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

Class MZTabColumnFactory

java.lang.Object

uk.ac.ebi.pride.jmztab2.model.MZTabColumnFactory

public class MZTabColumnFactory
extends Object

This is a static factory class which used to generate a couple of MZTabColumn objects, and organizes them into "logicalPosition, MZTabColumn" pairs. Currently, mzTab table including three kinds of columns:

1. Stable column with stable order: header name, data type, logical position and order are stable in these columns. All of them are defined in SmallMoleculeColumn, SmallMoleculeFeatureColumn, and SmallMoleculeEvidenceColumn.
2. Optional column with stable order: column name, data type and order are defined in the SmallMoleculeColumn, SmallMoleculeFeatureColumn, and SmallMoleculeEvidenceColumn. But header name, logical position dynamically depend on IndexedElement.
3. Optional columns which are placed at the end of a table-based section. There are three types of optional column: AbundanceColumn, OptionColumn and ParameterOptionColumn, which always are added at the end of the table. These optional columns have no stable column name, data type or order. In this factory, we use addOptionalColumn(String, Class) to create OptionColumn; and #addOptionalColumn(de.isas.mztab2.model.IndexedElement, java.lang.String, java.lang.Class) or #addOptionalColumn(IndexedElement, Parameter, Class) to create ParameterOptionColumn.

Since:

23/05/13

Author:

qingwei, nilshoffmann

Method Summary

Modifier and Type	Method	Description
String	addAbundanceOptionalColumn(Assay assay, String order)	addAbundanceOptionalColumn.
String	addAbundanceOptionalColumn(StudyVariable studyVariable, String columnHeader, String order)	Add an AbundanceColumn into AbundanceColumn, optionalColumnMapping and columnMapping.
String	addIdConfidenceMeasureColumn(Parameter parameter, Integer index, Class columnType)	addIdConfidenceMeasureColumn.
String	addOptionalColumn(Parameter param, Class columnType)	Add global ParameterOptionColumn into optionalColumnMapping and columnMapping.
String	addOptionalColumn(String name, Class columnType)	Add global OptionColumn into optionalColumnMapping and columnMapping.
<T> String	addOptionalColumn(T columnEntity, Parameter param, Class columnType)	Add ParameterOptionColumn followed by an indexed element (study variable, assay, ms run) into optionalColumnMapping and columnMapping.
<T> String	addOptionalColumn(T columnEntity, String name, Class columnType)	Add OptionColumn followed by an indexed element (study variable, assay, ms run) into optionalColumnMapping and columnMapping.
IMZTabColumn	findColumnByHeader(String header)	Query the MZTabColumn in factory, based on column header with case-insensitive.
SortedMap<String,IMZTabColumn>	getColumnMapping()	Get all columns in the factory.
static MZTabColumnFactory	getInstance(Section section)	Retrieves the MZTabColumnFactory accordingly to the section
SortedMap<Integer,IMZTabColumn>	getOffsetColumnsMap()	The offset record the position of MZTabColumn in header line.
SortedMap<String,IMZTabColumn>	getOptionalColumnMapping()	Get all optional columns, including option column with stable order and name, abundance columns, optional columns and cv param optional columns.
SortedMap<String,IMZTabColumn>	getStableColumnMapping()	Get stable columns mapping.

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static MZTabColumnFactory getInstance(Section section)

Retrieves the MZTabColumnFactory accordingly to the section

Parameters:

section - SHOULD be Section.Protein_Header, Section.Peptide_Header Section.PSM_Header or Section.Small_Molecule_Header.

Returns:

a MZTabColumnFactory object.

getStableColumnMapping

public SortedMap<String,IMZTabColumn> getStableColumnMapping()

Get stable columns mapping. Key is logical position, and value is MZTabColumn object. Stable column with stable order: header name, data type, logical position and order are stable in these columns. All of them have been defined in null SmallMoleculeColumn, SmallMoleculeFeatureColumn, SmallMoleculeEvidenceColumn.

Returns:

a SortedMap object.

getOptionalColumnMapping

public SortedMap<String,IMZTabColumn> getOptionalColumnMapping()

Get all optional columns, including option column with stable order and name, abundance columns, optional columns and cv param optional columns. Key is logical position, and value is MZTabColumn object.

Returns:

a SortedMap object.

See Also:

AbundanceColumn, OptionColumn, ParameterOptionColumn

getColumnMapping

public SortedMap<String,IMZTabColumn> getColumnMapping()

Get all columns in the factory. In this class, we maintain the following constraint at any time:

Returns:

a SortedMap object.

addOptionalColumn

public String addOptionalColumn(String name,
                                Class columnType)

Add global OptionColumn into optionalColumnMapping and columnMapping. The header like: opt_global_{name}

Parameters:

name - SHOULD NOT be empty.

columnType - SHOULD NOT be empty.

Returns:

the column's logic position.

addOptionalColumn

public <T> String addOptionalColumn(T columnEntity,
                                    String name,
                                    Class columnType)

Add OptionColumn followed by an indexed element (study variable, assay, ms run) into optionalColumnMapping and columnMapping. The header will look like: opt_study_variable[1]_{name} for a study variable

Type Parameters:

T - the type of the columnEntity.

Parameters:

columnEntity - SHOULD NOT be empty.

name - SHOULD NOT be empty.

columnType - SHOULD NOT be empty.

Returns:

the column's logic position.

addOptionalColumn

public String addOptionalColumn(Parameter param,
                                Class columnType)

Add global ParameterOptionColumn into optionalColumnMapping and columnMapping. The header like: opt_global_cv_{accession}_{parameter name}

Parameters:

param - SHOULD NOT empty.

columnType - SHOULD NOT empty.

Returns:

the column's logic position.

addOptionalColumn

public <T> String addOptionalColumn(T columnEntity,
                                    Parameter param,
                                    Class columnType)

Add ParameterOptionColumn followed by an indexed element (study variable, assay, ms run) into optionalColumnMapping and columnMapping. The header will look like: opt_assay[1]_cv_{accession}_{parameter name} for an assay.

Type Parameters:

T - the type of the columnEntity.

Parameters:

columnEntity - SHOULD NOT empty.

param - SHOULD NOT empty.

columnType - SHOULD NOT empty.

Returns:

the column's logic position.

addAbundanceOptionalColumn

public String addAbundanceOptionalColumn(Assay assay,
                                         String order)

addAbundanceOptionalColumn.

Parameters:

assay - a Assay object.

order - the order string for this column.

Returns:

the column's logic position.

addAbundanceOptionalColumn

public String addAbundanceOptionalColumn(StudyVariable studyVariable,
                                         String columnHeader,
                                         String order)

Add an AbundanceColumn into AbundanceColumn, optionalColumnMapping and columnMapping. The header can be one of abundance_study_variable[1], abundance_coeffvar_study_variable[1].

Parameters:

studyVariable - SHOULD NOT empty.

columnHeader - the column header without the 'abundance_' prefix.

order - the order string for this column.

Returns:

the column's logic position.

See Also:

AbundanceColumn.createOptionalColumns(uk.ac.ebi.pride.jmztab2.model.Section, de.isas.mztab2.model.StudyVariable, java.lang.String, java.lang.String)

addIdConfidenceMeasureColumn

public String addIdConfidenceMeasureColumn(Parameter parameter,
                                           Integer index,
                                           Class columnType)

addIdConfidenceMeasureColumn.

Parameters:

parameter - a Parameter object.

index - a Integer object.

columnType - the class of values in this column.

Returns:

the column's logic position.

getOffsetColumnsMap

public SortedMap<Integer,IMZTabColumn> getOffsetColumnsMap()

The offset record the position of MZTabColumn in header line. For example, protein header line, the relationships between Logical Position, MZTabColumn, offset and order are like following structure: Logical Position MZTabColumn offset order "01" accession 1 01 "02" description 2 02 ...... "08" best_search_engine_score 8 08 "091" search_engine_score_ms_run[1] 9 09 "092" search_engine_score_ms_run[2] 10 09 "10" reliability 11 10 "111" num_psms_ms_run[1] 12 11 "112" num_psms_ms_run[2] 13 11

Returns:

a SortedMap object with the offsets for each column.

findColumnByHeader

public IMZTabColumn findColumnByHeader(String header)

Query the MZTabColumn in factory, based on column header with case-insensitive. Notice: for optional columns, header name maybe flexible. For example, num_psms_ms_run[1]. At this time, user SHOULD BE provide the full header name to query MZTabColumn. If just provide num_psms_ms_run, return null.

Parameters:

header - the column header to use as the search key.

Returns:

a IMZTabColumn object or null.