fr.curie.BiNoM.pathways.utils
Class BioPAXGraphQuery

java.lang.Object
  fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

public class BioPAXGraphQuery
extends java.lang.Object

A simple container of the BioPAX standard query

Field Summary

static int	ADD_ALL_REACTIONS For all species adds all reactions in which they participate
static int	ADD_COMPLEXES_EXPAND For a set of entities in the input adds all complexes in which at list one participates
static int	ADD_COMPLEXES_NOEXPAND For a set of entities in the input adds all their complexes
static int	ADD_CONNECTING_REACTIONS For all chemical species adds reactions in which at least one of the species participates as reactants and another one as product
static int	ADD_PUBLICATIONS Simply connects all publicationXrefs to the entities
static int	ADD_SPECIES For all entities adds all their forms (chemical species)
static int	COMPLETE_REACTIONS For all reactions, attaches all connected nodes from the index (species, publications, pathway steps, etc.)
Graph	input Input for the query
static int	LIST_COMPLEXES Simply lists the proteins from the input to the query log
static int	LIST_GENES Simply lists the dnas from the input to the query log
static int	LIST_PROTEINS Simply lists the proteins from the input to the query log
static int	LIST_PUBLICATIONS Simply lists the publications from the input to the query log
static int	LIST_REACTIONS Simply lists the reactions from the input to the query log
static int	LIST_SMALL_MOLECULES Simply lists the smallMolecules from the input to the query log
int	queryType Predefined query type
Graph	result Output of the query
static int	SELECT_ENTITIES Identifying entities by names and XREFs in the index

Constructor Summary

BioPAXGraphQuery()

Method Summary

static BioPAXGraphQuery	convertListOfNamesToQuery(java.util.Vector names, java.util.Vector IDs) Utility converting vector of names and ids to a BioPAXGraphQuery object
void	parseAccessionTable(java.lang.String fn) deprecated
static BioPAXGraphQuery	parseXGMML(java.lang.String fn) Loads BioPAXGraphQuery from a XGMML file

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

input

public Graph input

Input for the query

result

public Graph result

Output of the query

queryType

public int queryType

Predefined query type

SELECT_ENTITIES

public static int SELECT_ENTITIES

Identifying entities by names and XREFs in the index

ADD_COMPLEXES_EXPAND

public static int ADD_COMPLEXES_EXPAND

For a set of entities in the input adds all complexes in which at list one participates

ADD_COMPLEXES_NOEXPAND

public static int ADD_COMPLEXES_NOEXPAND

For a set of entities in the input adds all their complexes

ADD_PUBLICATIONS

public static int ADD_PUBLICATIONS

Simply connects all publicationXrefs to the entities

ADD_SPECIES

public static int ADD_SPECIES

For all entities adds all their forms (chemical species)

ADD_CONNECTING_REACTIONS

public static int ADD_CONNECTING_REACTIONS

For all chemical species adds reactions in which at least one of the species participates as reactants and another one as product

COMPLETE_REACTIONS

public static int COMPLETE_REACTIONS

For all reactions, attaches all connected nodes from the index (species, publications, pathway steps, etc.)

ADD_ALL_REACTIONS

public static int ADD_ALL_REACTIONS

For all species adds all reactions in which they participate

LIST_PUBLICATIONS

public static int LIST_PUBLICATIONS

Simply lists the publications from the input to the query log

LIST_PROTEINS

public static int LIST_PROTEINS

Simply lists the proteins from the input to the query log

LIST_COMPLEXES

public static int LIST_COMPLEXES

Simply lists the proteins from the input to the query log

LIST_REACTIONS

public static int LIST_REACTIONS

Simply lists the reactions from the input to the query log

LIST_GENES

public static int LIST_GENES

Simply lists the dnas from the input to the query log

LIST_SMALL_MOLECULES

public static int LIST_SMALL_MOLECULES

Simply lists the smallMolecules from the input to the query log

Constructor Detail

BioPAXGraphQuery

public BioPAXGraphQuery()

Method Detail

convertListOfNamesToQuery

public static BioPAXGraphQuery convertListOfNamesToQuery(java.util.Vector names,
                                                         java.util.Vector IDs)

Utility converting vector of names and ids to a BioPAXGraphQuery object

parseXGMML

public static BioPAXGraphQuery parseXGMML(java.lang.String fn)
                                   throws java.lang.Exception

Loads BioPAXGraphQuery from a XGMML file

Throws:

java.lang.Exception

parseAccessionTable

public void parseAccessionTable(java.lang.String fn)
                         throws java.lang.Exception

deprecated

Parameters:

fn -

Throws:

java.lang.Exception