Uses of Class
fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option

Packages that use BioPAXToCytoscapeConverter.Option

fr.curie.BiNoM.cytoscape.biopax	Cytoscape interface for working with BioPAX files
fr.curie.BiNoM.pathways	Set of converters for conversion of one systems biology format into an other.

Uses of BioPAXToCytoscapeConverter.Option in fr.curie.BiNoM.cytoscape.biopax

Constructors in fr.curie.BiNoM.cytoscape.biopax with parameters of type BioPAXToCytoscapeConverter.Option

BioPAXImport(java.io.File file, java.net.URL url, java.lang.String name, int[] algos, BioPAXToCytoscapeConverter.Option option)

BioPAXImportTask(java.io.File file, java.net.URL url, java.lang.String name, int[] algos, BioPAXToCytoscapeConverter.Option option, boolean applyLayout)

Uses of BioPAXToCytoscapeConverter.Option in fr.curie.BiNoM.pathways

Methods in fr.curie.BiNoM.pathways with parameters of type BioPAXToCytoscapeConverter.Option

edu.rpi.cs.xgmml.GraphicNode	BioPAXToCytoscapeConverter.addPathwayNode(edu.rpi.cs.xgmml.GraphicGraph grf, pathway p, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes, java.util.HashMap edges, BioPAXToCytoscapeConverter.Option option) Adds a pathway node to Pathway Structure interface
edu.rpi.cs.xgmml.GraphicNode	BioPAXToCytoscapeConverter.addPathwayStepNode(edu.rpi.cs.xgmml.GraphicGraph grf, pathwayStep ps, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes, java.util.HashMap edges, BioPAXToCytoscapeConverter.Option option) Adds a 'pathway step' node to Pathway Structure interface
static BioPAXToCytoscapeConverter.Graph	BioPAXToCytoscapeConverter.convert(int algo, BioPAXToCytoscapeConverter b2c, java.lang.String name, BioPAXToCytoscapeConverter.Option option) Convert using BioPAXToCytoscapeConverter and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
static BioPAXToCytoscapeConverter.Graph	BioPAXToCytoscapeConverter.convert(int algo, java.io.InputStream is, java.lang.String name, BioPAXToCytoscapeConverter.Option option) Convert from InputStream and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
static BioPAXToCytoscapeConverter.Graph	BioPAXToCytoscapeConverter.convert(int algo, java.lang.String file, BioPAXToCytoscapeConverter.Option option) Convert from file (specified by path) and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
static BioPAXToCytoscapeConverter.Graph	BioPAXToCytoscapeConverter.convert(int algo, java.lang.String file, java.lang.String name, BioPAXToCytoscapeConverter.Option option) Convert using file name and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
edu.rpi.cs.xgmml.GraphDocument	BioPAXToCytoscapeConverter.getXGMMLPathwayGraph(java.lang.String name, BioPAX biopax, BioPAXToCytoscapeConverter.Option option) Implementation of extracting Pathway Structure interface (requires first conversion from BioPAX to SBML, from which the interface is converted).
edu.rpi.cs.xgmml.GraphDocument	BioPAXToCytoscapeConverter.getXGMMLProteinGraph(java.lang.String name, BioPAX biopax, BioPAXToCytoscapeConverter.Option option) Implementation of extracting Protein Interaction interface (requires first conversion from BioPAX to SBML, from which the interface is converted).