Java ListOf.size方法代码示例

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Creates the sampled domain order.
 *
 * @param losv the losv
 */
private void createSampledDomainOrder(ListOf<SampledVolume> losv){
	int numDom = (int) losv.size();
	List<Double> sampleList = new ArrayList<Double>();
	for(int i = 0; i < numDom ; i++){
		sampleList.add(losv.get(i).getSampledValue());
	}
	Collections.sort(sampleList);
	for(int i = 0; i < numDom ; i++){
		for(int j = 0 ; j < numDom ; j++){
			SampledVolume sv = losv.get(j);
			if(sampleList.get(i) == sv.getSampledValue()){
				orderedList.add(sv.getDomainType());		
			}
		}
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Adds the coord parameter.
 */
public void addCoordParameter() {
	ListOf<CoordinateComponent> lcc = geometry.getListOfCoordinateComponents();
	Parameter p;
	CoordinateComponent cc;
	for (int i = 0; i < lcc.size(); i++) {
		cc = (CoordinateComponent) lcc.get(i);
		p = model.createParameter();
		p.setId("coordinate" + cc.getSpatialId());
		p.setConstant(true);
		p.setValue(0d);
		SpatialParameterPlugin spp = (SpatialParameterPlugin) p.getPlugin(SpatialConstants.namespaceURI);
		SpatialSymbolReference ssr = new SpatialSymbolReference();
		ssr.setSpatialRef(cc.getSpatialId());
		spp.setParamType(ssr);
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
@Override
protected void createImage(){
	ListOf<SampledField> losf = g.getListOfSampledFields();
	//TODO : be able create image with multiple sampledfield
	if(losf.size() > 1)
		System.err.println("not able to compute multiple sampledfields at this point");

	SampledField sf = losf.get(0);
	if(sf.getDataType() != DataKind.UINT8)
		System.err.println("Image data is automatically changed to 8 bit image");
	getSize(sf);
	getArray(sf);

	ImageStack is = createStack();
	img.setStack(is);
	img.setTitle(title);
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Units to string.
 *
 * @param lou the lou
 * @return the string
 */
private String unitsToString(ListOf<Unit> lou){
	StringBuilder sb = new StringBuilder();
	
	for(int i = 0; i< lou.size(); i++){
		Unit unit = lou.get(i);
		String mul = unit.getMultiplier() == 1 ? "" : String.valueOf(unit.getMultiplier()) + " *";
		String scale =  unit.getScale() == 0 ? "" : "10^" + unit.getScale() + " *";
		String exp = unit.getExponent() == 1 ? "" : "^" + String.valueOf(unit.getExponent());
		String kind = SBMLProcessUtil.unitIndexToString(unit.getKind()); 
		sb.append("(" + mul  + scale +  " " + kind + " )" + exp);
		if(i < lou.size() - 1) 
			sb.append(" * ");
	}
	
	return sb.toString();
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Reorder species references list.
 *
 * @param srList
 *        the sr list
 * @return the list
 */
private ListOf<SpeciesReference> reorderSpeciesReferencesList(
  ListOf<SpeciesReference> srList) {
  SpeciesReference sr = srList.get(0);
  SpeciesWrapper sw = mWrapper.getSpeciesWrapperById(sr.getSpecies());
  if (sw.getClazz().equals("PROTEIN") || sw.getClazz().equals("GENE")
      || sw.getClazz().equals("RNA") || sw.getClazz().equals("ANTISENSE_RNA")) {
    return srList;
  }
  for (int i = 1; i < srList.size(); i++) {
    sr = srList.get(i);
    sw = mWrapper.getSpeciesWrapperById(sr.getSpecies());
    if (sw.getClazz().equals("PROTEIN") || sw.getClazz().equals("GENE")
        || sw.getClazz().equals("RNA") || sw.getClazz().equals("ANTISENSE_RNA")) {
      Collections.swap(srList, 0, i);
    }
  }
  return srList;
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Creates the analytic domain order.
 *
 * @param listOf the list of
 */
private void createAnalyticDomainOrder(ListOf<AnalyticVolume> listOf){
	int numDom = (int) listOf.size();
	
	for(int i = 0 ; i < numDom ; i++){
		for(int j = 0; j < numDom ; j++){
			AnalyticVolume	av = listOf.get(j);
			if(av.getOrdinal() == i){
				orderedList.add(av.getDomainType());
			}
		}
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Edge.
 * TODO change to a better algorithm since this assumes the order of load to be specified
 *
 * @param load the load
 */
public void addEdge(ListOf<AdjacentDomains> load){
	for(int i = 0; i < load.size(); i+=2){
		String dom1 = ((AdjacentDomains)load.get(i)).getDomain2();
		String dom2 = ((AdjacentDomains)load.get(i+1)).getDomain2();
		lod.get(dom1);
		if(getOrder(dom1, dom2))
			graphStruct.addEdge(dom1, dom2);
		else
			graphStruct.addEdge(dom2, dom1);
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Vertex.
 *
 * @param lod the lod
 */
public void addVertex(ListOf<Domain> lod) {
	Domain dom;
	for (int i = 0; i < lod.size(); i++) {
		dom = lod.get(i);
		if(getDomainType(dom.getDomainType()).getSpatialDimensions() == dimension)
			graphStruct.addVertex(dom.getSpatialId());
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Createsp img list.
 */
protected void createspImgList(){
	ListOf<GeometryDefinition> logd = geometry.getListOfGeometryDefinitions();
	SpatialImage spImg; 
	for(int i = 0 ; i < logd.size() ; i++){
		GeometryDefinition gd = logd.get(i);
		spImg = getSpImgFromGeo(gd);
		if(spImg != null)
			spImgList.add(spImg);
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Sets the parameter to list.
 *
 * @param lop the new parameter to list
 */
private void setParameterToList(ListOf<Parameter> lop){
	long max = lop.size();
	for(int i = 0; i < max; i++){
		Parameter p = lop.get(i);
		SpatialParameterPlugin sp = (SpatialParameterPlugin) p.getPlugin("spatial");
		if(!(sp.getParamType() instanceof DiffusionCoefficient)) continue;
		memberList.add(p.clone());
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
@Override
void getSampledValues() {
	ListOf<AnalyticVolume> loav = ag.getListOfAnalyticVolumes();
	int numDom = (int) loav.size();
	int intervalVal = (int) Math.floor(255 / (numDom - 1));		//divide 255 by num of domains excluding EC
	
	for(int i = 0 ; i < numDom ; i++){
		AnalyticVolume av = loav.get(i);
		hashSampledValue.put(av.getDomainType(), av.getOrdinal() * intervalVal);
	}		
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * List id to string array.
 *
 * @param lo the lo
 * @return the string[]
 */
public static String[] listIdToStringArray(ListOf<?> lo){
	String[] str = new String[(int)lo.size()];
			
	for(int i = 0; i < lo.size(); i++)
		str[i] = ((Symbol)lo.get(i)).getId();
	
	return str;
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Sets the parameter to list.
 *
 * @param lop the new parameter to list
 */
private void setParameterToList(ListOf<Parameter> lop){
	long max = lop.size();
	for(int i = 0; i < max; i++){
		Parameter p = lop.get(i);
		SpatialParameterPlugin sp = (SpatialParameterPlugin) p.getPlugin("spatial");
		if(!(sp.getParamType() instanceof AdvectionCoefficient)) continue;
		memberList.add(p.clone());
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Sets the unit definition to list.
 *
 * @param loud the new unit definition to list
 */
private void setUnitDefinitionToList(ListOf<UnitDefinition> loud){
	long max = loud.size();
	for(int i = 0; i < max; i++){
		UnitDefinition ud = loud.get(i);
		memberList.add(ud.clone());
	}
}
 

import org.sbml.jsbml.ListOf; //导入方法依赖的package包/类
/**
 * Bool species in S reference.
 *
 * @param los the los
 * @param losr the losr
 * @return the boolean[]
 */
private boolean[] boolSpeciesInSReference(ListOf<Species> los, ListOf<SpeciesReference> losr){
	boolean[] bool = new boolean[(int)los.size()];
	
	for(int i = 0; i < los.size(); i++)
		for(int j = 0; j < losr.size(); j++)
			if(los.get(i).getId().equals(losr.get(j).getSpecies()))
				bool[i] = true;
		
	return bool;
}