Package psidev.psi.mi.jami.crosslink.io.parser

Class AbstractCsvInteractionEvidenceParser<T extends InteractionEvidence>

java.lang.Object

psidev.psi.mi.jami.crosslink.io.parser.AbstractCsvInteractionEvidenceParser<T>

All Implemented Interfaces:

com.googlecode.jcsv.reader.CSVEntryParser<T>

Direct Known Subclasses:

CsvBinaryInteractionEvidenceParser, CsvInteractionEvidenceParser

public abstract class AbstractCsvInteractionEvidenceParser<T extends InteractionEvidence>
extends Object
implements com.googlecode.jcsv.reader.CSVEntryParser<T>

Abstract class for crosslink CSV parser

Since:

22/08/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
AbstractCsvInteractionEvidenceParser()

Method Summary

Modifier and Type	Method	Description
protected CsvFeatureEvidence	createCrossLinkFeatureEvidence(CsvRange range)	createCrossLinkFeatureEvidence.
protected CsvExperimentalParticipantPool	createExperimentalParticipantPool(List<CsvProtein> csvProteins, int lineNumber, int columnNumber, List<CsvRange> csvRanges)	createExperimentalParticipantPool.
protected ParticipantEvidence	createParticipantEvidence(String protein1, int protein1Index, String pepPos, int pepPos1Index, String linkedPos, int linkedPosIndex)	createParticipantEvidence.
protected CsvParticipantEvidence	createParticipantEvidence(CsvProtein csvProtein, int lineNumber, int columnNumber, CsvRange range)	createParticipantEvidence.
protected CsvProtein	createProteinFromNameAndIdentifier(String protein, int lineNumber, int columnNumber)	createProteinFromNameAndIdentifier.
protected List<CsvProtein>	createProteinsFromString(String protein1, int lineNumber, int columnNumber)	createProteinsFromString.
CsvParserListener	getParserListener()	Getter for the field parserListener.
void	initialiseColumnNames(List<String> data)	initialiseColumnNames.
protected abstract T	instantiateInteractionEvidence(int linePosition, String bait)	instantiateInteractionEvidence.
boolean	isStarted()	isStarted.
protected List<CsvRange>	parseCrossLinkingFeatures(String pepPos, String linkedPos, int lineNumber, int pepColumnNumber, int linkedColumnNumber)	parseCrossLinkingFeatures.
T	parseEntry(String... data)	parseEntry.
protected List<CsvRange>	parsePositions(String pos, int lineNumber, int colNumber)	parsePositions.
protected void	processInvalidPosition(String message, FileSourceContext context)	processInvalidPosition.
protected void	processMismatchPeptidePositions(List<CsvRange> peptidePositions, List<CsvRange> linkedPositions)	processMismatchPeptidePositions.
protected void	processMismatchProteinPositions(List<CsvRange> rangePositions, List<CsvProtein> proteins)	processMismatchProteinPositions.
protected void	processNoProtein1Error(int lineNumber)	processNoProtein1Error.
protected void	processProteinIdentifiersError(String[] identifiers, int lineNumber, int columnNumber)	processProteinIdentifiersError.
void	setParserListener(CsvParserListener parserListener)	Setter for the field parserListener.

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractCsvInteractionEvidenceParser

public AbstractCsvInteractionEvidenceParser()

Method Detail

parseEntry

public T parseEntry(String... data)

parseEntry.

Specified by:

parseEntry in interface com.googlecode.jcsv.reader.CSVEntryParser<T extends InteractionEvidence>

Parameters:

data - a String object.

Returns:

a T object.

getParserListener

public CsvParserListener getParserListener()

Getter for the field parserListener.

Returns:

a CsvParserListener object.

setParserListener

public void setParserListener(CsvParserListener parserListener)

Setter for the field parserListener.

Parameters:

parserListener - a CsvParserListener object.

isStarted

public boolean isStarted()

isStarted.

Returns:

a boolean.

createParticipantEvidence

protected ParticipantEvidence createParticipantEvidence(String protein1,
                                                        int protein1Index,
                                                        String pepPos,
                                                        int pepPos1Index,
                                                        String linkedPos,
                                                        int linkedPosIndex)

createParticipantEvidence.

Parameters:

protein1 - a String object.

protein1Index - a int.

pepPos - a String object.

pepPos1Index - a int.

linkedPos - a String object.

linkedPosIndex - a int.

Returns:

a ParticipantEvidence object.

parseCrossLinkingFeatures

protected List<CsvRange> parseCrossLinkingFeatures(String pepPos,
                                                   String linkedPos,
                                                   int lineNumber,
                                                   int pepColumnNumber,
                                                   int linkedColumnNumber)

parseCrossLinkingFeatures.

Parameters:

pepPos - a String object.

linkedPos - a String object.

lineNumber - a int.

pepColumnNumber - a int.

linkedColumnNumber - a int.

Returns:

a List object.

parsePositions

protected List<CsvRange> parsePositions(String pos,
                                        int lineNumber,
                                        int colNumber)

parsePositions.

Parameters:

pos - a String object.

lineNumber - a int.

colNumber - a int.

Returns:

a List object.

createParticipantEvidence

protected CsvParticipantEvidence createParticipantEvidence(CsvProtein csvProtein,
                                                           int lineNumber,
                                                           int columnNumber,
                                                           CsvRange range)

createParticipantEvidence.

Parameters:

csvProtein - a CsvProtein object.

lineNumber - a int.

columnNumber - a int.

range - a CsvRange object.

Returns:

a CsvParticipantEvidence object.

createCrossLinkFeatureEvidence

protected CsvFeatureEvidence createCrossLinkFeatureEvidence(CsvRange range)

createCrossLinkFeatureEvidence.

Parameters:

range - a CsvRange object.

Returns:

a CsvFeatureEvidence object.

createExperimentalParticipantPool

protected CsvExperimentalParticipantPool createExperimentalParticipantPool(List<CsvProtein> csvProteins,
                                                                           int lineNumber,
                                                                           int columnNumber,
                                                                           List<CsvRange> csvRanges)

createExperimentalParticipantPool.

Parameters:

csvProteins - a List object.

lineNumber - a int.

columnNumber - a int.

csvRanges - a List object.

Returns:

a CsvExperimentalParticipantPool object.

createProteinsFromString

protected List<CsvProtein> createProteinsFromString(String protein1,
                                                    int lineNumber,
                                                    int columnNumber)

createProteinsFromString.

Parameters:

protein1 - a String object.

lineNumber - a int.

columnNumber - a int.

Returns:

a List object.

createProteinFromNameAndIdentifier

protected CsvProtein createProteinFromNameAndIdentifier(String protein,
                                                        int lineNumber,
                                                        int columnNumber)

createProteinFromNameAndIdentifier.

Parameters:

protein - a String object.

lineNumber - a int.

columnNumber - a int.

Returns:

a CsvProtein object.

instantiateInteractionEvidence

protected abstract T instantiateInteractionEvidence(int linePosition,
                                                    String bait)

instantiateInteractionEvidence.

Parameters:

linePosition - a int.

bait - a String object.

Returns:

a T object.

processMismatchPeptidePositions

protected void processMismatchPeptidePositions(List<CsvRange> peptidePositions,
                                               List<CsvRange> linkedPositions)

processMismatchPeptidePositions.

Parameters:

peptidePositions - a List object.

linkedPositions - a List object.

processMismatchProteinPositions

protected void processMismatchProteinPositions(List<CsvRange> rangePositions,
                                               List<CsvProtein> proteins)

processMismatchProteinPositions.

Parameters:

rangePositions - a List object.

proteins - a List object.

processInvalidPosition

protected void processInvalidPosition(String message,
                                      FileSourceContext context)

processInvalidPosition.

Parameters:

message - a String object.

context - a FileSourceContext object.

processProteinIdentifiersError

protected void processProteinIdentifiersError(String[] identifiers,
                                              int lineNumber,
                                              int columnNumber)

processProteinIdentifiersError.

Parameters:

identifiers - an array of String objects.

lineNumber - a int.

columnNumber - a int.

processNoProtein1Error

protected void processNoProtein1Error(int lineNumber)

processNoProtein1Error.

Parameters:

lineNumber - a int.

initialiseColumnNames

public void initialiseColumnNames(List<String> data)

initialiseColumnNames.

Parameters:

data - a List object.