Java PathwayElement.createPathwayElement方法代码示例

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void actionPerformed(ActionEvent arg0)
{
	List<Graphics> selection = vPathway.getSelectedGraphics();
	if(selection.size() > 0) {
		vPathway.getUndoManager().newAction("Add State");
		for(Graphics g : selection) {
			if(g instanceof GeneProduct) {
				GeneProduct gp = (GeneProduct)g;
				PathwayElement elt = PathwayElement.createPathwayElement(STATE);
				elt.setInitialSize();
				((MState)elt).linkTo (gp.getPathwayElement(), 1.0, 1.0); 
				elt.setShapeType(ShapeType.OVAL);
				engine.getActivePathway().add(elt);
				elt.setGeneratedGraphId();
			}
		}
	}			
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public PathwayElement[] addElements(Pathway p, double mx, double my) {
			PathwayElement e = PathwayElement.createPathwayElement(ObjectType.SHAPE);
			e.setShapeType(type);
			e.setMCenterX(mx);
			e.setMCenterY(my);
			e.setMWidth(1);
			e.setMHeight(1);
			e.setRotation(0);
			e.setGraphId(p.getUniqueGraphId());
			addElement(e, p);

			//brace
//			gdata.setOrientation(OrientationType.RIGHT);

			return new PathwayElement[] { e };
		}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void setUp()
{
	data = new Pathway();
	PathwayElement o = PathwayElement.createPathwayElement(ObjectType.DATANODE);
	data.add (o);

	elementManager = data.getBiopax();
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void testEmpty()
{
	data = new Pathway();
	PathwayElement o = PathwayElement.createPathwayElement(ObjectType.DATANODE);
	data.add (o);
	elementManager = data.getBiopax();

	assertNotNull (elementManager);
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void setUp()
{
	PreferenceManager.init();
	vpwy = new VPathway(null);
	pwy = new Pathway();
	vpwy.fromModel(pwy);

	for (int i = 0; i < DATANODE_COUNT; ++i)
	{
		dn[i] = PathwayElement.createPathwayElement(ObjectType.DATANODE);
		dn[i].setMCenterX(i * 1000);
		dn[i].setMCenterY(3000);
		dn[i].setMWidth(500);
		dn[i].setMHeight(500);
		vDn[i] = (GeneProduct)addElement (vpwy, dn[i]);
		dn[i].setGeneratedGraphId();
	}
	vLn[0] = (Line)addConnector (vpwy, dn[0], dn[1]);
	vLn[1] = (Line)addConnector (vpwy, dn[0], dn[2]);

	vpwy.clearSelection();
	assertNull (dn[0].getGroupRef());
	assertNull (dn[1].getGroupRef());
	vDn[0].select();
	vDn[1].select();
	vLn[0].select();
	// create a group
	vpwy.toggleGroup(vpwy.getSelectedGraphics());
	String ref1 = dn[0].getGroupRef();
	assertNotNull(ref1);
	assertEquals (ref1, dn[1].getGroupRef());
	grp1 = vpwy.getPathwayModel().getGroupById(ref1);
	vGrp1 = (Group)vpwy.getPathwayElementView(grp1);
	grp1.setGeneratedGraphId();
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/** helper for adding connectors to a vpathway */
private VPathwayElement addConnector (VPathway vpwy, PathwayElement l1, PathwayElement l2)
{
	PathwayElement elt = PathwayElement.createPathwayElement(ObjectType.LINE);
	elt.setConnectorType(ConnectorType.ELBOW);
	elt.setStartGraphRef(l1.getGraphId());
	elt.setEndGraphRef(l2.getGraphId());
	elt.setMStartX(l1.getMCenterX());
	elt.setMStartY(l1.getMCenterY());
	elt.setMEndX(l2.getMCenterX());
	elt.setMEndY(l2.getMCenterY());

	return addElement (vpwy, elt);
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void testReadWrite() throws IOException {
	//Add to datanode
	PathwayElement pwElm = PathwayElement.createPathwayElement(ObjectType.DATANODE);
	data.add(pwElm);
	BiopaxReferenceManager dnRefManager = new BiopaxReferenceManager(pwElm);
	pwRefManager = new BiopaxReferenceManager(data.getMappInfo());

	//Test 1:
	//Add two identical publication references, one to the pathway,
	//the other to the pathway element.
	//Expected behaviour:
	//The pathway should have 1 reference with two authors
	//There should only be one reference instance in the biopax element

	//Reference information
	String title = "title1";
	String author1 = "author1";
	String author2 = "author2";

	//Add to pathway element
	PublicationXref xrefObject = new PublicationXref();
	//Add one title and two authors
	xrefObject.setTitle(title);
	xrefObject.addAuthor(author1);
	xrefObject.addAuthor(author2);

	dnRefManager.addElementReference(xrefObject);

	//Add to pathway
	PublicationXref xrefPathway = new PublicationXref();
	//Add one title and two authors
	xrefPathway.setTitle(title);
	xrefPathway.addAuthor(author1);
	xrefPathway.addAuthor(author2);

	pwRefManager.addElementReference(xrefPathway);

	writeRead(data);

	List<PublicationXref> references = pwRefManager.getPublicationXRefs();
	//There has to be one reference
	assertTrue("Should have one literature reference, has " + references.size(), references.size() == 1);
	//With two authors
	assertTrue("Two authors", references.get(0).getAuthors().size() == 2);

	//There should be one publicationxref element total
	int nrElm = elementManager.getElements().size();
	assertTrue("Should have one element total, has " + nrElm, nrElm == 1);


	//Test added 30-08, because of bug where biopax was lost after
	//saving/loading/saving sequence
	//Add another reference to Pathway
	xrefPathway = new PublicationXref();
	//Add one title and one author
	xrefPathway.setTitle("title3");
	xrefPathway.addAuthor("author3");

	pwRefManager.addElementReference(xrefPathway);

	writeRead(data);

	references = pwRefManager.getPublicationXRefs();
	//There have to be two references now
	assertTrue("Two literature references, has " + references.size(), references.size() == 2);
	//Where the one we last added has one author
	PublicationXref xref = (PublicationXref)elementManager.getElement(xrefPathway.getId());
	assertTrue("One author", xref.getAuthors().size() == 1);

}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void setUp()
{
	PreferenceManager.init();
   	pwy = new Pathway();
   	eltDn = PathwayElement.createPathwayElement(ObjectType.DATANODE);
   	eltDn.setMCenterX(3000);
   	eltDn.setMCenterY(3000);
   	eltDn.setElementID("1234");
   	eltDn.setTextLabel("Gene");
   	eltDn.setMWidth(1000);
   	eltDn.setMHeight(1000);
   	eltSh = PathwayElement.createPathwayElement(ObjectType.SHAPE);
   	eltSh.setMCenterX(6000);
   	eltSh.setMCenterY(3000);
   	eltSh.setMWidth(300);
   	eltSh.setMHeight(700);
   	eltLi = PathwayElement.createPathwayElement(ObjectType.LINE);
   	eltLi.setMStartX(500);
   	eltLi.setMStartY(1000);
   	eltLi.setMEndX(2500);
   	eltLi.setMEndY(4000);
   	eltLa = PathwayElement.createPathwayElement(ObjectType.LABEL);
   	eltLa.setMCenterX(6000);
   	eltLa.setMCenterY(6000);
   	eltLa.setMWidth(300);
   	eltLa.setMHeight(700);
   	eltLa.setTextLabel("Test");
   	pwy.add(eltDn);
   	pwy.add(eltSh);
   	pwy.add(eltLi);
   	pwy.add(eltLa);
   	vPwy = new VPathway(null);
   	vPwy.fromModel(pwy);

   	for(VPathwayElement e : vPwy.getDrawingObjects())
   	{
   		if(e instanceof Graphics) {
   			PathwayElement pe = ((Graphics)e).getPathwayElement();
   			if			(pe == eltDn) {
   				vDn = (Graphics)e;
   			} else if 	(pe == eltSh) {
   				vSh = (Graphics)e;
   			} else if	(pe == eltLi) {
   				vLi = (Graphics)e;
   			} else if	(pe == eltLa) {
   				vLa = (Graphics)e;
   			}
   		}
   	}

   	assertFalse(vDn == null);
   	assertFalse(vSh == null);
   	assertFalse(vLi == null);
   	assertFalse(vLa == null);
}