Java PathwayElement.getObjectType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 e) {
	vPathway.resetHighlight();
		for(PathwayElement pe : vPathway.getPathwayModel().getDataObjects()) {
			if(pe.getObjectType() == ObjectType.LINE) {
				Line vl = (Line)vPathway.getPathwayElementView(pe);
				String grs = pe.getStartGraphRef();
				String gre = pe.getEndGraphRef();
				if(grs == null || "".equals(grs)) {
					vl.getStart().highlight();
				}
				if(gre == null || "".equals(gre)) {
					vl.getEnd().highlight();
				}
			}
		}
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
protected Point2D getVPosition() {
	PathwayElement mParent = parent.getPathwayElement();

	Point2D vp = null;
	//Check for mappinfo object, needs a special treatment,
	//since it has no bounds in the model
	if(mParent.getObjectType() == ObjectType.MAPPINFO) {
		Rectangle2D vb = parent.getVBounds();
		double x = rPosition.getX();
		double y = rPosition.getY();
		if(vb.getWidth() != 0) x *= vb.getWidth() / 2;
		if(vb.getHeight() != 0) y *= vb.getHeight() / 2;
		x += vb.getCenterX();
		y += vb.getCenterY();
		vp = new Point2D.Double(x, y);
	} else { //For other objects, use the model bounds
		Point2D mp = mParent.toAbsoluteCoordinate(rPosition);
		vp = new Point2D.Double(vFromM(mp.getX()), vFromM(mp.getY()));
	}
	return vp;
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * Generate new id's for a bunch of elements to be pasted, but do not actually set them.
 * Instead, store these new ids in a map, so that we can later update
 * both the graphIds and graphReferences,
 * as well as groupIds and groupReferences.
 *
 * idMap and newIds should be an empty map / set.
 * It will be filled by this method.
 */
private void generateNewIds(List<PathwayElement> elements,
		Map<String, String> idmap, Set<String> newids)
{
	for (PathwayElement o : elements)
	{
		String id = o.getGraphId();
		String groupId = o.getGroupId();
		generatePasteId(id, data.getGraphIds(), idmap, newids);
		generatePasteId(groupId, data.getGroupIds(), idmap, newids);

		//For a line, also process the point ids
		if(o.getObjectType() == ObjectType.LINE || o.getObjectType() == ObjectType.GRAPHLINE) {
			for(MPoint mp : o.getMPoints())
				generatePasteId(mp.getGraphId(), data.getGraphIds(), idmap, newids);
			for(MAnchor ma : o.getMAnchors())
				generatePasteId(ma.getGraphId(), data.getGraphIds(), idmap, newids);
		}
	}
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void vPathwayEvent(VPathwayEvent e) {
	if(e.getType() == VPathwayEventType.ELEMENT_DRAWN) {
		VPathwayElement vpwe = e.getAffectedElement();
		if(vpwe instanceof Graphics) {
			PathwayElement pwe = ((Graphics)vpwe).getPathwayElement();
			List<Color> elmColors = colors.get(pwe);
			if(elmColors != null && elmColors.size() > 0) {
				Logger.log.info("Coloring " + pwe + " with " + elmColors);
				switch(pwe.getObjectType()) {
				case DATANODE:
					doColor(e.getGraphics2D(), (Graphics)vpwe, elmColors);
					drawLabel(e.getGraphics2D(), (Graphics)vpwe);
					break;
				case GROUP:
					doColor(e.getGraphics2D(), (Graphics)vpwe, elmColors);
					break;
				}
			}
		}
	}
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * Returns the top left corner of the bounding box around the elements
 * @param elements = list of PathwayElement objects
 * @return
 */
private Point2D.Double getTopLeftCorner(List<PathwayElement> elements) {
	
	Rectangle2D vr = null;
	for (PathwayElement o : elements)
	{
		if (o.getObjectType() == ObjectType.INFOBOX) continue;
		if (o.getObjectType() == ObjectType.BIOPAX) continue;
		else {
			if (vr == null) vr = o.getMBounds();
			else vr.add(o.getMBounds());
		}
	}
	
	return new Point2D.Double(vr.getX(), vr.getY());
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * generates html for a given PathwayElement. Combines the base
 * header with fragments from all BackpageHooks into one html String.
 */
public String getBackpageHTML(PathwayElement e)
{
	if (e == null) {
		return "<p>No pathway element is selected.</p>";
	} else if (e.getObjectType() != ObjectType.DATANODE && e.getObjectType() != ObjectType.LINE) {
		return "<p>Backpage is not available for this type of element.<BR>Only DataNodes or Interactions can have a backpage.</p>";
	} else if (e.getDataSource() == null || e.getXref().getId().equals("")) {
		return "<p>There is no annotation for this pathway element defined.</p>";
	}
	StringBuilder builder = new StringBuilder(backpagePanelHeader);
	for (BackpageHook h : hooks)
	{
		builder.append(h.getHtml(e));
	}
	builder.append ("</body></html>");
	return builder.toString();
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的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.pathvisio.core.model.PathwayElement; //导入方法依赖的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.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * generates html for a given PathwayElement. Combines the base header with
 * fragments from all BackpageHooks into one html String.
 */
public String getAnnotationHTML(PathwayElement e) {
	if (e == null) {
		return "<p>No pathway element is selected.</p>";
	} else if (e.getObjectType() != ObjectType.DATANODE
			&& e.getObjectType() != ObjectType.LINE) {
		return "<p>It is currently not possible to annotate this type of pathway element." +
				"<BR>Only DataNodes and Interactions can be annotated.</p>";
	} else if (e.getDataSource() == null || e.getXref().getId().equals("")) {
		return "<p>This pathway element has not yet been annotated.</p>";
	}
	StringBuilder builder = new StringBuilder(backpagePanelHeader);
	for (DataHook h : hooks) {
		builder.append(h.getHtml(e));
	}
	builder.append("</body></html>");
	return builder.toString();
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * Map the contents of a single data object to this VPathway.
 */
private Graphics fromModelElement(PathwayElement o)
{
	Graphics result = null;
	switch (o.getObjectType())
	{
	case DATANODE:
		result = new GeneProduct(this, o);
		break;
	case SHAPE:
		result = new Shape(this, o);
		break;
	case LINE:
		result = new Line(this, o);
		break;
	case GRAPHLINE:
		result = new Line(this, o);
		break;	
	case MAPPINFO:
		InfoBox mi = new InfoBox(this, o);
		result = mi;
		mi.markDirty();
		break;
	case LABEL:
		result = new Label(this, o);
		break;
	case GROUP:
		result = new Group(this, o);
		break;
	case STATE:
		result = new State (this, o);
		break;
	case LEGEND:
		result = new Legend(this, o);
		break;
	default:
		break;
	}
	return result;
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
public void selectObjectsByObjectType(ObjectType ot) {
	clearSelection();
	selection.startSelecting();
	for(PathwayElement pe : getPathwayModel().getDataObjects()) {
		if(pe.getObjectType() == ot) {
			selection.addToSelection(getPathwayElementView(pe));
		}
	}
	selection.stopSelecting();
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
Set<PathwayElement> addElement(PathwayElement pwe, Set<PathwayElement> set) {
	Set<PathwayElement> added = new HashSet<PathwayElement>();
	
	if(pwe != null) {
		//If it's a group, add all subelements
		if(pwe.getObjectType() == ObjectType.GROUP) {
			for(PathwayElement ge : pwe.getParent().getGroupElements(pwe.getGroupId())) {
				added.addAll(addElement(ge, set));
			}
		}
		set.add(pwe);
		added.add(pwe);
	}
	return added;
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * Highlight all object but DataNodes and Groups. Only the first color
 * from the hashmap will be used.
 */
private void doHighlight() {
	for(VPathwayElement vpe : vPathway.getDrawingObjects()) {
		if(vpe instanceof Graphics) {
			PathwayElement pwe = ((Graphics)vpe).getPathwayElement();
			List<Color> elmColors = colors.get(pwe);
			if(elmColors != null && elmColors.size() > 0) {
				ObjectType ot = pwe.getObjectType();
				if(ot != ObjectType.DATANODE && ot != ObjectType.GROUP) {
					vpe.highlight(elmColors.get(0));
				}
			}
		}
	}
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * Creates a pathway from the data in the provided {@link Transferable}.
 * @param t
 * @return
 * @throws ConverterException
 * @throws MalformedURLException
 * @throws UnsupportedFlavorException
 * @throws IOException
 */
public static Pathway pathwayFromTransferable(Transferable t) throws ConverterException, MalformedURLException, UnsupportedFlavorException, IOException {
	Pathway pnew = new Pathway();

	String xml = getText(t);
	if(xml != null) {
		GpmlFormat.readFromXml(pnew, new StringReader(xml), true);

		List<PathwayElement> elements = new ArrayList<PathwayElement>();
		for(PathwayElement elm : pnew.getDataObjects()) {
			if(elm.getObjectType() != ObjectType.MAPPINFO) {
				elements.add(elm);
			} else {
				//Only add mappinfo if it's not generated by the transferable
				String source = elm.getMapInfoDataSource();
				if(!PathwayTransferable.INFO_DATASOURCE.equals(source)) {
					elements.add(elm);
				}
			}
		}
		return pnew;
	}

	URL url = getFileURL(t);
	if(url != null) {
		File file = new File(url.getFile());
		pnew.readFromXml(file, true);
		return pnew;
	}
	return null;
}
 

import org.pathvisio.core.model.PathwayElement; //导入方法依赖的package包/类
/**
 * Get all managed dynamic properties that fall within the scope of the
 * given pathway element.
 *
 * @see #setPropertyScope(Property, EnumSet) for info on how to configure the property
 *      scope.
 */
private static Collection<Property> getManagedDynamicProperties(PathwayElement e) {
	Set<Property> props = new HashSet<Property>();

	ObjectType type = e.getObjectType();
	for (Property p : MANAGED_DYNAMIC_PROPERTIES) {
		EnumSet<ObjectType> scope = PROPERTY_SCOPE.get(p);
		if (scope == null || scope.contains(type))
			props.add(p);
	}
	return props;
}