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

Class MZTabUtils

java.lang.Object

uk.ac.ebi.pride.jmztab2.model.MZTabUtils

public class MZTabUtils
extends Object

Provide a couple of functions for translating, parsing and printing formatted strings defined in the mzTab specification.

Since:

30/01/13

Author:

qingwei, nilshoffmann

Constructor Summary

Constructors

Constructor	Description
MZTabUtils()

Method Summary

Modifier and Type	Method	Description
static Double	parseDouble(String target)	NOTICE: If ratios are included and the denominator is zero, the "INF" value MUST be used.
static List<Double>	parseDoubleList(String target)	parseDoubleList.
static String	parseEmail(String target)	Parse the target string, and check is obey the email format or not.
static List<String>	parseGOTermList(String target)	A '|' delimited list of GO accessions
static IndexedElement	parseIndexedElement(String target, MetadataElement element)	parse the target into a IndexedElement object.
static Integer	parseInteger(String target)	parseInteger.
static List<Integer>	parseIntegerList(String target)	parseIntegerList.
static Long	parseLong(String target)	parseLong.
static String	parseMzTabVersion(String target)	Parse the target string, and check it follows the mzTab Version format.
static Parameter	parseParam(String target)	Parameters are always reported as [CV label, accession, name, value].
static List<Parameter>	parseParamList(String target)	A list of '|' separated parameters
static Publication	parsePublicationItems(Publication publication, int lineNumber, String target)	A publication on this unit.
static List<IndexedElement>	parseRefList(String target, MetadataElement element)	Parse the target into a IndexedElement list.
static List<SpectraRef>	parseSpectraRefList(MZTabParserContext context, Metadata metadata, String target)	Parse a SpectraRef list.
static List<String>	parseStringList(char splitChar, String target)	Multiple identifiers MUST be separated by splitChar.
static URI	parseURI(String target)	parseURI.
static String	printDouble(Double value)	If ratios are included and the denominator is zero, the "INF" value MUST be used.
static String	removeDoubleQuotes(String value)	If there exists reserved characters in value, like comma, the string need to be escape.
static String	translateCommaToTab(String target)	locate param label [label, accession, name, value], translate ',' to '\t'
static String	translateLastToTab(String target)	translateLastToTab.
static String	translateMinusInCVtoUnicode(String target)	translateMinusInCVtoUnicode.
static String	translateMinusToTab(String target)	translateMinusToTab.
static String	translateMinusToUnicode(String target)	Solve the conflict about minus char between modification position and CHEMMOD charge.
static String	translateTabToComma(String target)	solve the conflict about comma char which used in split modification and split cv param components.
static String	translateTabToMinus(String target)	solve the conflict about comma char which used in split modification and split cv param components.
static String	translateUnicodeCVTermMinus(String target)	translateUnicodeCVTermMinus.
static String	translateUnicodeToMinus(String target)	Solve the conflict about minus char between modification position and CHEMMOD charge.

Methods inherited from class java.lang.Object

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

Constructor Detail

MZTabUtils

public MZTabUtils()

Method Detail

printDouble

public static String printDouble(Double value)

If ratios are included and the denominator is zero, the "INF" value MUST be used. If the result leads to calculation errors (for example 0/0), this MUST be reported as "not a number" ("NaN").

Parameters:

value - a Double object.

Returns:

a String object.

See Also:

parseDouble(String)

parseEmail

public static String parseEmail(String target)

Parse the target string, and check is obey the email format or not. If not, return null.

Parameters:

target - a String object.

Returns:

a String object.

parseMzTabVersion

public static String parseMzTabVersion(String target)

Parse the target string, and check it follows the mzTab Version format. If not, return null.

Parameters:

target - a String object.

Returns:

a String object.

parseParam

public static Parameter parseParam(String target)

Parameters are always reported as [CV label, accession, name, value]. Any field that is not available MUST be left empty. If the name or value of param contains comma, quotes MUST be added to avoid problems. Nested double quotes are not supported. Notice: name cell never set null.

Parameters:

target - a String object.

Returns:

a Parameter object.

parseStringList

public static List<String> parseStringList(char splitChar,
                                           String target)

Multiple identifiers MUST be separated by splitChar.

Parameters:

splitChar - a char.

target - a String object.

Returns:

a List object.

parseIndexedElement

public static IndexedElement parseIndexedElement(String target,
                                                 MetadataElement element)

parse the target into a IndexedElement object.

Parameters:

target - a String object.

element - a MetadataElement object.

Returns:

a IndexedElement object.

parseRefList

public static List<IndexedElement> parseRefList(String target,
                                                MetadataElement element)

Parse the target into a IndexedElement list. target is a '|' separated list of entries.

Parameters:

target - a String object.

element - a MetadataElement object.

Returns:

a List object.

parseParamList

public static List<Parameter> parseParamList(String target)

A list of '|' separated parameters

Parameters:

target - a String object.

Returns:

a List object.

parseGOTermList

public static List<String> parseGOTermList(String target)

A '|' delimited list of GO accessions

Parameters:

target - a String object.

Returns:

a List object.

parseInteger

public static Integer parseInteger(String target)

parseInteger.

Parameters:

target - a String object.

Returns:

a Integer object.

parseDouble

public static Double parseDouble(String target)

NOTICE: If ratios are included and the denominator is zero, the "INF" value MUST be used. If the result leads to calculation errors (for example 0/0), this MUST be reported as "not a number" ("NaN").

Parameters:

target - a String object.

Returns:

a Double object.

parseLong

public static Long parseLong(String target)

parseLong.

Parameters:

target - a String object.

Returns:

a Long object.

parseDoubleList

public static List<Double> parseDoubleList(String target)

parseDoubleList.

Parameters:

target - a String object.

Returns:

a List object.

parseIntegerList

public static List<Integer> parseIntegerList(String target)

parseIntegerList.

Parameters:

target - a String object.

Returns:

a List object.

parseURI

public static URI parseURI(String target)

parseURI.

Parameters:

target - a String object.

Returns:

a URI object.

parsePublicationItems

public static Publication parsePublicationItems(Publication publication,
                                                int lineNumber,
                                                String target)
                                         throws MZTabException

A publication on this unit. PubMed ids must be prefixed by "pubmed:", DOIs by "doi:". Multiple identifiers MUST be separated by "|".

Parameters:

publication - a Publication object.

lineNumber - the line number while parsing.

target - a String object.

Returns:

a Publication object.

Throws:

MZTabException - in case of parsing or formatting issues of the publication string.

parseSpectraRefList

public static List<SpectraRef> parseSpectraRefList(MZTabParserContext context,
                                                   Metadata metadata,
                                                   String target)

Parse a SpectraRef list.

Parameters:

context - a MZTabParserContext object.

metadata - a Metadata object.

target - a String object.

Returns:

a List object.

translateMinusToUnicode

public static String translateMinusToUnicode(String target)

Solve the conflict about minus char between modification position and CHEMMOD charge. For example: 13-CHEMMOD:-159

Parameters:

target - a String object.

Returns:

a String object.

translateMinusInCVtoUnicode

public static String translateMinusInCVtoUnicode(String target)

translateMinusInCVtoUnicode.

Parameters:

target - a String object.

Returns:

a String object.

translateUnicodeCVTermMinus

public static String translateUnicodeCVTermMinus(String target)

translateUnicodeCVTermMinus.

Parameters:

target - a String object.

Returns:

a String object.

translateUnicodeToMinus

public static String translateUnicodeToMinus(String target)

Solve the conflict about minus char between modification position and CHEMMOD charge. For example: 13-CHEMMOD:-159

Parameters:

target - a String object.

Returns:

a String object.

translateCommaToTab

public static String translateCommaToTab(String target)

locate param label [label, accession, name, value], translate ',' to '\t'

Parameters:

target - a String object.

Returns:

a String object.

translateTabToComma

public static String translateTabToComma(String target)

solve the conflict about comma char which used in split modification and split cv param components.

Parameters:

target - a String object.

Returns:

a String object.

translateMinusToTab

public static String translateMinusToTab(String target)

translateMinusToTab.

Parameters:

target - a String object.

Returns:

a String object.

translateLastToTab

public static String translateLastToTab(String target)

translateLastToTab.

Parameters:

target - a String object.

Returns:

a String object.

translateTabToMinus

public static String translateTabToMinus(String target)

solve the conflict about comma char which used in split modification and split cv param components.

Parameters:

target - a String object.

Returns:

a String object.

removeDoubleQuotes

public static String removeDoubleQuotes(String value)

If there exists reserved characters in value, like comma, the string need to be escape. However the escaping char is not store because it will be write back in the writer. Nested double quotes are not supported.

Parameters:

value - a String object.

Returns:

a String object.