org.helm.notation2.tools

Class AminoAcidParser

java.lang.Object

org.helm.notation2.tools.AminoAcidParser

public class AminoAcidParser
extends Object

AminoAcidParser

Author:

hecht

Field Summary

Fields

Modifier and Type	Field and Description
static String[]	SEQUENCE_DELIMETERS

Constructor Summary

Constructors

Constructor and Description
AminoAcidParser()

Method Summary

Methods

Modifier and Type	Method and Description
static String	cleanup(String sequence) remove white space, and convert all lower case to upper case
static List<String>	getAminoAcidList(String peptideSequence) This method converts peptide sequence into a List of amino acid
static List<String>	getAminoAcidList(String peptideSequence, String delimiter) This method converts peptide sequence into a List of amino acid with optional delimiter

Methods inherited from class java.lang.Object

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

Field Detail

SEQUENCE_DELIMETERS

public static final String[] SEQUENCE_DELIMETERS

Constructor Detail

AminoAcidParser

public AminoAcidParser()

Method Detail

getAminoAcidList

public static List<String> getAminoAcidList(String peptideSequence)
                                     throws MonomerException,
                                            NotationException,
                                            MonomerLoadingException,
                                            ChemistryException

This method converts peptide sequence into a List of amino acid

Parameters:

peptideSequence - given peptide sequence

Returns:

list of amino acid

Throws:

MonomerException - if peptide contains unknown monomers

NotationException - if peptide sequence is null

MonomerLoadingException - monomer store could not be loaded

ChemistryException - if chemistry could not be initialized

getAminoAcidList

public static List<String> getAminoAcidList(String peptideSequence,
                            String delimiter)
                                     throws MonomerException,
                                            NotationException,
                                            MonomerLoadingException,
                                            ChemistryException

This method converts peptide sequence into a List of amino acid with optional delimiter

Parameters:

peptideSequence - input sequence

delimiter - optional delimeter in the input sequence

Returns:

list of amino acid

Throws:

MonomerException - if monomer is not valid

NotationException - if notation is not valid

MonomerLoadingException - if monomer could not be read from the source

ChemistryException - if chemistry could not be initialized

cleanup

public static String cleanup(String sequence)

remove white space, and convert all lower case to upper case

Parameters:

sequence - given sequence

Returns:

cleaned sequence without withspace and all characters are in uppercase