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

Class OptionColumn

java.lang.Object

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

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

All Implemented Interfaces:

IMZTabColumn

Direct Known Subclasses:

ParameterOptionColumn

public class OptionColumn
extends MZTabColumn

Additional columns can be added to the end of the protein table. These column headers MUST start with the prefix "opt_". Column names MUST only contain the following characters: 'A'-'Z', 'a'-'z', '0'-'9', '_', '-', '[', ']', and ':'.

Since:

28/05/13

Author:

qingwei

Field Summary

Fields

Modifier and Type	Field	Description
static String	GLOBAL	Constant GLOBAL="global"
static String	OPT	Constant OPT="opt"

Constructor Summary

Constructors

Constructor	Description
OptionColumn(de.isas.mztab2.model.IndexedElement element, String value, Class columnType, int offset)	Create a optional column.

Method Summary

Modifier and Type	Method	Description
static String	getHeader(de.isas.mztab2.model.IndexedElement element, String name)	Get the optional column header, which start with the prefix "opt_". the format: opt_{indexedElement[id]}_{name}.

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

OPT

public static final String OPT

Constant OPT="opt"

See Also:

Constant Field Values

GLOBAL

public static final String GLOBAL

Constant GLOBAL="global"

See Also:

Constant Field Values

Constructor Detail

OptionColumn

public OptionColumn(de.isas.mztab2.model.IndexedElement element,
                    String value,
                    Class columnType,
                    int offset)

Create a optional column. Which header start with the prefix "opt_", logical position always stay the end of table.

Parameters:

element - if the value relates to all replicates, we use "global" in header. Here, if user set element is null for define for all replicates.

value - SHOULD NOT be empty.

columnType - SHOULD NOT be empty.

offset - SHOULD be positive integer.

See Also:

generate optional column header.

Method Detail

getHeader

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

Get the optional column header, which start with the prefix "opt_". the format: opt_{indexedElement[id]}_{name}. Spaces within the parameter's name MUST be replaced by '_'.

Parameters:

element - if the name relates to all replicates, we use "global" in header. Here, if user set element to null, the definition applies for all replicates.

name - SHOULD NOT be empty.

Returns:

a String object.