public class BioPAXGraphQuery
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
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 and Description |
---|
BioPAXGraphQuery() |
Modifier and Type | Method and Description |
---|---|
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
|
public Graph input
public Graph result
public int queryType
public static int SELECT_ENTITIES
public static int ADD_COMPLEXES_EXPAND
public static int ADD_COMPLEXES_NOEXPAND
public static int ADD_PUBLICATIONS
public static int ADD_SPECIES
public static int ADD_CONNECTING_REACTIONS
public static int COMPLETE_REACTIONS
public static int ADD_ALL_REACTIONS
public static int LIST_PUBLICATIONS
public static int LIST_PROTEINS
public static int LIST_COMPLEXES
public static int LIST_REACTIONS
public static int LIST_GENES
public static int LIST_SMALL_MOLECULES
public static BioPAXGraphQuery convertListOfNamesToQuery(java.util.Vector names, java.util.Vector IDs)
public static BioPAXGraphQuery parseXGMML(java.lang.String fn) throws java.lang.Exception
java.lang.Exception
public void parseAccessionTable(java.lang.String fn) throws java.lang.Exception
fn
- java.lang.Exception