org.expasy.mzjava.glycomics.io.mol.glycoct

Class GlycoCTReader

java.lang.Object

org.expasy.mzjava.glycomics.io.mol.glycoct.GlycoCTReader

public class GlycoCTReader
extends Object

Created with IntelliJ IDEA. User: jmarieth Date: 10/29/13 Time: 4:32 PM

Constructor Summary

Constructors

Constructor and Description
GlycoCTReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected Map<Integer,String>	findLinkages(Map<Integer,String> allLinkages, int anomericResidueId)
protected Integer	getAnomericCarbon(String glycoctLinkageLine)
protected Character	getAnomericCompsition(String glycoctLinkageLine)
protected Integer	getAnomericResidueId(String glycoctLinkageLine)
protected Integer	getGlycoctIndex(String glycoctLine)
protected Character	getGlycoctResidueAnomer(String glycoctLine)
protected char	getGlycoctResidueType(String glycoctLine)
protected Integer	getLinkedCarbon(String glycoctLinkageLine)
protected Character	getLinkedCompsition(String glycoctLinkageLine)
protected Integer	getLinkedResidueId(String glycoctLinkageLine)
protected Monosaccharide	getMonosaccharide(String glycoctResidueLine)
protected Integer	getNumericValue(String glycoctLine, int offset)
protected com.google.common.base.Optional<Character>	getOptionalCharacter(Character value)
protected com.google.common.base.Optional<Integer>	getOptionalInteger(Integer value)
protected int	getStartIndex(List<String> al, String startTag)
protected int	getStopIndex(List<String> al, String stopTag)
protected Substituent	getSubstituent(String glycoctResidueLine)
protected Glycan	glycoctListsToSugar(String databaseIdentifier, List<String> residuesList, List<String> linkagesList)
protected Map<Integer,String>	glycoctListToMap(List<String> glycoctList)
protected List<String>	glycoctToList(String glycoct)
Glycan	read(String glycoct, String databaseIdentifier)
protected List<String>	readLIN(List<String> glycoctList)
protected List<String>	readRES(List<String> glycoctList)

Methods inherited from class java.lang.Object

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

Constructor Detail

GlycoCTReader

public GlycoCTReader()

Method Detail

read

public Glycan read(String glycoct,
          String databaseIdentifier)

glycoctListsToSugar

protected Glycan glycoctListsToSugar(String databaseIdentifier,
                         List<String> residuesList,
                         List<String> linkagesList)

glycoctListToMap

protected Map<Integer,String> glycoctListToMap(List<String> glycoctList)

getSubstituent

protected Substituent getSubstituent(String glycoctResidueLine)

getMonosaccharide

protected Monosaccharide getMonosaccharide(String glycoctResidueLine)

getNumericValue

protected Integer getNumericValue(String glycoctLine,
                      int offset)

getOptionalInteger

protected com.google.common.base.Optional<Integer> getOptionalInteger(Integer value)

getOptionalCharacter

protected com.google.common.base.Optional<Character> getOptionalCharacter(Character value)

getGlycoctIndex

protected Integer getGlycoctIndex(String glycoctLine)

getAnomericResidueId

protected Integer getAnomericResidueId(String glycoctLinkageLine)

getAnomericCarbon

protected Integer getAnomericCarbon(String glycoctLinkageLine)

getAnomericCompsition

protected Character getAnomericCompsition(String glycoctLinkageLine)

getLinkedResidueId

protected Integer getLinkedResidueId(String glycoctLinkageLine)

getLinkedCarbon

protected Integer getLinkedCarbon(String glycoctLinkageLine)

getLinkedCompsition

protected Character getLinkedCompsition(String glycoctLinkageLine)

findLinkages

protected Map<Integer,String> findLinkages(Map<Integer,String> allLinkages,
                               int anomericResidueId)

getGlycoctResidueType

protected char getGlycoctResidueType(String glycoctLine)

getGlycoctResidueAnomer

protected Character getGlycoctResidueAnomer(String glycoctLine)

glycoctToList

protected List<String> glycoctToList(String glycoct)

readRES

protected List<String> readRES(List<String> glycoctList)

readLIN

protected List<String> readLIN(List<String> glycoctList)

getStartIndex

protected int getStartIndex(List<String> al,
                String startTag)

getStopIndex

protected int getStopIndex(List<String> al,
               String stopTag)