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

Class SmallMoleculeEvidenceColumn

java.lang.Object

uk.ac.ebi.pride.jmztab2.model.SmallMoleculeEvidenceColumn

All Implemented Interfaces:

IMZTabColumn, ISmallMoleculeColumn, ISmallMoleculeEvidenceColumn

public class SmallMoleculeEvidenceColumn
extends Object
implements ISmallMoleculeEvidenceColumn

Define the stable columns which have stable order in the small molecule evidence header line. Refactored to contain an enum for stable columns.

Since:

11/09/17

Author:

nilshoffmann

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SmallMoleculeEvidenceColumn.Stable	Stable SmallMoleculeEvidenceColumn definition templates.

Method Summary

Modifier and Type	Method	Description
Class<?>	getDataType()	Get the column data type Class.
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(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.

Methods inherited from class java.lang.Object

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

Method Detail

getDataType

public Class<?> getDataType()

Get the column data type Class.

Specified by:

getDataType in interface IMZTabColumn

Returns:

a Class object.

getElement

public 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.

Specified by:

getElement in interface IMZTabColumn

Returns:

a IndexedElement object.

See Also:

IMZTabColumn.getHeader(), IMZTabColumn.getLogicPosition(), IMZTabColumn.getHeader(), IMZTabColumn.getLogicPosition()

getHeader

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

Specified by:

getHeader in interface IMZTabColumn

Returns:

a String object.

See Also:

IMZTabColumn.getName(), IMZTabColumn.setElement(IndexedElement), IMZTabColumn.getName(), IMZTabColumn.setElement(IndexedElement)

getLogicPosition

public 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.

Specified by:

getLogicPosition in interface IMZTabColumn

Returns:

a String object.

See Also:

IMZTabColumn.getOrder()

getName

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

Specified by:

getName in interface IMZTabColumn

Returns:

a String object.

See Also:

IMZTabColumn.getHeader(), IMZTabColumn.setElement(IndexedElement), IMZTabColumn.getHeader(), IMZTabColumn.setElement(IndexedElement)

getOrder

public 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.

Specified by:

getOrder in interface IMZTabColumn

Returns:

a String object.

See Also:

IMZTabColumn.getLogicPosition()

isOptional

public boolean isOptional()

Judge this column belong to stable column or optional column.

Specified by:

isOptional in interface IMZTabColumn

Returns:

a boolean.

setHeader

public void setHeader(String header)

setHeader.

Specified by:

setHeader in interface IMZTabColumn

Parameters:

header - a String object.

setLogicPosition

public void setLogicPosition(String logicPosition)

setLogicPosition.

Specified by:

setLogicPosition in interface IMZTabColumn

Parameters:

logicPosition - a String object.

setOrder

public void setOrder(String order)

setOrder.

Specified by:

setOrder in interface IMZTabColumn

Parameters:

order - a String object.

setElement

public void setElement(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.

Specified by:

setElement in interface IMZTabColumn

Parameters:

element - SHOULD NOT set null.

See Also:

IMZTabColumn.getHeader(), IMZTabColumn.getLogicPosition(), IMZTabColumn.getHeader(), IMZTabColumn.getLogicPosition()