本文整理汇总了Java中org.sbml.jsbml.Species.setSBOTerm方法的典型用法代码示例。如果您正苦于以下问题:Java Species.setSBOTerm方法的具体用法?Java Species.setSBOTerm怎么用?Java Species.setSBOTerm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.sbml.jsbml.Species
的用法示例。
在下文中一共展示了Species.setSBOTerm方法的5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: isPromoterSpecies
import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public static boolean isPromoterSpecies(Species species) {
if (species.isSetSBOTerm()) {
if (species.getSBOTerm()==GlobalConstants.SBO_OLD_PROMOTER_SPECIES) {
species.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
return true;
}
if (species.getSBOTerm()==GlobalConstants.SBO_PROMOTER_SPECIES) {
species.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
return true;
} else if (species.getSBOTerm()==GlobalConstants.SBO_PROMOTER_BINDING_REGION) {
return true;
} else if (species.getSBOTermID().equals(GlobalConstants.SBO_DNA_SEGMENT)) {
//species.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
return true;
// TODO: assuming DNA_SEGMENT is promoter
}
}
if (AnnotationUtility.checkObsoleteAnnotation(species,GlobalConstants.TYPE+"="+GlobalConstants.PROMOTER)) {
species.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
AnnotationUtility.removeObsoleteAnnotation(species);
return true;
}
return false;
}
示例2: generateSpecies
import org.sbml.jsbml.Species; //导入方法依赖的package包/类
/**
* Convert the given SBOL FunctionalComponent to its equivalent SBML species.
* SBO terms will be assigned to the generated SBML species to retain the type of SBOL FunctionalComponent.
* Annotation will be performed on the species for any FunctionalComponent information that can't be mapped directly to the SBML species.
*
* @param species - The SBOL FunctionalComponent to convert to SBML species.
* @param sbolDoc - The SBOL Document that contains the SBOL objects to convert to SBML promoter species.
* @param targetModel - The SBML model to store the SBML promoter species created from the conversion.
*/
private static void generateSpecies(FunctionalComponent species, SBOLDocument sbolDoc, BioModel targetModel) {
targetModel.createSpecies(getDisplayID(species), -1, -1);
Species sbmlSpecies = targetModel.getSBMLDocument().getModel().getSpecies(getDisplayID(species));
sbmlSpecies.setBoundaryCondition(species.getDirection().equals(DirectionType.IN));
if (isDNAComponent(species,sbolDoc)) {
sbmlSpecies.setSBOTerm(GlobalConstants.SBO_DNA_SEGMENT);
} else if (isRNAComponent(species,sbolDoc)) {
sbmlSpecies.setSBOTerm(GlobalConstants.SBO_RNA_SEGMENT);
} else if (isProteinComponent(species,sbolDoc)) {
sbmlSpecies.setSBOTerm(GlobalConstants.SBO_PROTEIN);
} else if (isComplexComponent(species,sbolDoc)) {
sbmlSpecies.setSBOTerm(GlobalConstants.SBO_NONCOVALENT_COMPLEX);
} else if (isSmallMoleculeComponent(species,sbolDoc)) {
sbmlSpecies.setSBOTerm(GlobalConstants.SBO_SIMPLE_CHEMICAL);
}
// Annotate SBML species with SBOL component and component definition
annotateSpecies(sbmlSpecies, species, sbolDoc);
}
示例3: createPromoterFromGCM
import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public void createPromoterFromGCM(String s,Properties property) {
Species promoter = sbml.getModel().getSpecies(s);
if (promoter==null) {
promoter = sbml.getModel().createSpecies();
promoter.setId(s);
}
if (property != null && property.containsKey(GlobalConstants.PROMOTER_COUNT_STRING)) {
promoter.setInitialAmount(Double.parseDouble(property.getProperty(GlobalConstants.PROMOTER_COUNT_STRING)));
} else {
promoter.setInitialAmount(sbml.getModel().getParameter(GlobalConstants.PROMOTER_COUNT_STRING).getValue());
}
promoter.setCompartment(getDefaultCompartment());
promoter.setBoundaryCondition(false);
promoter.setConstant(false);
promoter.setHasOnlySubstanceUnits(true);
promoter.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
if (property==null) {
createProductionReaction(s,GlobalConstants.ACTIVATED_STRING,
GlobalConstants.STOICHIOMETRY_STRING,
GlobalConstants.OCR_STRING,
GlobalConstants.KBASAL_STRING,
GlobalConstants.RNAP_BINDING_STRING,
GlobalConstants.ACTIVATED_RNAP_BINDING_STRING,false,null);
} else {
createProductionReaction(s,property.getProperty(GlobalConstants.ACTIVATED_STRING),
property.getProperty(GlobalConstants.STOICHIOMETRY_STRING),
property.getProperty(GlobalConstants.OCR_STRING),
property.getProperty(GlobalConstants.KBASAL_STRING),
property.getProperty(GlobalConstants.RNAP_BINDING_STRING),
property.getProperty(GlobalConstants.ACTIVATED_RNAP_BINDING_STRING),false,null);
}
}
示例4: isMRNASpecies
import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public static boolean isMRNASpecies(SBMLDocument doc, Species species) {
for (int i = 0; i < doc.getModel().getReactionCount(); i++) {
Reaction r = doc.getModel().getReaction(i);
if (isProductionReaction(r)) continue;
for (int j = 0; j < r.getReactantCount(); j++) {
if (r.getReactant(j).getSpecies().equals(species.getId())) return false;
}
for (int j = 0; j < r.getModifierCount(); j++) {
if (r.getModifier(j).getSpecies().equals(species.getId())) return false;
}
for (int j = 0; j < r.getProductCount(); j++) {
if (r.getProduct(j).getSpecies().equals(species.getId())) return false;
}
}
if (species.isSetSBOTerm()) {
if (species.getSBOTerm()==GlobalConstants.SBO_MRNA || species.getSBOTerm()==GlobalConstants.SBO_MRNA_OLD) {
species.setSBOTerm(GlobalConstants.SBO_MRNA);
return species.getId().endsWith("_mRNA");
}
}
if (AnnotationUtility.checkObsoleteAnnotation(species,GlobalConstants.TYPE+"="+GlobalConstants.MRNA)) {
species.setSBOTerm(GlobalConstants.SBO_MRNA);
AnnotationUtility.removeObsoleteAnnotation(species);
return species.getId().endsWith("_mRNA");
}
return false;
}
示例5: createPromoter
import org.sbml.jsbml.Species; //导入方法依赖的package包/类
public String createPromoter(String promoterId, float x, float y, boolean isExplicit,
boolean createProduction, String reactionId) {
createProductionDefaultParameters();
String compartment;
compartment = getCompartmentByLocation(x,y,GlobalConstants.DEFAULT_SPECIES_WIDTH,GlobalConstants.DEFAULT_SPECIES_HEIGHT);
if (compartment.equals("")) {
if (sbml.getModel().getCompartmentCount()==0) {
message.setErrorDialog("Compartment Required", "Species must be placed within a compartment.");
this.notifyObservers(message);
return "";
}
compartment = sbml.getModel().getCompartment(0).getId();
}
Species promoter = sbml.getModel().createSpecies();
// Set default species ID
if (promoterId == null) {
do {
creatingPromoterID++;
promoterId = "P" + String.valueOf(creatingPromoterID);
}
while (SBMLutilities.getElementBySId(sbml, promoterId)!=null);
}
promoter.setId(promoterId);
// Set default promoter metaID
metaIDIndex = SBMLutilities.setDefaultMetaID(sbml, promoter, metaIDIndex);
promoter.setSBOTerm(GlobalConstants.SBO_PROMOTER_BINDING_REGION);
promoter.setInitialAmount(sbml.getModel().getParameter(GlobalConstants.PROMOTER_COUNT_STRING).getValue());
promoter.setCompartment(compartment);
SBMLutilities.cloneDimensionAddIndex(sbml.getModel().getCompartment(compartment),promoter,"compartment");
promoter.setBoundaryCondition(false);
promoter.setConstant(false);
promoter.setHasOnlySubstanceUnits(true);
if (createProduction)
createProductionReaction(promoterId, reactionId, null, null, null, null, null, null, false, null);
if (isExplicit) {
Layout layout = getLayout();
SpeciesGlyph speciesGlyph = null;
if (layout.getSpeciesGlyph(GlobalConstants.GLYPH+"__"+promoterId)!=null) {
speciesGlyph = layout.getSpeciesGlyph(GlobalConstants.GLYPH+"__"+promoterId);
} else {
speciesGlyph = layout.createSpeciesGlyph(GlobalConstants.GLYPH+"__"+promoterId);
speciesGlyph.createBoundingBox();
speciesGlyph.getBoundingBox().createDimensions();
speciesGlyph.getBoundingBox().createPosition();
speciesGlyph.setSpecies(promoterId);
}
speciesGlyph.getBoundingBox().getPosition().setX(x);
speciesGlyph.getBoundingBox().getPosition().setY(y);
speciesGlyph.getBoundingBox().getDimensions().setWidth(GlobalConstants.DEFAULT_SPECIES_WIDTH);
speciesGlyph.getBoundingBox().getDimensions().setHeight(GlobalConstants.DEFAULT_SPECIES_HEIGHT);
TextGlyph textGlyph = layout.createTextGlyph(GlobalConstants.TEXT_GLYPH+"__"+promoterId);
textGlyph.createBoundingBox();
textGlyph.getBoundingBox().createDimensions();
textGlyph.getBoundingBox().createPosition();
textGlyph.setGraphicalObject(GlobalConstants.GLYPH+"__"+promoterId);
textGlyph.setText(SBMLutilities.getArrayId(sbml,promoterId));
textGlyph.setBoundingBox(speciesGlyph.getBoundingBox().clone());
}
return promoterId;
}