/**
* @param uniprotDoc
* @return
* @throws Exception
*/
private String getSequence(Document uniprotDoc) throws Exception {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
Element sequenceElement = XMLHelper.selectSingleElement(entryElement, "sequence");
String seqdata = sequenceElement.getTextContent();
return seqdata;
}
/** @return */
public AccessionID getAccession() {
AccessionID accessionID = new AccessionID();
if (uniprotDoc == null) {
return accessionID;
}
try {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
Element nameElement = XMLHelper.selectSingleElement(entryElement, "name");
accessionID = new AccessionID(nameElement.getTextContent(), DataSource.UNIPROT);
} catch (Exception e) {
logger.error("Exeception: ", e);
}
return accessionID;
}
/**
* The Uniprot mappings to other database identifiers for this sequence
*
* @return
* @throws Exception
*/
public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()
throws Exception {
LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferencesHashMap =
new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
if (uniprotDoc == null) {
return databaseReferencesHashMap;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> dbreferenceElementList =
XMLHelper.selectElements(entryElement, "dbReference");
for (Element element : dbreferenceElementList) {
String type = element.getAttribute("type");
String id = element.getAttribute("id");
ArrayList<DBReferenceInfo> idlist = databaseReferencesHashMap.get(type);
if (idlist == null) {
idlist = new ArrayList<DBReferenceInfo>();
databaseReferencesHashMap.put(type, idlist);
}
DBReferenceInfo dbreferenceInfo = new DBReferenceInfo(type, id);
ArrayList<Element> propertyElementList = XMLHelper.selectElements(element, "property");
for (Element propertyElement : propertyElementList) {
String propertyType = propertyElement.getAttribute("type");
String propertyValue = propertyElement.getAttribute("value");
dbreferenceInfo.addProperty(propertyType, propertyValue);
}
idlist.add(dbreferenceInfo);
}
return databaseReferencesHashMap;
}
/**
* Get the organism name assigned to this sequence
*
* @return
* @throws Exception
*/
public String getOrganismName() throws Exception {
if (uniprotDoc == null) {
return "";
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
Element organismElement = XMLHelper.selectSingleElement(entryElement, "organism");
if (organismElement == null) {
return "";
}
Element nameElement = XMLHelper.selectSingleElement(organismElement, "name");
if (nameElement == null) {
return "";
}
return nameElement.getTextContent();
}
/**
* Pull uniprot key words which is a mixed bag of words associated with this sequence
*
* @return
* @throws Exception
*/
public ArrayList<String> getKeyWords() throws Exception {
ArrayList<String> keyWordsList = new ArrayList<String>();
if (uniprotDoc == null) {
return keyWordsList;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(entryElement, "keyword");
for (Element element : keyWordElementList) {
keyWordsList.add(element.getTextContent());
}
return keyWordsList;
}