org.helm.notation2.tools

Class RNAUtils

java.lang.Object

org.helm.notation2.tools.RNAUtils

public class RNAUtils
extends Object

RNAUtils, class to provide methods for rna polymer

Author:

hecht

Field Summary

Fields

Modifier and Type	Field and Description
static int	MINUMUM_MATCH_FRAGMENT_LENGTH

Method Summary

Methods

Modifier and Type	Method and Description
static void	addLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to add a phosphate to the last polymer's nucleotide
static boolean	areAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymerOne, org.helm.notation2.parser.notation.polymer.PolymerNotation polymerTwo) method to check if two given polymers are complement to each other
static org.helm.notation2.parser.notation.polymer.PolymerNotation	getAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the antiparallel polymer for a rna/dna polymer
static org.helm.notation2.parser.notation.polymer.PolymerNotation	getComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the normal complement polymer for a given rna/dna polymer
static org.helm.notation2.parser.notation.polymer.PolymerNotation	getInverse(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the polymer with the inverse sequence of the current polymer
static String	getMaxMatchFragment(String seq1, String seq2) method to get the largest matched fragment between two sequences, replace T with U before Match
static String	getMaxMatchFragment(String seq1, String seq2, int minLength) This method returns the largest matched fragment between two sequences, replace T with U before match
static String	getModifiedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the modifiedNucleotideSequence of the given PolymerNotation
static String	getNaturalAnalogSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to generate the natural analogue sequence of a rna/dna of a given polymer
static List<Nucleotide>	getNucleotideList(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get all nucleotides for one polymer
static String	getNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the nucleotide sequence for the polymer
static org.helm.notation2.parser.notation.polymer.PolymerNotation	getReverseComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the polymer with the reverse complement sequence of the current polymer
static String	getReverseSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to generate the reverse rna/dna sequence of a given polymer
static String	getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation one) method to get the rna sequence of the given PolymerNotation
static String	getTrimmedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to get the trimmed nucleotide sequence
static boolean	hasNucleotideModification(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to check if the given PolymerNotation has a nucleotide Modification
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation>	hybridize(org.helm.notation2.parser.notation.polymer.PolymerNotation one, org.helm.notation2.parser.notation.polymer.PolymerNotation two) method to hybridize two given PolymerNotations together
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation>	hybridizeAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation one, org.helm.notation2.parser.notation.polymer.PolymerNotation two) method to hybridize two PolymerNotations together if they are antiparallel
static void	removeLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to remove the phosphate of the last nucleotide

Methods inherited from class java.lang.Object

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

Field Detail

MINUMUM_MATCH_FRAGMENT_LENGTH

public static final int MINUMUM_MATCH_FRAGMENT_LENGTH

See Also:

Constant Field Values

Method Detail

getReverseSequence

public static String getReverseSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                 throws RNAUtilsException,
                                        HELM2HandledException,
                                        NotationException,
                                        ChemistryException

method to generate the reverse rna/dna sequence of a given polymer

Parameters:

polymer - PolymerNotation

Returns:

sequence reverse rna/dna sequence

Throws:

RNAUtilsException - if the polymer is not a RNA/DNA

HELM2HandledException - if the polymer contains HELM2 features

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

getNaturalAnalogSequence

public static String getNaturalAnalogSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                       throws HELM2HandledException,
                                              RNAUtilsException,
                                              ChemistryException

method to generate the natural analogue sequence of a rna/dna of a given polymer

Parameters:

polymer - PolymerNotation

Returns:

sequence natural analogue sequence

Throws:

HELM2HandledException - if the polymer contains HELM2 features

RNAUtilsException - if the polymer is not RNA or DNA

ChemistryException - if the Chemistry Engine can not be initialized

areAntiparallel

public static boolean areAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymerOne,
                      org.helm.notation2.parser.notation.polymer.PolymerNotation polymerTwo)
                               throws RNAUtilsException,
                                      HELM2HandledException,
                                      ChemistryException,
                                      NucleotideLoadingException

method to check if two given polymers are complement to each other

Parameters:

polymerOne - PolymerNotation of the first polymer

polymerTwo - PolymerNotation of the second polymer

Returns:

true, if they are opposite to each other, false otherwise

Throws:

RNAUtilsException - if the polymers are not rna/dna or the antiparallel strand can not be built from polymerOne

HELM2HandledException - if the polymers contain HELM2 features

ChemistryException - if the Chemistry Engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

getMaxMatchFragment

public static String getMaxMatchFragment(String seq1,
                         String seq2)
                                  throws org.helm.notation2.parser.exceptionparser.NotationException

method to get the largest matched fragment between two sequences, replace T with U before Match

Parameters:

seq1 - single letter, all upper case nucleotide sequence

seq2 - single letter, all upper case nucleotide sequence

Returns:

maximal match fragment of seq1 and seq2

Throws:

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

getMaxMatchFragment

public static String getMaxMatchFragment(String seq1,
                         String seq2,
                         int minLength)
                                  throws org.helm.notation2.parser.exceptionparser.NotationException

This method returns the largest matched fragment between two sequences, replace T with U before match

Parameters:

seq1 - single letter, all upper case nucleotide sequence

seq2 - single letter, all upper case nucleotide sequence

minLength - - minimum fragment length

Returns:

largest match fragment

Throws:

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

removeLastP

public static void removeLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                        throws RNAUtilsException,
                               org.helm.notation2.parser.exceptionparser.NotationException,
                               HELM2HandledException

method to remove the phosphate of the last nucleotide

Parameters:

polymer - PolymerNotation

Throws:

RNAUtilsException - if the PolmyerNotation is not a rna or dna

org.helm.notation2.parser.exceptionparser.NotationException - if the changed notation object can not be generated

HELM2HandledException - if HELM2 features are involved

addLastP

public static void addLastP(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                     throws RNAUtilsException,
                            org.helm.notation2.parser.exceptionparser.NotationException,
                            HELM2HandledException

method to add a phosphate to the last polymer's nucleotide

Parameters:

polymer - PolymerNotation

Throws:

RNAUtilsException - if the polymer is no rna or dna

org.helm.notation2.parser.exceptionparser.NotationException - if the changed notation object can not be generated

HELM2HandledException - if HELM2 features are involved

getAntiparallel

public static org.helm.notation2.parser.notation.polymer.PolymerNotation getAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                                                                  throws RNAUtilsException,
                                                                                         ChemistryException,
                                                                                         NucleotideLoadingException

method to get the antiparallel polymer for a rna/dna polymer

Parameters:

polymer - PolymerNotation

Returns:

antiparallel polymer

Throws:

RNAUtilsException - if the polymer is not rna or dna or the reverse polymer can not be built

ChemistryException - if the Chemistry Engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

getInverse

public static org.helm.notation2.parser.notation.polymer.PolymerNotation getInverse(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                                                             throws RNAUtilsException,
                                                                                    NotationException,
                                                                                    ChemistryException,
                                                                                    NucleotideLoadingException

method to get the polymer with the inverse sequence of the current polymer

Parameters:

polymer - PolymerNotation

Returns:

inverse sequence

Throws:

RNAUtilsException - if the polymer is not rna or dna or the inverse strand can not be built

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

getReverseComplement

public static org.helm.notation2.parser.notation.polymer.PolymerNotation getReverseComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                                                                       throws RNAUtilsException,
                                                                                              NotationException,
                                                                                              ChemistryException,
                                                                                              NucleotideLoadingException

method to get the polymer with the reverse complement sequence of the current polymer

Parameters:

polymer - PolymerNotation

Returns:

PolymerNotation with the reverse complement

Throws:

RNAUtilsException - if the polymer is not rna or dna or the inverse strand can not be built

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

NucleotideLoadingException - can not be loaded

getComplement

public static org.helm.notation2.parser.notation.polymer.PolymerNotation getComplement(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                                                                throws RNAUtilsException,
                                                                                       ChemistryException,
                                                                                       NucleotideLoadingException

method to get the normal complement polymer for a given rna/dna polymer

Parameters:

polymer - given polymernotation

Returns:

complement polymernotation of the given polymernotation

Throws:

RNAUtilsException - if the polymer is not rna or dna or the complement polymer can not be built

ChemistryException - if the Chemistry Engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

hasNucleotideModification

public static boolean hasNucleotideModification(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                         throws org.helm.notation2.parser.exceptionparser.NotationException

method to check if the given PolymerNotation has a nucleotide Modification

Parameters:

polymer - PolymerNotation

Returns:

true if the polymer contains at least one modifcation, false otherwise

Throws:

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

hybridizeAntiparallel

public static List<org.helm.notation2.parser.notation.connection.ConnectionNotation> hybridizeAntiparallel(org.helm.notation2.parser.notation.polymer.PolymerNotation one,
                                                                                           org.helm.notation2.parser.notation.polymer.PolymerNotation two)
                                                                                                    throws RNAUtilsException,
                                                                                                           org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                                           HELM2HandledException,
                                                                                                           ChemistryException,
                                                                                                           NucleotideLoadingException

method to hybridize two PolymerNotations together if they are antiparallel

Parameters:

one - PolymerNotation first

two - PolymerNotation second

Returns:

List of ConnectionNotations

Throws:

RNAUtilsException - if the polymer is not a RNA/DNA

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

HELM2HandledException - if it contains helm2 specific features can not be downcasted to HELM1 format

ChemistryException - if the Chemistry Engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

getSequence

public static String getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation one)
                          throws RNAUtilsException,
                                 HELM2HandledException,
                                 ChemistryException

method to get the rna sequence of the given PolymerNotation

Parameters:

one - PolymerNotation

Returns:

sequence

Throws:

RNAUtilsException - if the polymer is not a RNA/DNA

HELM2HandledException - if it contains helm2 specific features can not be casted to HELM1 Format

ChemistryException - if chemistry engine can not be initialized

getModifiedNucleotideSequence

public static String getModifiedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                            throws RNAUtilsException,
                                                   HELM2HandledException,
                                                   ChemistryException

method to get the modifiedNucleotideSequence of the given PolymerNotation

Parameters:

polymer - PolymerNotation

Returns:

modified nucleotide sequence

Throws:

RNAUtilsException - if the polymer is not a RNA/DNA

HELM2HandledException - if it contains HELM2 specific features, it can not be casted to HELM1Format

ChemistryException - if the chemistry engine can not be initialized

hybridize

public static List<org.helm.notation2.parser.notation.connection.ConnectionNotation> hybridize(org.helm.notation2.parser.notation.polymer.PolymerNotation one,
                                                                               org.helm.notation2.parser.notation.polymer.PolymerNotation two)
                                                                                        throws RNAUtilsException,
                                                                                               org.helm.notation2.parser.exceptionparser.NotationException,
                                                                                               HELM2HandledException,
                                                                                               NotationException,
                                                                                               ChemistryException

method to hybridize two given PolymerNotations together

Parameters:

one - PolymerNotaiton

two - PolymerNotation

Returns:

List of ConnectionNotations

Throws:

RNAUtilsException - if the polymer is not a RNA/DNA

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

HELM2HandledException - if it contains specific HELM2 features, so that it can not casted to HELM1Format

NotationException - if notation is not valid

ChemistryException - if chemistry engine can not be initialized

getNucleotideSequence

public static String getNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                    throws org.helm.notation2.parser.exceptionparser.NotationException,
                                           RNAUtilsException,
                                           HELM2HandledException,
                                           NucleotideLoadingException,
                                           ChemistryException

method to get the nucleotide sequence for the polymer

Parameters:

polymer - PolymerNotation

Returns:

nucleotide sequence

Throws:

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

RNAUtilsException - if the polymer is not a RNA/DNA

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

NucleotideLoadingException - if nucleotides can not be loaded

ChemistryException - if chemistry engine can not be initialized

getNucleotideList

public static List<Nucleotide> getNucleotideList(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                          throws RNAUtilsException,
                                                 HELM2HandledException,
                                                 ChemistryException

method to get all nucleotides for one polymer

Parameters:

polymer - PolymerNotation

Returns:

List of nucleotides of the polmyer

Throws:

RNAUtilsException - if the polymer is not rna or dna or the nucleotide can not be read

HELM2HandledException - if the polymer contains HELM2 features

ChemistryException - if chemistry engine can not be initialized

getTrimmedNucleotideSequence

public static String getTrimmedNucleotideSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                           throws RNAUtilsException,
                                                  HELM2HandledException,
                                                  ChemistryException

method to get the trimmed nucleotide sequence

Parameters:

polymer - given rna/dna polymer

Returns:

trimmed nucleotide sequence

Throws:

RNAUtilsException - if the polymer is not a RNA/DNA

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

ChemistryException - if chemistry engine can not be initialized