Package uk.ac.ebi.pride.jmztab2.utils.parser

Class MZTabHeaderLineParser

java.lang.Object

uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser

uk.ac.ebi.pride.jmztab2.utils.parser.MZTabHeaderLineParser

Direct Known Subclasses:

SEHLineParser, SFHLineParser, SMHLineParser

public abstract class MZTabHeaderLineParser
extends MZTabLineParser

A couple of common method used to parse a header line into MZTabColumnFactory structure. NOTICE: MZTabColumnFactory maintain a couple of MZTabColumn which have internal logical position and order. In physical mzTab file, we allow user not obey this logical position organized way, and provide their date with own order. In order to distinguish them, we use physical position (a positive integer) to record the column location in mzTab file. And use PositionMapping structure the maintain the mapping between them.

Since:

11/02/13

Author:

qingwei

See Also:

SMHLineParser, SMFLineParser, SMELineParser

Field Summary

Fields

Modifier and Type	Field	Description
protected MZTabColumnFactory	factory
protected de.isas.mztab2.model.Metadata	metadata

Fields inherited from class uk.ac.ebi.pride.jmztab2.utils.parser.MZTabLineParser

context, errorList, items, line, lineNumber, section

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	MZTabHeaderLineParser(MZTabParserContext context, MZTabColumnFactory factory, de.isas.mztab2.model.Metadata metadata)	Parse a header line into MZTabColumnFactory structure.

Method Summary

Modifier and Type	Method	Description
protected int	checkAbundanceColumns(int offset, String order)	checkAbundanceColumns.
protected boolean	checkOptColumnName(String nameLabel)	Additional columns can be added to the end of the protein table.
protected String	fromIndexToOrder(Integer index)	fromIndexToOrder.
MZTabColumnFactory	getFactory()	Getter for the field factory.
void	parse(int lineNumber, String line, uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)	We assume that user before call this method, have parse the raw line is not empty line and start with section prefix.
protected abstract int	parseColumns()	This methods delegates to the subclasses the parsing of the columns.
protected int	parseIndex(String header, String id)	Parse header to a index id number.
protected abstract void	refine()	Some validate operation need to be done after the whole MZTabColumnFactory created.
protected void	refineOptionalColumn(Section section, String columnHeader)	Refine optional columns and check, whether they were properly defined.

Methods inherited from class java.lang.Object

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

Field Detail

factory

protected MZTabColumnFactory factory

metadata

protected de.isas.mztab2.model.Metadata metadata

Constructor Detail

MZTabHeaderLineParser

protected MZTabHeaderLineParser(MZTabParserContext context,
                                MZTabColumnFactory factory,
                                de.isas.mztab2.model.Metadata metadata)

Parse a header line into MZTabColumnFactory structure.

Parameters:

context - the parser context, keeping dynamic state and lookup associations.

factory - SHOULD NOT set null

metadata - SHOULD NOT set null

Method Detail

parse

public void parse(int lineNumber,
                  String line,
                  uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList errorList)
           throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

We assume that user before call this method, have parse the raw line is not empty line and start with section prefix. Parse a header line into MZTabColumnFactory structure. There are several steps in this method: Step 1: parseColumns() focus on validate and parse all columns. Step 2: refine()

Overrides:

parse in class MZTabLineParser

Parameters:

lineNumber - a int.

line - a String object.

errorList - a MZTabErrorList object.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any.

parseColumns

protected abstract int parseColumns()
                             throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

This methods delegates to the subclasses the parsing of the columns. All of the columns are defined in SmallMoleculeColumn, SmallMoleculeFeatureColumn, or SmallMoleculeEvidenceColumn.

Returns:

the next physical index of column available after the parsing.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

refine

protected abstract void refine()
                        throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Some validate operation need to be done after the whole MZTabColumnFactory created. Thus, user can add them, and called at the end of the parse(int, String, MZTabErrorList) method.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

refineOptionalColumn

protected void refineOptionalColumn(Section section,
                                    String columnHeader)
                             throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Refine optional columns and check, whether they were properly defined. These re-validate operation will called in refine() method.

Parameters:

section - a Section object defining the part of the document.

columnHeader - a String object.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

fromIndexToOrder

protected String fromIndexToOrder(Integer index)

fromIndexToOrder.

Parameters:

index - a Integer object.

Returns:

a String object.

checkOptColumnName

protected boolean checkOptColumnName(String nameLabel)
                              throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

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 ':'. the format: opt_{IndexedElement[id]}_{value}. Spaces within the parameter's name MUST be replaced by '_'.

Parameters:

nameLabel - a String object.

Returns:

a boolean.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

checkAbundanceColumns

protected int checkAbundanceColumns(int offset,
                                    String order)
                             throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

checkAbundanceColumns.

Parameters:

offset - a int.

order - a String object.

Returns:

a int.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

parseIndex

protected int parseIndex(String header,
                         String id)
                  throws uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException

Parse header to a index id number. If exists parse error, stop validate and throw MZTabException directly.

Parameters:

header - a String object.

id - a String object.

Returns:

a int.

Throws:

uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException - if any structural or logical errors are encountered that prohibit further processing.

getFactory

public MZTabColumnFactory getFactory()

Getter for the field factory.

Returns:

a MZTabColumnFactory object.