uk.ac.ebi.intact.util
Class InsertComplexMerck

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

public class InsertComplexMerck

extends java.lang.Object

Insert binary iteraction data (customize to MERCK format). Custom version for IntAct Merck installation for initial * insertion of Merck and Mint data. Data is read from an input text file. Input file format: Line records, elements are space-delimited: Prey Bait ExperimentLabel addionalInformation * Q05524 P00330 hyb Various data additions, e.g. full Mint record. * The experimentLabel may be a pubmed id. IMPORTANT! The order is prey bait

Version:

$Id: InsertComplexMerck.java,v 1.6 2004/02/26 11:59:29 skerrien Exp $

Author:

Henning Hermjakob, hhe@ebi.ac.uk

, Samuel Kerrien, skerrien@ebi.ac.uk

Field Summary

static java.lang.String

NEW_LINE

Constructor Summary

InsertComplexMerck()
basic constructor - sets up intact helper and protein factory

Method Summary

void	closeHelper() Close the database connexion if it has been opened.
void	insert(java.lang.String filename, java.lang.String taxId, java.lang.String interactionType)
void	insertComplex(java.lang.String baitAC, java.util.ArrayList preyACs, java.lang.String experimentLabel, java.lang.String commentTopicLabel, java.lang.String commentTopicDescription) Inserts a complex into the database If the complex already exists, it is skipped!
void	insertComponent(Interaction interaction, java.lang.String spAc, java.lang.String taxId, CvComponentRole role) Insert a Component object linking an Interactor to an Interaction.
static void	main(java.lang.String[] args) Read complex data from flat file and insert it into the database.

Methods inherited from class java.lang.Object

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

Field Detail

NEW_LINE

public static final java.lang.String NEW_LINE

Constructor Detail

InsertComplexMerck

public InsertComplexMerck()
                   throws java.lang.Exception

basic constructor - sets up intact helper and protein factory

Method Detail

insertComponent

public void insertComponent(Interaction interaction,
                            java.lang.String spAc,
                            java.lang.String taxId,
                            CvComponentRole role)
                     throws java.lang.Exception

Insert a Component object linking an Interactor to an Interaction.

Parameters:

interaction - The interaction to add the Interactor to

spAc - Swiss-Prot accession number of the Protein to add. If the protein does not yet exist, it will be created.

taxId - The tax Id of the target proteins.

role - Role of the protein in the interaction.

Throws:

java.lang.Exception

insertComplex

public void insertComplex(java.lang.String baitAC,
                          java.util.ArrayList preyACs,
                          java.lang.String experimentLabel,
                          java.lang.String commentTopicLabel,
                          java.lang.String commentTopicDescription)
                   throws java.lang.Exception

Inserts a complex into the database If the complex already exists, it is skipped!

Parameters:

baitAC - Swiss-Prot accession number of the bait protein.

preyACs - Swiss-Prot accession numbers of the prey proteins.

experimentLabel - The short label of the experiment the complex belongs to.

Throws:

java.lang.Exception

insert

public void insert(java.lang.String filename,
                   java.lang.String taxId,
                   java.lang.String interactionType)
            throws java.lang.Exception

Parameters:

filename - the filename to parse

taxId - the taxId

interactionType - the CvInteractionType shortlabel which will allow to retreive the right object from the database and then to link it to the created interactions.

Throws:

java.lang.Exception

closeHelper

public void closeHelper()

Close the database connexion if it has been opened.

main

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

Read complex data from flat file and insert it into the database.

Format of the file: One line describe one binary interaction as follow, PREY BAIT EXPERIMENT DESCRIPTION, PREY and BAIT are swiss-prot ACs, EXPERIMENT is preferably a PUBMED id, DESCRIPTION is the rest of the line (stored as an Annotation).

Warning: there is no managment of transaction isolation, they have been removed because nothing were written in the database. So, if anything goes wrong during the loading, the program doesn't stop and some objects may hang around.

Usage of the program: InsertComplexMerck -file -taxId -interactionType

Developper note: the command line interface uses common-cli (jakarta)

Parameters:

args - [0] InputFileName, [1] the tax id of the target proteins, [2] the interaction type of the experiment.

Throws:

java.lang.Exception - for any errors.