uk.ac.ebi.intact.util
Class InsertGo

java.lang.Object
  |
  +--uk.ac.ebi.intact.util.InsertGo

public class InsertGo

extends java.lang.Object

Create GO crossreferences for Protein objects. Data is read from an input text file. Input file format: Line records, elements are tab-delimited SP AC SGD SGD AC Systematic GO ac References GO name from evidence SGD P04710 SGD S0004660 AAC1 GO:0005743 SGD_REF:12031|PMID:2167309 TAS C ADP/ATP translocator YMR056C gene taxon:4932 20010118

Author:

Henning Hermjakob, hhe@ebi.ac.uk

Field Summary

static int

MAX_ID_LEN

Constructor Summary

InsertGo()
basic constructor - sets up (hard-coded) data source and an intact helper

Method Summary

void	addNewXref(AnnotatedObject current, Xref xref) Add a new xref to an annotatedObject.
static void	main(java.lang.String[] args)
java.util.HashMap	parseGoDefs(java.lang.String aUrl) Reads a GO definition file from a URL.
Protein	updateProtein(java.lang.String shortLabel, java.lang.String spAc, java.lang.String sgdAc, java.lang.String goAc, java.lang.String pubmedAc) Insert or update a protein object.

Methods inherited from class java.lang.Object

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

Field Detail

MAX_ID_LEN

public static final int MAX_ID_LEN

See Also:

Constant Field Values

Constructor Detail

InsertGo

public InsertGo()
         throws java.lang.Exception

basic constructor - sets up (hard-coded) data source and an intact helper

Method Detail

addNewXref

public void addNewXref(AnnotatedObject current,
                       Xref xref)
                throws CreateException

Add a new xref to an annotatedObject.

CreateException

updateProtein

public Protein updateProtein(java.lang.String shortLabel,
                             java.lang.String spAc,
                             java.lang.String sgdAc,
                             java.lang.String goAc,
                             java.lang.String pubmedAc)
                      throws IntactException,
                             CreateException,
                             UpdateException

Insert or update a protein object. Set the shortLabel, add SP ac, SGD ac, GO term(s) and Pubmed IDs as crossreferences.

IntactException

CreateException

UpdateException

parseGoDefs

public java.util.HashMap parseGoDefs(java.lang.String aUrl)

Reads a GO definition file from a URL.

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

java.lang.Exception