Ejemplo n.º 1
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 2
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 3
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;
  }
Ejemplo n.º 4
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 5
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 6
0
  /**
   * @param accession
   * @return
   * @throws Exception
   */
  private Document getUniprotXML(String accession) throws Exception {
    int index = accession.lastIndexOf(".");
    String key = accession;
    if (index != -1) {
      key = accession.substring(0, index);
    }
    StringBuilder sb = new StringBuilder();
    File f = null;
    if (uniprotDirectoryCache != null && uniprotDirectoryCache.length() > 0) {
      f = new File(uniprotDirectoryCache + File.separatorChar + key + ".xml");
      if (f.exists()) {
        FileReader fr = new FileReader(f);
        int size = (int) f.length();
        char[] data = new char[size];
        fr.read(data);
        fr.close();
        sb.append(data);
        index = sb.indexOf("xmlns="); // strip out name space stuff to make it easier on xpath
        if (index != -1) {
          int lastIndex = sb.indexOf(">", index);
          sb.replace(index, lastIndex, "");
        }
      }
    }

    // http://www.uniprot.org/uniprot/?query=SORBIDRAFT_03g027040&format=xml
    if (sb.length() == 0) {
      String uniprotURL = getUniprotbaseURL() + "/uniprot/?query=" + key + "&format=xml";
      // String uniprotURL = getUniprotbaseURL() + "/uniprot/" + key + ".xml";
      logger.info("Loading: {}", uniprotURL);
      URL uniprot = new URL(uniprotURL);
      URLConnection uniprotConnection = uniprot.openConnection();
      uniprotConnection.setRequestProperty("User-Agent", "BioJava");
      BufferedReader in =
          new BufferedReader(new InputStreamReader(uniprotConnection.getInputStream()));
      String inputLine;

      while ((inputLine = in.readLine()) != null) {
        sb.append(inputLine);
      }
      in.close();
      index = sb.indexOf("xmlns="); // strip out name space stuff to make it easier on xpath
      if (index != -1) {
        int lastIndex = sb.indexOf(">", index);
        sb.replace(index, lastIndex, "");
      }
      if (f != null) {
        FileWriter fw = new FileWriter(f);
        fw.write(sb.toString());
        fw.close();
      }
    }

    logger.info("Load complete");
    try {
      //       logger.debug(sb.toString());
      Document document =
          XMLHelper.inputStreamToDocument(new ByteArrayInputStream(sb.toString().getBytes()));
      return document;
    } catch (Exception e) {
      logger.error("Exception on xml parse of: {}", sb.toString());
    }
    return null;
  }