Ejemplo n.º 1
0
  /**
   * @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;
  }
Ejemplo n.º 2
0
 /** @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;
 }
Ejemplo n.º 3
0
  /**
   * 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;
  }
Ejemplo n.º 4
0
 /**
  * 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();
 }
Ejemplo n.º 5
0
  /**
   * 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;
  }