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

Interface IMZTabColumn

All Known Subinterfaces:

ISmallMoleculeColumn, ISmallMoleculeEvidenceColumn, ISmallMoleculeFeatureColumn

All Known Implementing Classes:

AbundanceColumn, MZTabColumn, OptionColumn, ParameterOptionColumn, SmallMoleculeColumn, SmallMoleculeEvidenceColumn, SmallMoleculeFeatureColumn

public interface IMZTabColumn

IMZTabColumn interface.

Since:

2.0

Author:

nilshoffmann

Method Summary

Modifier and Type	Method	Description
Class<?>	getDataType()	Get the column data type Class.
de.isas.mztab2.model.IndexedElement	getElement()	Indexed element used in optional column header and logical position definition.
String	getHeader()	Get the column name.
String	getLogicPosition()	Get the column logical position.
String	getName()	Get the column name.
String	getOrder()	Get the column internal order.
boolean	isOptional()	Judge this column belong to stable column or optional column.
void	setElement(de.isas.mztab2.model.IndexedElement element)	Indexed element used in optional column header and logical position definition.
void	setHeader(String header)	setHeader.
void	setLogicPosition(String logicPosition)	setLogicPosition.
void	setOrder(String order)	setOrder.

Method Detail

getDataType

Class<?> getDataType()

Get the column data type Class.

Returns:

a Class object.

getElement

de.isas.mztab2.model.IndexedElement getElement()

Indexed element used in optional column header and logical position definition. In stable column, the return is null. Notice: this design pattern not fit for AbundanceColumn, OptionColumn and ParameterOptionColumn. These optional columns need be generated by calling MZTabColumnFactory 's methods.

Returns:

a IndexedElement object.

See Also:

getHeader(), getLogicPosition(), getHeader(), getLogicPosition()

getHeader

String getHeader()

Get the column name. For stable column, name and header are same. While for optional column, name is part of its header. For example, optional column which header is search_engine_score_ms_run[1-n], and its name is search_engine_score. Besides this, ms_run[1-n] is kind of getElement() Notice: this design pattern not fit for AbundanceColumn, OptionColumn and ParameterOptionColumn. These optional columns need be generated by calling MZTabColumnFactory 's methods.

Returns:

a String object.

See Also:

getName(), setElement(IndexedElement), getName(), setElement(IndexedElement)

getLogicPosition

String getLogicPosition()

Get the column logical position. For stable column, order and logical position are same. But for optional column, the logical position need to calculate by concatenate order and index element id. For example, optional column search_engine_score_ms_run[2] in Protein section, its order is 09, and the logical position is 092. Because the element ms_run[2] 's index is 2.

Notice: this design pattern not fit for AbundanceColumn, OptionColumn and ParameterOptionColumn. These optional columns need be generated by calling MZTabColumnFactory 's methods.

Notice: in MZTabColumnFactory, we use logical position to maintain the logical consistence with in MzTab. During the process of parsing mzTab file, we create a mapping between physical position and internal logical position.

Returns:

a String object.

See Also:

getOrder()

getName

String getName()

Get the column name. For stable column, name and header are same. But for optional column, name is part of its header. For example, optional column which header is search_engine_score_ms_run[1-n], and its name is search_engine_score. Besides this, ms_run[1-n] is kind of getElement() Notice: this design pattern not fit for AbundanceColumn, OptionColumn and ParameterOptionColumn. These optional columns need be generated by calling MZTabColumnFactory 's methods.

Returns:

a String object.

See Also:

getHeader(), setElement(IndexedElement), getHeader(), setElement(IndexedElement)

getOrder

String getOrder()

Get the column internal order. For stable column, order and logical position are same. But for optional column, the logical position need to be calculated by concatenating order and index element id. For example, optional column search_engine_score_ms_run[2] in Protein section, its order is 09, and the logical position is 092. Because the element ms_run[2] 's index is 2. Notice: this design pattern not fit for AbundanceColumn, OptionColumn and ParameterOptionColumn. These optional columns need be generated by calling MZTabColumnFactory 's methods.

Returns:

a String object.

See Also:

getLogicPosition()

isOptional

boolean isOptional()

Judge this column belong to stable column or optional column.

Returns:

a boolean.

setHeader

void setHeader(String header)

setHeader.

Parameters:

header - a String object.

setLogicPosition

void setLogicPosition(String logicPosition)

setLogicPosition.

Parameters:

logicPosition - a String object.

setOrder

void setOrder(String order)

setOrder.

Parameters:

order - a String object.

setElement

void setElement(de.isas.mztab2.model.IndexedElement element)

Indexed element used in optional column header and logical position definition. In stable column, the return is null. Notice: this design pattern not fit for AbundanceColumn, OptionColumn and ParameterOptionColumn. These optional columns need be generated by calling MZTabColumnFactory 's methods.

Parameters:

element - SHOULD NOT set null.

See Also:

getHeader(), getLogicPosition(), getHeader(), getLogicPosition()