uk.ac.ebi.intact.application.goDensity.business.binaryInteractions
Class CalcBinInteractionData

java.lang.Object
  |
  +--uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet
        |
        +--uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.CalcBinInteractionData

public class CalcBinInteractionData

extends Key2HashSet

CalcBinInteractionData can be used to generate binary interactions from intAct core model. The generated binary interactions will be stored in a seperate redundant (speed) table which look like this:
bait | prey | gobait | goprey

bait is a fictive bait protein within a binary interacction. prey is the corresponding proteins to the bait. go-bait/prey are the corresponding goIds to the proteins within a interaction

Version:

$Id: CalcBinInteractionData.java,v 1.3 2003/11/14 14:59:51 skerrien Exp $

Author:

Markus Brosch (markus @ brosch.cc)

Field Summary

Fields inherited from class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet

_key2HashSet, _values

Constructor Summary

CalcBinInteractionData(IntactHelper helper, boolean ifABait, boolean ifNoBait, boolean baitBait)
Constructor of CalcBinaryInteractionData
The parameter CalcBinaryInteractionData(helper, true, true, false) is for us at the moment the best way to generate BinaryInteractions with biological significant sense.

Method Summary

void	dbPopulate(boolean addIfProteinNoGoId) populate database with binary interaction data - but only if bait and prey are annotated by go.

Methods inherited from class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet

add, containsKey, getAll, getKeys, getValueByKey, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

CalcBinInteractionData

public CalcBinInteractionData(IntactHelper helper,
                              boolean ifABait,
                              boolean ifNoBait,
                              boolean baitBait)
                       throws IntactException

Constructor of CalcBinaryInteractionData
The parameter CalcBinaryInteractionData(helper, true, true, false) is for us at the moment the best way to generate BinaryInteractions with biological significant sense.

Parameters:

helper - IntactHelper instance

ifABait - if there is a bait for a Interaction (Complex) then:
- true: crossproduct (spokes model)
- false: allVsAll (clique model)

ifNoBait - is there is no bait for a Interaction (Complex) then:
- true: crossproduct (choose random bait)
- false: allVsAll (clique model)

baitBait - if there are more baits for this Interaction (Complex)
(btw: no real biological sense, but for the case there are ...)
- true: connect if more bait: clique on bait-bait
- false: don't connect bait-bait

Method Detail

dbPopulate

public void dbPopulate(boolean addIfProteinNoGoId)
                throws java.sql.SQLException,
                       IntactException,
                       KeyNotFoundException

populate database with binary interaction data - but only if bait and prey are annotated by go. Every bait-prey-gobait-goprey entry is unique and will be modeled only once, even if the data in the model itself would provide duplicate data.

Parameters:

addIfProteinNoGoId - if bait and/or prey have no annotated GO:ID, then for:
- true -> only bait, prey will be added to db and goBait, goPrey are ""
- false -> if either bait or prey or both have no GO:ID, then this pair is not added to db!

java.sql.SQLException

IntactException

KeyNotFoundException