本文整理汇总了Java中org.pathvisio.core.model.PathwayElement.getObjectType方法的典型用法代码示例。如果您正苦于以下问题:Java PathwayElement.getObjectType方法的具体用法?Java PathwayElement.getObjectType怎么用?Java PathwayElement.getObjectType使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类org.pathvisio.core.model.PathwayElement
的用法示例。
在下文中一共展示了PathwayElement.getObjectType方法的15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,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: actionPerformed
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();
}
}
}
}
示例2: getVPosition
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;
}
示例3: generateNewIds
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);
}
}
}
示例4: vPathwayEvent
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;
}
}
}
}
}
示例5: getTopLeftCorner
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());
}
示例6: getBackpageHTML
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();
}
示例7: usesOldEnsembl
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;
}
示例8: convertEnsembl
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));
}
}
}
示例9: getAnnotationHTML
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();
}
示例10: fromModelElement
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;
}
示例11: selectObjectsByObjectType
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();
}
示例12: addElement
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;
}
示例13: doHighlight
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));
}
}
}
}
}
示例14: pathwayFromTransferable
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;
}
示例15: getManagedDynamicProperties
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;
}