uk.ac.ebi.intact.util
Class InsertComplexGiot

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

public class InsertComplexGiot

extends java.lang.Object

Insert of the Giot data in IntAct

Version:

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

Author:

Samuel Kerrien (skerrien@ebi.ac.uk)

Field Summary

static java.lang.String	ANNOTATION_cDNA
static java.lang.String	ANNOTATION_cDNA_BAIT_3_UTR
static java.lang.String	ANNOTATION_cDNA_BAIT_5_UTR
static java.lang.String	ANNOTATION_cDNA_PREY_3_UTR
static java.lang.String	ANNOTATION_cDNA_PREY_5_UTR
static java.lang.String	ANNOTATION_CONFIDENCE
static java.lang.String	ANNOTATION_NEED_TO_BE_REVISITED
static java.lang.String	ANNOTATION_ORIENTATION

Constructor Summary

InsertComplexGiot(java.lang.String giotUrl, java.lang.String cgSptrMappingUrl, java.lang.String sptrGeneMappingUrl, IntactHelper helper)

Method Summary

java.lang.String	createInteractionShortLabel(java.lang.String bait, java.lang.String prey) Creata an interaction shortlabel.
void	displayStatistics()
void	displayUnmappedIds()
java.lang.String	getGNLine(java.lang.String ac)
BeanStreamReader	getLineBrowser()
java.lang.String	getUrl(java.lang.String sptrAC)
static void	main(java.lang.String[] args) D E M O
void	process(java.lang.String outputFilename)

Methods inherited from class java.lang.Object

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

Field Detail

ANNOTATION_cDNA

public static final java.lang.String ANNOTATION_cDNA

See Also:

Constant Field Values

ANNOTATION_NEED_TO_BE_REVISITED

public static final java.lang.String ANNOTATION_NEED_TO_BE_REVISITED

See Also:

Constant Field Values

ANNOTATION_cDNA_BAIT_5_UTR

public static final java.lang.String ANNOTATION_cDNA_BAIT_5_UTR

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Constant Field Values

ANNOTATION_cDNA_BAIT_3_UTR

public static final java.lang.String ANNOTATION_cDNA_BAIT_3_UTR

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Constant Field Values

ANNOTATION_cDNA_PREY_5_UTR

public static final java.lang.String ANNOTATION_cDNA_PREY_5_UTR

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Constant Field Values

ANNOTATION_cDNA_PREY_3_UTR

public static final java.lang.String ANNOTATION_cDNA_PREY_3_UTR

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Constant Field Values

ANNOTATION_CONFIDENCE

public static final java.lang.String ANNOTATION_CONFIDENCE

See Also:

Constant Field Values

ANNOTATION_ORIENTATION

public static final java.lang.String ANNOTATION_ORIENTATION

See Also:

Constant Field Values

Constructor Detail

InsertComplexGiot

public InsertComplexGiot(java.lang.String giotUrl,
                         java.lang.String cgSptrMappingUrl,
                         java.lang.String sptrGeneMappingUrl,
                         IntactHelper helper)
                  throws java.net.MalformedURLException,
                         java.io.IOException,
                         IntactException,
                         java.lang.NoSuchMethodException,
                         UpdateProteinsI.UpdateException

Method Detail

getLineBrowser

public BeanStreamReader getLineBrowser()

displayStatistics

public void displayStatistics()

displayUnmappedIds

public void displayUnmappedIds()

process

public void process(java.lang.String outputFilename)
             throws java.io.IOException,
                    IntactException,
                    java.lang.IllegalAccessException,
                    java.lang.reflect.InvocationTargetException,
                    java.lang.InstantiationException

java.io.IOException

IntactException

java.lang.IllegalAccessException

java.lang.reflect.InvocationTargetException

java.lang.InstantiationException

getUrl

public final java.lang.String getUrl(java.lang.String sptrAC)

getGNLine

public java.lang.String getGNLine(java.lang.String ac)

createInteractionShortLabel

public java.lang.String createInteractionShortLabel(java.lang.String bait,
                                                    java.lang.String prey)
                                             throws IntactException

Creata an interaction shortlabel.
Take care about the maximum length of the field.

Parameters:

bait -

prey -

Returns:

IntactException

main

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

D E M O

Parameters:

args - [0] fileParsing URL from which we'll read the data

java.lang.Exception