsKey(this.orgTaxonId)) {
Map<String, String> attrMapOrg = config_attr.get(this.orgTaxonId);
Map<String, String> attrMapClone = new HashMap<String, String>();
// Deep copy of a map
for (Entry<String, String> e : attrMapOrg.entrySet()) {
attrMapClone.put(e.getKey(), e.getValue());
}
for (String pa : primeAttrList) {
attrMapClone.remove(pa);
}
for (Entry<String, String> e : attrMapClone.entrySet()) {
String cls = config_attr_class.get(this.orgTaxonId).get(e.getKey());
if ("all".equals(cls) || term.equals(cls)) {
String attr = e.getValue();
if (attr.contains("Dbxref") && record.getDbxrefs() != null) {
String attrPrefix = attr.split("\\.")[1];
for (Iterator<?> i = record.getDbxrefs().iterator(); i.hasNext(); ) {
String xref = (String) i.next();
if (xref.contains(attrPrefix)) {
if (feature.checkAttribute(e.getKey())) {
feature.setAttribute(e.getKey(), xref.split(":")[1]);
}
break;
}
}
} else {
if (record.getAttributes().get(attr) != null) {
String attrVal = record.getAttributes().get(attr).get(0);
if (attrVal != null) {
if (feature.checkAttribute(e.getKey())) {
feature.setAttribute(e.getKey(), attrVal);
}
}
}
}
}
}
}
List<String> parents = record.getParents();
if (parents != null && !parents.isEmpty()) {
setRefsAndCollections(parents, feature);
}
feature.addReference(getOrgRef());
feature.addToCollection("dataSets", dataSet);
handler.addDataSet(dataSet);
Double score = record.getScore();
if (score != null && !"".equals(String.valueOf(score))) {
feature.setAttribute("score", String.valueOf(score));
feature.setAttribute("scoreType", record.getSource());
}
for (Item synonym : synonymsToAdd) {
handler.addItem(synonym);
}
handler.process(record);
if (handler.getDataSetReferenceList().getRefIds().size() > 0) {
feature.addCollection(handler.getDataSetReferenceList());
}
handler.clearDataSetReferenceList();
if (handler.getPublicationReferenceList().getRefIds().size() > 0) {
feature.addCollection(handler.getPublicationReferenceList());
}
handler.clearPublicationReferenceList();
try {
Iterator<Item> iter = handler.getItems().iterator();
while (iter.hasNext()) {
store(iter.next());
}
} catch (ObjectStoreException e) {
LOG.error("Problem writing item to the itemwriter");
throw e;
}
}