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

Class AbundanceColumn

java.lang.Object

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

uk.ac.ebi.pride.jmztab2.model.AbundanceColumn

All Implemented Interfaces:

IMZTabColumn

public class AbundanceColumn
extends MZTabColumn

If the data exporter wishes to report only final results for 'Summary' files (i.e. following averaging over replicates), then these MUST be reported as quantitative values in the columns associated with the study_variable[1-n] (e.g. abundance_study_variable[1]). mzTab allows the reporting of abundance, standard deviation, and standard error for any study_variable. The unit of values in the abundance column MUST be specified in the metadata section of the mzTab file. The reported values SHOULD represent the final result of the performed data analysis. The exact meaning of the values will thus depend on the used analysis pipeline and quantitation method and is not expected to be comparable across multiple mzTab files.

Since:

23/05/13

Author:

qingwei, nilshoffmann

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	AbundanceColumn.Field

Method Summary

Modifier and Type	Method	Description
static MZTabColumn	createOptionalColumn(Section section, Assay assay, int offset)	Generate a abundance optional column as measured in the given assay.The column header like protein_abundance_assay[1-n], the position always stay the most right of the tabled section, and the data type is Double.
static SortedMap<String,MZTabColumn>	createOptionalColumns(Section section, StudyVariable studyVariable, Integer lastOrder)	createOptionalColumns.
static SortedMap<String,MZTabColumn>	createOptionalColumns(Section section, StudyVariable studyVariable, String columnHeader, String order)	Generate an abundance optional column as measured in the given study variable.

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

Method Detail

createOptionalColumn

public static MZTabColumn createOptionalColumn(Section section,
                                               Assay assay,
                                               int offset)

Generate a abundance optional column as measured in the given assay.The column header like protein_abundance_assay[1-n], the position always stay the most right of the tabled section, and the data type is Double.

Parameters:

section - SHOULD be Section.Protein, Section.Peptide, Section.PSM, or Section.Small_Molecule.

assay - SHOULD not be null.

offset - Normally the last column's position in header, MZTabColumnFactory.getColumnMapping(),

Returns:

an abundance optional column as measured in the given assay.

createOptionalColumns

public static SortedMap<String,MZTabColumn> createOptionalColumns(Section section,
                                                                        StudyVariable studyVariable,
                                                                        String columnHeader,
                                                                        String order)

Generate an abundance optional column as measured in the given study variable. The header can be one of abundance_study_variable[1], abundance_coeffvar_study_variable[1]. The position always stay the most right of the tabled section, and the data type is Double.

Parameters:

section - SHOULD be Section.Protein, Section.Peptide, Section.PSM, or Section.Small_Molecule.

studyVariable - SHOULD not be null.

order - position in header for the new columns MZTabColumnFactory.getColumnMapping()

columnHeader - a processed column header with abundance_ removed.

Returns:

an abundance optional column as measured in the given study variable.

createOptionalColumns

public static SortedMap<String,MZTabColumn> createOptionalColumns(Section section,
                                                                        StudyVariable studyVariable,
                                                                        Integer lastOrder)

createOptionalColumns.

Parameters:

section - a Section object.

studyVariable - a StudyVariable object.

lastOrder - a Integer object.

Returns:

a SortedMap object.