org.helm.notation2.tools

Class NucleotideParser

java.lang.Object

org.helm.notation2.tools.NucleotideParser

public class NucleotideParser
extends Object

NucleotideParser

Author:

hecht

Field Summary

Fields

Modifier and Type	Field and Description
static char	BRANCH_END_SYMBOL
static char	BRANCH_START_SYMBOL
static Map<String,String>	complementMap
static String	DEFAULT_NOTATION_SOURCE Deprecated.
static int	MINUMUM_MATCH_FRAGMENT_LENGTH
static char	MODIFICATION_END_SYMBOL
static char	MODIFICATION_START_SYMBOL
static String	RNA_DESIGN_DICER_27_L
static String	RNA_DESIGN_DICER_27_R
static String	RNA_DESIGN_NONE
static String	RNA_DESIGN_TUSCHL_19_PLUS_2
static List<String>	SUPPORTED_DESIGN_LIST

Constructor Summary

Constructors

Constructor and Description
NucleotideParser()

Method Summary

Methods

Modifier and Type	Method and Description
static Nucleotide	convertToNucleotide(String id, boolean last) method to convert an string to an nucleotide
static int	getMatchingBracketPosition(char[] characters, int position, char openingBracket, char closingBracket)
static int	getMonomerCountForRNA(String notation)
static List<String>	getMonomerIDListFromNucleotide(String element)
static Nucleotide	getNucleotide(org.jdom2.Element nucleotideElement)
static Nucleotide	getNucleotide(String nucleotideXML)
static Map<String,Map<String,String>>	getNucleotideTemplates(org.jdom2.Element templatesElement)
static String	getNucleotideTemplatesXML(Map<String,Map<String,String>> templates)
static boolean	validateSimpleNotationForRNA(String polymerNotation) validate RNA simple notation

Methods inherited from class java.lang.Object

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

Field Detail

MODIFICATION_START_SYMBOL

public static final char MODIFICATION_START_SYMBOL

See Also:

Constant Field Values

MODIFICATION_END_SYMBOL

public static final char MODIFICATION_END_SYMBOL

See Also:

Constant Field Values

BRANCH_START_SYMBOL

public static final char BRANCH_START_SYMBOL

See Also:

Constant Field Values

BRANCH_END_SYMBOL

public static final char BRANCH_END_SYMBOL

See Also:

Constant Field Values

DEFAULT_NOTATION_SOURCE

@Deprecated
public static final String DEFAULT_NOTATION_SOURCE

Deprecated.

See Also:

Constant Field Values

MINUMUM_MATCH_FRAGMENT_LENGTH

public static final int MINUMUM_MATCH_FRAGMENT_LENGTH

See Also:

Constant Field Values

complementMap

public static Map<String,String> complementMap

RNA_DESIGN_NONE

public static final String RNA_DESIGN_NONE

See Also:

Constant Field Values

RNA_DESIGN_TUSCHL_19_PLUS_2

public static final String RNA_DESIGN_TUSCHL_19_PLUS_2

See Also:

Constant Field Values

RNA_DESIGN_DICER_27_R

public static final String RNA_DESIGN_DICER_27_R

See Also:

Constant Field Values

RNA_DESIGN_DICER_27_L

public static final String RNA_DESIGN_DICER_27_L

See Also:

Constant Field Values

SUPPORTED_DESIGN_LIST

public static final List<String> SUPPORTED_DESIGN_LIST

Constructor Detail

NucleotideParser

public NucleotideParser()

Method Detail

getNucleotideTemplates

public static Map<String,Map<String,String>> getNucleotideTemplates(org.jdom2.Element templatesElement)

getNucleotide

public static Nucleotide getNucleotide(org.jdom2.Element nucleotideElement)

getNucleotide

public static Nucleotide getNucleotide(String nucleotideXML)
                                throws org.jdom2.JDOMException,
                                       IOException

Throws:

org.jdom2.JDOMException

IOException

getNucleotideTemplatesXML

public static String getNucleotideTemplatesXML(Map<String,Map<String,String>> templates)

getMonomerIDListFromNucleotide

public static List<String> getMonomerIDListFromNucleotide(String element)
                                                   throws org.helm.notation2.parser.exceptionparser.NotationException

Throws:

org.helm.notation2.parser.exceptionparser.NotationException

convertToNucleotide

public static Nucleotide convertToNucleotide(String id,
                             boolean last)
                                      throws MonomerException,
                                             NotationException,
                                             ChemistryException,
                                             NucleotideLoadingException,
                                             org.helm.notation2.parser.exceptionparser.NotationException

method to convert an string to an nucleotide

Parameters:

id - given input string

last - if the nucleotide is the last element of an rna

Returns:

nucleotide

Throws:

ChemistryException - if the chemistry engine could not be initialized

NotationException - if notation is not valid

MonomerException - if the monomer is not valid

NucleotideLoadingException - if nucleotides can not be loaded

org.helm.notation2.parser.exceptionparser.NotationException - if the notation is not valid

getMonomerCountForRNA

public static int getMonomerCountForRNA(String notation)
                                 throws org.helm.notation2.parser.exceptionparser.NotationException

Parameters:

notation - given notation

Returns:

count of rna monomers

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

validateSimpleNotationForRNA

public static boolean validateSimpleNotationForRNA(String polymerNotation)
                                            throws org.helm.notation2.parser.exceptionparser.NotationException

validate RNA simple notation

Parameters:

polymerNotation - notation to be checked

Returns:

true if the polymyer notation is valid, otherwise throws an exception

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

getMatchingBracketPosition

public static int getMatchingBracketPosition(char[] characters,
                             int position,
                             char openingBracket,
                             char closingBracket)