Package org.helm.notation2.tools
Class AminoAcidParser
java.lang.Object
org.helm.notation2.tools.AminoAcidParser
public class AminoAcidParser extends Object
AminoAcidParser
- Author:
- hecht
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Field Summary
Fields Modifier and Type Field Description static String[]SEQUENCE_DELIMETERS -
Constructor Summary
Constructors Constructor Description AminoAcidParser() -
Method Summary
Modifier and Type Method Description static Stringcleanup(String sequence)remove white space, and convert all lower case to upper casestatic List<String>getAminoAcidList(String peptideSequence)This method converts peptide sequence into a List of amino acidstatic List<String>getAminoAcidList(String peptideSequence, String delimiter)This method converts peptide sequence into a List of amino acid with optional delimiter
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Field Details
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Constructor Details
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AminoAcidParser
public AminoAcidParser()
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Method Details
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getAminoAcidList
public static List<String> getAminoAcidList(String peptideSequence) throws MonomerException, NotationException, MonomerLoadingException, ChemistryExceptionThis 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 monomersNotationException- if peptide sequence is nullMonomerLoadingException- monomer store could not be loadedChemistryException- if chemistry could not be initialized
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getAminoAcidList
public static List<String> getAminoAcidList(String peptideSequence, String delimiter) throws MonomerException, NotationException, MonomerLoadingException, ChemistryExceptionThis method converts peptide sequence into a List of amino acid with optional delimiter- Parameters:
peptideSequence- input sequencedelimiter- optional delimeter in the input sequence- Returns:
- list of amino acid
- Throws:
MonomerException- if monomer is not validNotationException- if notation is not validMonomerLoadingException- if monomer could not be read from the sourceChemistryException- if chemistry could not be initialized
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cleanup
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
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