本文整理汇总了Java中org.bridgedb.bio.Organism类的典型用法代码示例。如果您正苦于以下问题：Java Organism类的具体用法？Java Organism怎么用？Java Organism使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
Organism类属于org.bridgedb.bio包，在下文中一共展示了Organism类的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: usesOldEnsembl
import org.bridgedb.bio.Organism; //导入依赖的package包/类
private boolean usesOldEnsembl(Pathway pwy)
{
Organism org = Organism.fromLatinName(pwy.getMappInfo().getOrganism());
if (!ensSpecies.containsKey(org))
return false; // this pwy is not one of the species to be converted
for (PathwayElement elt : pwy.getDataObjects())
{
if (elt.getObjectType() == ObjectType.DATANODE &&
elt.getDataSource() == BioDataSource.ENSEMBL)
{
return true;
}
}
return false;
}
开发者ID:PathVisio，项目名称:pathvisio，代码行数:17，代码来源:Compat.java
示例2: convertEnsembl
import org.bridgedb.bio.Organism; //导入依赖的package包/类
/**
* Ensembl considers each species database as separate,
* and thus they should have separate system codes as well.
* This method will convert generic Ensembl datanodes
* to species specific datanodes if possible.
*/
private void convertEnsembl(Pathway pwy)
{
Organism org = Organism.fromLatinName(pwy.getMappInfo().getOrganism());
if (!ensSpecies.containsKey(org))
return; // this pwy is not one of the species to be converted
for (PathwayElement elt : pwy.getDataObjects())
{
if (elt.getObjectType() == ObjectType.DATANODE &&
elt.getDataSource() == BioDataSource.ENSEMBL)
{
elt.setDataSource (ensSpecies.get (org));
}
}
}
开发者ID:PathVisio，项目名称:pathvisio，代码行数:23，代码来源:Compat.java
示例3: getContents
import org.bridgedb.bio.Organism; //导入依赖的package包/类
@Get
public String getContents()
{
try
{
StringBuilder result = new StringBuilder();
for (Organism org : getGdbProvider().getOrganisms())
{
result.append (org.shortName());
result.append ("\t");
result.append (org.latinName());
result.append ("\n");
}
return result.toString();
}
catch( Exception e )
{
e.printStackTrace();
setStatus( Status.SERVER_ERROR_INTERNAL );
return e.getMessage();
}
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:23，代码来源:Contents.java
示例4: initIDMappers
import org.bridgedb.bio.Organism; //导入依赖的package包/类
private void initIDMappers() {
Organism org = Organism.fromLatinName(orgName);
if(org == null) { //Fallback on code
org = Organism.fromCode(orgName);
}
if(org == null) { //Fallback on shortname
org = Organism.fromShortName(orgName);
}
if(org == null) {
throw new IllegalArgumentException("Unknown organism: " + orgName + "<p><font size='+1'><i>Double check the spelling. We are expecting an entry like: Human</i></font></p>");
}
mappers = getGdbProvider().getStack(org);
if (mappers.getSize() == 0)
{
throw new IllegalArgumentException("No database found for: " + orgName +"<p><font size='+1'><i>Verify that the database is supported and properly referenced in gdb.config.</i></font></p>");
}
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:18，代码来源:IDMapperResource.java
示例5: scanPathway
import org.bridgedb.bio.Organism; //导入依赖的package包/类
protected Result scanPathway(File pathwayFile) throws BotException {
try {
ConnectorBotResult report = new ConnectorBotResult(
getCache().getPathwayInfo(pathwayFile));
Pathway pathway = new Pathway();
pathway.readFromXml(pathwayFile, true);
String orgName = pathway.getMappInfo().getOrganism();
Organism org = Organism.fromLatinName(orgName);
if(org == null) org = Organism.fromShortName(orgName);
for(PathwayElement pwe : pathway.getDataObjects()) {
if(pwe.getObjectType() == ObjectType.LINE) {
boolean valid =
pwe.getMStart().isLinked() &&
pwe.getMEnd().isLinked();
report.addLine(pwe, valid);
}
}
return report;
} catch(Exception e) {
throw new BotException(e);
}
}
开发者ID:wikipathways，项目名称:org.wikipathways.client，代码行数:27，代码来源:ConnectorBot.java
示例6: testListPathways
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public void testListPathways() {
try {
WSPathwayInfo[] r = client.listPathways();
Logger.log.trace("Get pathway list returned " + r.length + " pathways");
r = client.listPathways(Organism.HomoSapiens);
Logger.log.trace("Get pathway list for Homo sapiens returned " + r.length + " pathways");
//Check if all pathways are indeed human
for(WSPathwayInfo wpi : r) {
if(!Organism.HomoSapiens.latinName().equals(wpi.getSpecies())) {
fail("Get pathway list for Homo sapiens included non-human pathway: " +
wpi.getId() + " (" + wpi.getSpecies() + ")");
}
}
} catch(Exception e) {
e.printStackTrace();
fail(e.getMessage());
}
}
开发者ID:wikipathways，项目名称:org.wikipathways.client，代码行数:19，代码来源:WikiPathwaysClientTest.java
示例7: addContent
import org.bridgedb.bio.Organism; //导入依赖的package包/类
protected void addContent(JPanel panel) {
JPanel fieldPanel = new JPanel();
fieldPanel.setBorder(BorderFactory.createTitledBorder(""));
GridBagConstraints panelConstraints = new GridBagConstraints();
panelConstraints.fill = GridBagConstraints.BOTH;
panelConstraints.weightx = 1;
panelConstraints.weighty = 1;
panel.add(fieldPanel, panelConstraints);
fieldPanel.setLayout(new GridBagLayout());
JLabel titleFieldLabel = new JLabel("Title");
JLabel orgComboLabel = new JLabel ("Organism ");
titleField = new JTextField();
organismComboBox = new PermissiveComboBox(Organism.latinNamesArray());
GridBagConstraints c = new GridBagConstraints();
c.anchor = GridBagConstraints.FIRST_LINE_START;
c.weightx = 0;
c.gridx = 0;
c.gridy = GridBagConstraints.RELATIVE;
fieldPanel.add(titleFieldLabel, c);
fieldPanel.add(orgComboLabel, c);
c.gridx = 1;
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 1;
fieldPanel.add(titleField, c);
fieldPanel.add(organismComboBox, c);
}
开发者ID:PathVisio，项目名称:pathvisio，代码行数:32，代码来源:NewPathwayDialog.java
示例8: addCustomTabs
import org.bridgedb.bio.Organism; //导入依赖的package包/类
protected void addCustomTabs(JTabbedPane parent) {
JPanel panel = new JPanel();
panel.setLayout(new GridBagLayout());
JPanel fieldPanel = new JPanel();
fieldPanel.setBorder(BorderFactory.createTitledBorder(""));
GridBagConstraints panelConstraints = new GridBagConstraints();
panelConstraints.fill = GridBagConstraints.BOTH;
panelConstraints.weightx = 1;
panelConstraints.weighty = 1;
panel.add(fieldPanel, panelConstraints);
fieldPanel.setLayout(new GridBagLayout());
JLabel titleFieldLabel = new JLabel("Title");
JLabel orgComboLabel = new JLabel ("Organism ");
titleField = new JTextField();
titleField.setText(swingEngine.getEngine().getActivePathway().getMappInfo().getMapInfoName());
organismComboBox = new PermissiveComboBox(Organism.latinNamesArray());
organismComboBox.setSelectedItem(swingEngine.getEngine().getActivePathway().getMappInfo().getOrganism());
GridBagConstraints c = new GridBagConstraints();
c.anchor = GridBagConstraints.FIRST_LINE_START;
c.weightx = 0;
c.gridx = 0;
c.gridy = GridBagConstraints.RELATIVE;
fieldPanel.add(titleFieldLabel, c);
fieldPanel.add(orgComboLabel, c);
c.gridx = 1;
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 1;
fieldPanel.add(titleField, c);
fieldPanel.add(organismComboBox, c);
parent.add("Properties", panel);
parent.setSelectedComponent(panel);
}
开发者ID:PathVisio，项目名称:pathvisio，代码行数:40，代码来源:PathwayPropertiesDialog.java
示例9: Compat
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public Compat (SwingEngine swingEngine)
{
this.swingEngine = swingEngine;
ensSpecies.put (Organism.HomoSapiens, BioDataSource.ENSEMBL_HUMAN);
ensSpecies.put (Organism.CaenorhabditisElegans, BioDataSource.ENSEMBL_CELEGANS);
ensSpecies.put (Organism.DanioRerio, BioDataSource.ENSEMBL_ZEBRAFISH);
ensSpecies.put (Organism.DrosophilaMelanogaster, BioDataSource.ENSEMBL_ZEBRAFISH);
ensSpecies.put (Organism.MusMusculus, BioDataSource.ENSEMBL_MOUSE);
ensSpecies.put (Organism.RattusNorvegicus, BioDataSource.ENSEMBL_RAT);
ensSpecies.put (Organism.SaccharomycesCerevisiae, BioDataSource.ENSEMBL_SCEREVISIAE);
}
开发者ID:PathVisio，项目名称:pathvisio，代码行数:13，代码来源:Compat.java
示例10: findPathwaysByText
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public WSSearchResult[] findPathwaysByText(String query, Organism organism) throws RemoteException {
String species = null;
if(organism != null) {
species = organism.latinName();
}
WSSearchResult[] r = port.findPathwaysByText(query, species);
if(r == null) r = new WSSearchResult[0];
return r;
}
开发者ID:wikipathways，项目名称:wikipathways-api-client-java，代码行数:10，代码来源:WikiPathwaysClient.java
示例11: test
import org.bridgedb.bio.Organism; //导入依赖的package包/类
@Test
public void test() throws RemoteException {
WSPathwayInfo [] info = client.listPathways();
assertTrue(info.length > 1900);
WSPathwayInfo [] info2 = client.listPathways(Organism.HomoSapiens);
assertTrue(info2.length < info.length);
assertFalse(info.length == info2.length);
}
开发者ID:wikipathways，项目名称:wikipathways-api-client-java，代码行数:10，代码来源:TestListPathways.java
示例12: check
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public void check(String oldVal, String newVal)
{
if (newVal != null)
{
Organism o = Organism.fromLatinName(newVal);
if (o == null) System.out.println ("WARNING: species '" + newVal + "' is not a recognized latin name");
}
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:9，代码来源:BridgeQC.java
示例13: addOrganismGdb
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public void addOrganismGdb(Organism organism, IDMapper gdb) {
IDMapperStack l = organism2gdb.get(organism);
if(l == null) {
organism2gdb.put(organism, l = new IDMapperStack());
l.setTransitive(transitive);
for (IDMapper globalGdb : globalGdbs)
{
l.addIDMapper(globalGdb);
}
}
l.addIDMapper(gdb);
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:13，代码来源:GdbProvider.java
示例14: addGlobalGdb
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public void addGlobalGdb(IDMapper gdb) {
if(!globalGdbs.contains(gdb))
{
globalGdbs.add(gdb);
for (Organism org : organism2gdb.keySet())
{
organism2gdb.get(org).addIDMapper(gdb);
}
}
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:11，代码来源:GdbProvider.java
示例15: removeGlobalGdb
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public void removeGlobalGdb(IDMapper gdb) {
if (globalGdbs.contains(gdb))
{
globalGdbs.remove(gdb);
for (Organism org : organism2gdb.keySet())
{
organism2gdb.get(org).removeIDMapper(gdb);
}
}
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:11，代码来源:GdbProvider.java
示例16: add
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public static void add(RepositoryConnection repositoryConnection, Organism organism)
throws IOException, RepositoryException {
URI id = getResourceId(organism);
repositoryConnection.add(id, RdfConstants.TYPE_URI, BridgeDBConstants.ORGANISM_URI);
repositoryConnection.add(id, BridgeDBConstants.CODE_URI, new LiteralImpl(organism.code()));
repositoryConnection.add(id, BridgeDBConstants.SHORT_NAME_URI, new LiteralImpl(organism.shortName()));
repositoryConnection.add(id, BridgeDBConstants.LATIN_NAME_URI, new LiteralImpl(organism.latinName()));
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:9，代码来源:OrganismRdf.java
示例17: readRdf
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public static Object readRdf(Resource organismId, Set<Statement> allStatements) throws BridgeDBException {
for (Statement statement:allStatements){
if (statement.getPredicate().equals(BridgeDBConstants.LATIN_NAME_URI)){
String latinName = statement.getObject().stringValue();
Organism orgamism = Organism.fromLatinName(latinName);
if (orgamism != null){
return orgamism;
}
throw new BridgeDBException("No Orgamism with LatinName " + latinName + " for " + organismId);
}
}
throw new BridgeDBException("No Orgamism found for " + organismId);
}
开发者ID:bridgedb，项目名称:BridgeDb，代码行数:14，代码来源:OrganismRdf.java
示例18: testConnectorTag
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public void testConnectorTag() {
Pathway pathway = new Pathway();
pathway.getMappInfo().setOrganism(Organism.HomoSapiens.latinName());
//Add a pathway with an unconnected line
PathwayElement line = PathwayElement.createPathwayElement(ObjectType.LINE);
pathway.add(line);
WSPathwayInfo pwi = createConnectorPathway(pathway);
addConnectorTag(pwi.getId());
removeConnectorTag(pwi.getId());
overrideConnectorTag(pwi.getId());
}
开发者ID:wikipathways，项目名称:org.wikipathways.client，代码行数:12，代码来源:BotsTest.java
示例19: copyMappInfo
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public static void copyMappInfo(String[] row, Pathway data, String filename)
{
/* Data is lost when converting from GenMAPP to GPML:
*
* GenMAPP:
* "Title", "MAPP", "Version", "Author",
* "Maint", "Email", "Copyright","Modify",
* "Remarks", "BoardWidth", "BoardHeight","WindowWidth",
* "WindowHeight", "GeneDB", "Notes"
* GPML:
* "Name", NONE, Version, "Author",
* "MaintainedBy", "Email", "Availability", "LastModified",
* "Comment", "BoardWidth", "BoardHeight", NONE,
* NONE, NONE, "Notes"
*
*/
Logger.log.trace ("CONVERTING INFO TABLE TO GPML");
PathwayElement o = data.getMappInfo();
o.setMapInfoName(row[ICOL_TITLE]);
o.setMapInfoDataSource("GenMAPP 2.0");
o.setVersion(row[ICOL_VERSION]);
o.setAuthor(row[ICOL_AUTHOR]);
o.setMaintainer(row[ICOL_MAINT]);
o.setEmail(row[ICOL_EMAIL]);
o.setCopyright(row[ICOL_COPYRIGHT]);
o.setLastModified(row[ICOL_MODIFY]);
o.addComment(row[ICOL_NOTES], "GenMAPP notes");
o.addComment(row[ICOL_REMARKS], "GenMAPP remarks");
//Board size will be calculated
// o.setMBoardWidth(Double.parseDouble(row[icolBoardWidth]));
// o.setMBoardHeight(Double.parseDouble(row[icolBoardHeight]));
o.setDynamicProperty("org.pathvisio.model.WindowWidth", row[ICOL_WINDOWWIDTH]);
o.setDynamicProperty("org.pathvisio.model.WindowHeight", row[ICOL_WINDOWHEIGHT]);
// guess organism based on first two characters of filename
String shortCode = new File (filename).getName().substring(0, 2);
Organism org = Organism.fromCode(shortCode);
if (org != null)
{
o.setOrganism(org.latinName());
}
}
开发者ID:PathVisio，项目名称:pathvisio，代码行数:50，代码来源:MappFormat.java
示例20: setSpeciesFilter
import org.bridgedb.bio.Organism; //导入依赖的package包/类
public void setSpeciesFilter (Organism aOrganism)
{
organism = aOrganism;
initItems();
}
开发者ID:PathVisio，项目名称:pathvisio，代码行数:6，代码来源:DataSourceModel.java
注：本文中的org.bridgedb.bio.Organism类示例整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
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