Package uk.ac.ebi.pride.jmztab2.model

Class ParameterOptionColumn

java.lang.Object

uk.ac.ebi.pride.jmztab2.model.MZTabColumn

uk.ac.ebi.pride.jmztab2.model.OptionColumn

uk.ac.ebi.pride.jmztab2.model.ParameterOptionColumn

All Implemented Interfaces:

IMZTabColumn

public class ParameterOptionColumn
extends OptionColumn

An kind of OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}. Spaces within the parameter' s name MUST be replaced by '_'.

Since:

30/05/13

Author:

qingwei

Field Summary

Fields

Modifier and Type	Field	Description
static String	CV	Constant CV="cv_"

Fields inherited from class uk.ac.ebi.pride.jmztab2.model.OptionColumn

GLOBAL, OPT

Constructor Summary

Constructors

Constructor	Description
ParameterOptionColumn(de.isas.mztab2.model.IndexedElement element, de.isas.mztab2.model.Parameter param, Class columnType, int offset)	Define a OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}.

Method Summary

Modifier and Type	Method	Description
static String	getHeader(de.isas.mztab2.model.IndexedElement element, de.isas.mztab2.model.Parameter param)	get column header like: opt_{OBJECT_ID}_cv_{accession}_{parameter name} Spaces within the parameter's name MUST be replaced by '_'.

Methods inherited from class uk.ac.ebi.pride.jmztab2.model.OptionColumn

getHeader

Methods inherited from class uk.ac.ebi.pride.jmztab2.model.MZTabColumn

equals, getDataType, getElement, getHeader, getLogicPosition, getName, getOrder, hashCode, isOptional, setElement, setHeader, setLogicPosition, setOrder, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

CV

public static final String CV

Constant CV="cv_"

See Also:

Constant Field Values

Constructor Detail

ParameterOptionColumn

public ParameterOptionColumn(de.isas.mztab2.model.IndexedElement element,
                             de.isas.mztab2.model.Parameter param,
                             Class columnType,
                             int offset)

Define a OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}. Spaces within the parameter' s name MUST be replaced by '_'.

Parameters:

element - SHOULD not be null.

param - SHOULD not be null.

columnType - SHOULD not be null.

offset - SHOULD be non-negative integer.

Method Detail

getHeader

public static String getHeader(de.isas.mztab2.model.IndexedElement element,
                               de.isas.mztab2.model.Parameter param)

get column header like: opt_{OBJECT_ID}_cv_{accession}_{parameter name} Spaces within the parameter's name MUST be replaced by '_'.

Parameters:

element - Assay, StudyVariable, MsRun or "global" (if the value relates to all replicates).

param - SHOULD NOT be null.

Returns:

the string representation of this column's header.