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

Class MZTabColumn

java.lang.Object

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

All Implemented Interfaces:

IMZTabColumn

Direct Known Subclasses:

AbundanceColumn, OptionColumn

public class MZTabColumn
extends Object
implements IMZTabColumn

Define a column header which used in Section.Protein_Header, Section.Peptide_Header, Section.PSM_Header, or Section.Small_Molecule_Header. There are two kinds of columns: stable column and optional column. Stable column has stable position and header name, while optional column not. MZTabColumnFactory used to create and maintain these column objects.

Since:

23/05/13

Author:

qingwei, nilshoffmann

See Also:

MZTabColumnFactory, SmallMoleculeColumn, SmallMoleculeFeatureColumn, SmallMoleculeEvidenceColumn, OptionColumn, ParameterOptionColumn, AbundanceColumn

Constructor Summary

Constructors

Constructor	Description
MZTabColumn(String name, Class dataType, boolean optional, String order)	Create a column header object.
MZTabColumn(String name, Class dataType, boolean optional, String order, Integer id)	Create a column header object.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
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.
int	hashCode()
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.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

MZTabColumn

public MZTabColumn(String name,
                   Class dataType,
                   boolean optional,
                   String order)

Create a column header object. Default, the column header keep the same value with name, and logical position keep the same value with order.

Parameters:

name - define a stable name for column. For optional column, only set stable part for name.

dataType - define the data type for column.

optional - if false the column is stable type, otherwise is optional column.

order - internal order. Every non OptionColumn has stable order. Column order is used to maintain the logical position in MZTabColumnFactory

MZTabColumn

public MZTabColumn(String name,
                   Class dataType,
                   boolean optional,
                   String order,
                   Integer id)

Create a column header object. Default, the column header keep the same value with name, and logical position keep the same value with order.

Parameters:

name - define a stable name for column. For optional column, only set stable part for name.

dataType - define the data type for column.

optional - if false the column is stable type, otherwise is optional column.

order - internal order. Every non OptionColumn has stable order. Column order is used to maintain the logical position in MZTabColumnFactory

id - incremental index used for some optional columns like best_search_engine_score[1], best_search_engine_score[2]

Method Detail

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. 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 element 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:

getHeader(), setElement(IndexedElement), getHeader(), 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. 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:

getLogicPosition()

setOrder

public void setOrder(String order)

setOrder.

Specified by:

setOrder in interface IMZTabColumn

Parameters:

order - a String object.

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. 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 element 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:

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

setHeader

public void setHeader(String header)

setHeader.

Specified by:

setHeader in interface IMZTabColumn

Parameters:

header - a String object.

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.

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 within the MzTab file. 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:

getOrder()

setLogicPosition

public void setLogicPosition(String logicPosition)

setLogicPosition.

Specified by:

setLogicPosition in interface IMZTabColumn

Parameters:

logicPosition - a String object.

getDataType

public Class getDataType()

Get the column data type Class. Get the column data type Class.

Specified by:

getDataType in interface IMZTabColumn

Returns:

a Class object.

isOptional

public boolean isOptional()

Judge this column belong to stable column or optional column. Judge this column belong to stable column or optional column.

Specified by:

isOptional in interface IMZTabColumn

Returns:

a boolean.

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. 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:

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

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. 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:

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

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object