Java Organism类代码示例

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;
}
 

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));
		}
	}

}
 

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();
	}
}
 

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>");
	}
}
 

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);
	}
}
 

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());
	}
}
 

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);
}
 

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);
}
 

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);
}
 

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;
}
 

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);
}
 

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");
	}
}
 

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);
}
 

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);
		}
	}
}
 

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);
		}
	}
}