fr.curie.BiNoM.pathways.utils
Class AccessionNumberTable

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

public class AccessionNumberTable
extends java.lang.Object

Class for conversion from some accession numbers and names to the id- and namespace used by a database

Field Summary

java.util.HashMap	idname Map from id used by a database to the Vector of names in the table (id - is database identifier, name - some common name or accession number)
java.util.HashMap	nameid Map from name in the table used to the Vector of database ids/names

Constructor Summary

AccessionNumberTable()

Method Summary

void	addSynonyms(BioPAXGraphQuery query) To every node of query adds BIOPAX_NODE_SYNONYM attribute accordingly to found ids connected to the Node.Id
java.util.Vector	getIDList(java.util.Vector names)
void	loadTable(java.lang.String fn) Loads tab delimited two-columns table \t
void	print() Prints the whole table in the form \t

Methods inherited from class java.lang.Object

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

Field Detail

idname

public java.util.HashMap idname

Map from id used by a database to the Vector of names in the table (id - is database identifier, name - some common name or accession number)

nameid

public java.util.HashMap nameid

Map from name in the table used to the Vector of database ids/names

Constructor Detail

AccessionNumberTable

public AccessionNumberTable()

Method Detail

loadTable

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

Loads tab delimited two-columns table \t

Throws:

java.lang.Exception

getIDList

public java.util.Vector getIDList(java.util.Vector names)

Parameters:

names - list of some names

Returns:

list of all corresponding ids

print

public void print()

Prints the whole table in the form \t

addSynonyms

public void addSynonyms(BioPAXGraphQuery query)

To every node of query adds BIOPAX_NODE_SYNONYM attribute accordingly to found ids connected to the Node.Id