/**
* Add a new qualifier to a list of qualifiers
*
* @param qualifiers
* @param newQualifier
*/
private void addNewQualifier(QualifierVector qualifiers, Qualifier newQualifier) {
Qualifier qualifier;
if ((qualifier = qualifiers.getQualifierByName(newQualifier.getName())) != null) {
final StringVector newValues = newQualifier.getValues();
final StringVector values = qualifier.getValues();
if (newValues == null) return;
for (int j = 0; j < newValues.size(); j++) {
String newValue = (String) newValues.get(j);
if (!values.contains(newValue)) qualifier.addValue(newValue);
}
} else qualifiers.addElement(newQualifier);
}
public static void main(String argv[]) throws Exception {
RetsSession session = new RetsSession("http://www.dis.com:6103/rets/login");
if (!session.Login("Joe", "Schmoe")) {
System.out.println("Invalid login");
System.exit(2);
}
System.out.println("Action: " + session.GetAction());
RetsVersion version = session.GetDetectedRetsVersion();
System.out.println("RETS Version: " + ((version == RetsVersion.RETS_1_5) ? "1.5" : "1.0"));
SearchRequest searchRequest =
session.CreateSearchRequest("Property", "RES", "(ListPrice=300000-)");
searchRequest.SetSelect("ListingID,ListPrice,Beds,City");
searchRequest.SetLimit(SearchRequest.LIMIT_DEFAULT);
searchRequest.SetOffset(SearchRequest.OFFSET_NONE);
searchRequest.SetCountType(SearchRequest.CountType.RECORD_COUNT_AND_RESULTS);
searchRequest.SetStandardNames(true);
searchRequest.SetRestrictedIndicator("XXXX");
searchRequest.SetFormatType(SearchRequest.FormatType.COMPACT);
SearchResultSet results = session.Search(searchRequest);
System.out.println("Record count: " + results.GetCount());
StringVector columns = null;
while (results.HasNext()) {
if (columns == null) {
columns = results.GetColumns();
}
for (int i = 0; i < columns.size(); i++) {
System.out.format("%15s: %s\n", columns.get(i), results.GetString(columns.get(i)));
}
System.out.println();
}
LogoutResponse logout = session.Logout();
System.out.println("Billing info: " + logout.GetBillingInfo());
System.out.println("Logout Message: " + logout.GetLogoutMessage());
System.out.println("Connect time: " + logout.GetConnectTime());
}
public void natCheckStunServers(
StringVector stringVector, boolean z, SWIGTYPE_p_void sWIGTYPE_p_void) {
pjsua2JNI.Endpoint_natCheckStunServers(
this.swigCPtr,
this,
StringVector.getCPtr(stringVector),
stringVector,
z,
SWIGTYPE_p_void.getCPtr(sWIGTYPE_p_void));
}
public void natCheckStunServers(
StringVector prmServers, boolean prmWait, SWIGTYPE_p_void prmUserData)
throws java.lang.Exception {
pjsua2JNI.Endpoint_natCheckStunServers(
swigCPtr,
this,
StringVector.getCPtr(prmServers),
prmServers,
prmWait,
SWIGTYPE_p_void.getCPtr(prmUserData));
}
public static void main(String argv[]) throws Exception {
RetsSession session = new RetsSession("http://demo.crt.realtors.org:6103/rets/login");
if (!session.Login("Joe", "Schmoe")) {
System.out.println("Invalid login");
System.exit(2);
}
System.out.println("Action: " + session.GetAction());
RetsVersion version = session.GetDetectedRetsVersion();
System.out.println("RETS Version: " + ((version == RetsVersion.RETS_1_5) ? "1.5" : "1.0"));
SearchRequest searchRequest =
session.CreateSearchRequest("Property", "RES", "(ListPrice=300000-)");
searchRequest.SetSelect("ListingID,ListPrice,Beds,City");
searchRequest.SetLimit(SearchRequest.LIMIT_DEFAULT);
searchRequest.SetOffset(SearchRequest.OFFSET_NONE);
searchRequest.SetCountType(SearchRequest.CountType.RECORD_COUNT_AND_RESULTS);
searchRequest.SetFormatType(SearchRequest.FormatType.COMPACT);
searchRequest.SetStandardNames(true);
try {
File f = new File("rawsearch.xml");
FileOutputStream fop = new FileOutputStream(f);
byte[] data = session.SearchAsArray(searchRequest);
fop.write(data);
fop.flush();
fop.close();
} catch (IOException e) {
}
LogoutResponse logout = session.Logout();
SearchResultSet results = new SearchResultSet();
// Reopen the file now for input
try {
File f = new File("rawsearch.xml");
byte[] buffer = new byte[(int) f.length()];
FileInputStream fip = new FileInputStream(f);
int offset = 0;
int numRead = 0;
while (offset < buffer.length
&& (numRead = fip.read(buffer, offset, buffer.length - offset)) >= 0) offset += numRead;
results.SetEncoding(EncodingType.RETS_XML_DEFAULT_ENCODING);
results.SetDataAsArray(buffer);
} catch (IOException e) {
}
System.out.println("Record count: " + results.GetCount());
StringVector columns = results.GetColumns();
while (results.HasNext()) {
if (columns == null) {
columns = results.GetColumns();
}
for (int i = 0; i < columns.size(); i++) {
System.out.format("%15s: %s\n", columns.get(i), results.GetString(columns.get(i)));
}
System.out.println();
}
/*
* Prototype for returning data in a stream.
try
{
File f=new File("foobarty");
FileOutputStream fop=new FileOutputStream(f);
CppInputStream data = session.SearchAsStream(searchRequest);
byte [] buf = new byte[30];
int len;
while ((len = data.read(buf, 0, 30)) > 0)
{
fop.write(buf, 0, len);
}
fop.flush();
fop.close();
}
catch (IOException e) {}
* end prototype */
}
/** Read key and qualifier mappings for CHADO to EMBL */
private static void initDatabaseMappings() {
InputStream keyStream = Options.class.getResourceAsStream("/key_mapping");
if (keyStream == null) keyStream = Options.class.getResourceAsStream("/etc/key_mapping");
InputStream qualifierStream = Options.class.getResourceAsStream("/qualifier_mapping");
if (qualifierStream == null)
qualifierStream = Options.class.getResourceAsStream("/etc/qualifier_mapping");
final Properties keyMapProperties = new Properties();
final Properties qualifierMapProperties = new Properties();
try {
keyMapProperties.load(keyStream);
qualifierMapProperties.load(qualifierStream);
if (System.getProperty("nohistory") != null)
qualifierMapProperties.setProperty("history", "");
} catch (IOException e) {
e.printStackTrace();
}
// parse the keyMapProperties
DATABASE_MAP_KEYS = new Object[keyMapProperties.size()][3];
final Enumeration keysenum = keyMapProperties.propertyNames();
int n = 0;
while (keysenum.hasMoreElements()) {
String current_map_name = (String) keysenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(keyMapProperties, current_map_name);
DATABASE_MAP_KEYS[n][0] = current_map_name;
DATABASE_MAP_KEYS[n][1] = property_values.get(0);
if (property_values.size() == 2) {
String qualifierString[] = ((String) property_values.get(1)).split("=");
final uk.ac.sanger.artemis.io.Qualifier qualifier;
if (qualifierString.length == 2)
qualifier = new uk.ac.sanger.artemis.io.Qualifier(qualifierString[0], qualifierString[1]);
else qualifier = new uk.ac.sanger.artemis.io.Qualifier(qualifierString[0]);
DATABASE_MAP_KEYS[n][2] = qualifier;
} else DATABASE_MAP_KEYS[n][2] = null;
n++;
}
// parse the qualifier mappings
Enumeration qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
Vector qualifiersToRemove = new Vector();
while (qualifiersenum.hasMoreElements()) {
String current_map_name = (String) qualifiersenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(qualifierMapProperties, current_map_name);
if (property_values == null || property_values.size() == 0)
qualifiersToRemove.add(current_map_name);
else n++;
}
DATABASE_QUALIFIERS_TO_MAP = new String[n][2];
DATABASE_QUALIFIERS_TO_REMOVE = qualifiersToRemove.toArray();
qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
while (qualifiersenum.hasMoreElements()) {
String current_map_name = (String) qualifiersenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(qualifierMapProperties, current_map_name);
if (property_values != null && property_values.size() > 0) {
DATABASE_QUALIFIERS_TO_MAP[n][0] = current_map_name;
DATABASE_QUALIFIERS_TO_MAP[n][1] = (String) property_values.get(0);
n++;
}
}
}
/**
* Merge qualifiers
*
* @param qualifiers
* @param newQualifiers
*/
private void combineQualifiers(
final QualifierVector qualifiers, final QualifierVector newQualifiers, final boolean isGene) {
for (int i = 0; i < newQualifiers.size(); i++) {
Qualifier newQualifier = (Qualifier) newQualifiers.get(i);
if (newQualifier.getName().equals("ID") && !isGene) {
continue;
}
// convert GO evidence to codes (e.g. ND=No biological Data available)
if (newQualifier.getName().equals("GO")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
String val = GoBox.getEvidenceCodeGoTextFromText((String) newValues.get(j));
tmpNewValues.add(val);
}
newQualifier = new Qualifier("GO", tmpNewValues);
}
if (newQualifier.getName().equals("product")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
String val = (String) newValues.get(j);
int ind = 0;
if ((ind = val.indexOf(";db_xref=")) > -1) val = val.substring(0, ind);
if ((ind = val.indexOf(";evidence=")) > -1) val = val.substring(0, ind);
if (val.startsWith("term=")) val = val.substring(5, val.length());
if (val.endsWith(";")) val = val.substring(0, val.length() - 1);
tmpNewValues.add(val);
}
newQualifier = new Qualifier("product", tmpNewValues);
}
if (newQualifier.getName().equals("orthologous_to")
|| newQualifier.getName().equals("paralogous_to")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
if (!newValues.get(j).equals("")) tmpNewValues.add(newValues.get(j));
}
if (tmpNewValues.size() == 0) continue;
Pattern p = Pattern.compile("\\w+:link=\\w+");
for (int j = 0; j < tmpNewValues.size(); j++) {
String valueStr = (String) tmpNewValues.get(j);
String newValueStr;
int indexEnd = valueStr.indexOf(';');
String endStr = "";
if (indexEnd > -1) endStr = valueStr.substring(indexEnd);
Matcher m = p.matcher(valueStr);
while (m.find()) {
int index = valueStr.indexOf("link=", m.start());
newValueStr =
valueStr.substring(m.start(), index)
+ valueStr.substring(index + 5, m.end())
+ endStr;
if (newQualifier.getName().equals("orthologous_to"))
newQualifier = new Qualifier("orthologous_to", newValueStr);
else newQualifier = new Qualifier("paralogous_to", newValueStr);
qualifiers.addElement(newQualifier);
}
}
continue;
}
addNewQualifier(qualifiers, newQualifier);
}
}
/**
* Map GFF features to EMBL/Genbank
*
* @param feature
* @return
*/
private Object mapGffToNativeFeature(final Feature feature) {
if (DATABASE_MAP_KEYS == null) initDatabaseMappings();
Key key = feature.getKey();
QualifierVector qualifiers = feature.getQualifiers().copy();
// ignore if obsolete
if (IGNORE_OBSOLETE_FEATURES) {
Qualifier isObsoleteQualifier = qualifiers.getQualifierByName("isObsolete");
if (isObsoleteQualifier != null) {
String value = (String) isObsoleteQualifier.getValues().get(0);
if (Boolean.parseBoolean(value)) return null;
}
}
key = map(key, qualifiers);
if (getEntryInformation().isValidQualifier((String) DATABASE_QUALIFIERS_TO_REMOVE[0])) {
try {
if (this instanceof EmblDocumentEntry)
return new EmblStreamFeature(key, feature.getLocation(), qualifiers);
else return new GenbankStreamFeature(key, feature.getLocation(), qualifiers);
} catch (InvalidRelationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
Location location = joinUtrs(feature, key, qualifiers);
if (location == null) return null;
// flatten gene model - combining qualifiers
if (key.getKeyString().equals(DatabaseDocument.EXONMODEL)) {
ChadoCanonicalGene chadoGene = ((GFFStreamFeature) feature).getChadoGene();
final String name = GeneUtils.getUniqueName(feature);
final String transcriptName = chadoGene.getTranscriptFromName(name);
StringVector sv = new StringVector();
sv.add(transcriptName);
final Feature transcript = chadoGene.containsTranscript(sv);
if (transcript != null && GeneUtils.isNonCodingTranscripts(transcript.getKey())) return null;
qualifiers.removeQualifierByName("ID");
int ntranscripts = 0;
// add transcript & protein qualifiers to CDS
try {
final Feature protein = chadoGene.getProteinOfTranscript(transcriptName);
if (protein != null) combineQualifiers(qualifiers, protein.getQualifiers().copy(), false);
if (transcript != null)
ntranscripts = handleTranscripts(qualifiers, transcript, ntranscripts, chadoGene);
} catch (NullPointerException npe) {
}
// add gene qualifiers to CDS
QualifierVector geneQualifiers = chadoGene.getGene().getQualifiers().copy();
// multiple transcripts
if (ntranscripts > 1 && geneQualifiers.getQualifierByName("ID") != null) {
Qualifier newIDQualifier =
new Qualifier(
"shared_id", (String) geneQualifiers.getQualifierByName("ID").getValues().get(0));
addNewQualifier(qualifiers, newIDQualifier);
geneQualifiers.removeQualifierByName("ID");
}
combineQualifiers(qualifiers, geneQualifiers, true);
} else if (GeneUtils.isNonCodingTranscripts(key)) {
// use gene id for non-coding transcripts
ChadoCanonicalGene chadoGene = ((GFFStreamFeature) feature).getChadoGene();
if (chadoGene != null) {
qualifiers.removeQualifierByName("ID");
QualifierVector geneQualifiers = chadoGene.getGene().getQualifiers().copy();
combineQualifiers(qualifiers, geneQualifiers, true);
}
}
try {
for (int i = 0; i < DATABASE_QUALIFIERS_TO_MAP.length; i++) {
if (!getEntryInformation().isValidQualifier(DATABASE_QUALIFIERS_TO_MAP[i][0])) {
changeQualifierName(
qualifiers, DATABASE_QUALIFIERS_TO_MAP[i][0], DATABASE_QUALIFIERS_TO_MAP[i][1]);
}
}
if (qualifiers.getQualifierByName("stop_codon_redefined_as_selenocysteine") != null) {
handleSelenocysteine(qualifiers, feature);
}
for (int i = 0; i < DATABASE_QUALIFIERS_TO_REMOVE.length; i++) {
if (!getEntryInformation().isValidQualifier((String) DATABASE_QUALIFIERS_TO_REMOVE[i]))
qualifiers.removeQualifierByName((String) DATABASE_QUALIFIERS_TO_REMOVE[i]);
}
if (key.getKeyString().equals("polypeptide")) return null;
else if (key.getKeyString().equals("gene")) return null;
else if (key.getKeyString().equals("centromere")) return null;
else if (key.getKeyString().equals("transcript") || key.getKeyString().equals("mRNA"))
return null;
if (this instanceof EmblDocumentEntry)
return new EmblStreamFeature(key, location, qualifiers);
else return new GenbankStreamFeature(key, location, qualifiers);
} catch (InvalidRelationException e) {
e.printStackTrace();
if (feature instanceof DatabaseStreamFeature) return new EmblStreamFeature();
else return new GenbankStreamFeature();
}
}