org.helm.notation2.tools

Class HELM2NotationUtils

java.lang.Object

org.helm.notation2.tools.HELM2NotationUtils

public class HELM2NotationUtils
extends Object

HELM2NotationUtils

Author:

hecht

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_BASE_PAIR_CHAR
static String	DEFAULT_PADDING_CHAR

Method Summary

Methods

Modifier and Type	Method and Description
static void	combineHELM2notation(org.helm.notation2.parser.notation.HELM2Notation helm2notation, org.helm.notation2.parser.notation.HELM2Notation newHELM2Notation) method to add a new HELMNotation to another HELM2Notation, the new HELM2Notation will be merged to the first HELM2Notation
List<org.helm.notation2.parser.notation.HELM2Notation>	decompose(org.helm.notation2.parser.notation.HELM2Notation helm2notation) decompose the HELM2 into smaller HELM2 objects
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation>	getAllBasePairConnections(List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections) method to get all base pair connections of a given list of ConnectionNotation
static List<org.helm.notation2.parser.notation.connection.ConnectionNotation>	getAllEdgeConnections(List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections) method to get all edge connections of a given List of ConnectionNotation
static List<org.helm.notation2.parser.notation.polymer.PolymerNotation>	getBLOBPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to get all blob polymers given a list of PolymerNotation objects
static List<org.helm.notation2.parser.notation.polymer.PolymerNotation>	getCHEMPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to get all chem polymers given a list of PolymerNotation objects
static String[]	getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation) generate formated siRNA sequence with default padding char " " and base-pair char "|"
static String[]	getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation, String paddingChar, String basePairChar)
static List<org.helm.notation2.parser.notation.polymer.PolymerNotation>	getListOfPolymersSpecificType(String str, List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to get all polymers for one specific polymer type
static List<org.helm.notation2.parser.notation.polymer.PolymerNotation>	getPeptidePolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to get all peptide polymers given a list of PolymerNotation objects
static List<org.helm.notation2.parser.notation.polymer.PolymerNotation>	getRNAPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to get all rna polymers given a List of PolymerNotation objects
static int	getTotalMonomerCount(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to get the total number of MonomerNotationUnits in a HELMNotation object
static boolean	hasNucleotideModification(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method to check if any of the rna polymers have a modified nucleotide
static org.helm.notation2.parser.notation.HELM2Notation	readNotation(String notation)
static String	toJSON(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to generate a JSON-Object from the given HELM2Notation

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_PADDING_CHAR

public static final String DEFAULT_PADDING_CHAR

See Also:

Constant Field Values

DEFAULT_BASE_PAIR_CHAR

public static final String DEFAULT_BASE_PAIR_CHAR

See Also:

Constant Field Values

Method Detail

toJSON

public static final String toJSON(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                           throws com.fasterxml.jackson.core.JsonProcessingException

method to generate a JSON-Object from the given HELM2Notation

Parameters:

helm2notation - HELM2Notation object

Returns:

NotationContainer in JSON-Format

Throws:

com.fasterxml.jackson.core.JsonProcessingException - json could not produced

getAllEdgeConnections

public static final List<org.helm.notation2.parser.notation.connection.ConnectionNotation> getAllEdgeConnections(List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections)

method to get all edge connections of a given List of ConnectionNotation

Parameters:

connections - List of ConnectionNotation objects

Returns:

all edge connections

getAllBasePairConnections

public static final List<org.helm.notation2.parser.notation.connection.ConnectionNotation> getAllBasePairConnections(List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections)

method to get all base pair connections of a given list of ConnectionNotation

Parameters:

connections - List of ConnectionNotation objects

Returns:

all base pair connections

getRNAPolymers

public static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getRNAPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)

method to get all rna polymers given a List of PolymerNotation objects

Parameters:

polymers - List of PolymerNotation

Returns:

list of rna polymers

getPeptidePolymers

public static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getPeptidePolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)

method to get all peptide polymers given a list of PolymerNotation objects

Parameters:

polymers - List of PolymerNotation objects

Returns:

list of peptide polymers

getCHEMPolymers

public static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getCHEMPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)

method to get all chem polymers given a list of PolymerNotation objects

Parameters:

polymers - List of PolymerNotation objects

Returns:

list of chem polymers

getBLOBPolymers

public static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getBLOBPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)

method to get all blob polymers given a list of PolymerNotation objects

Parameters:

polymers - List of PolymerNotation objects

Returns:

list of blob polymers

combineHELM2notation

public static final void combineHELM2notation(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
                        org.helm.notation2.parser.notation.HELM2Notation newHELM2Notation)
                                       throws org.helm.notation2.parser.exceptionparser.NotationException

method to add a new HELMNotation to another HELM2Notation, the new HELM2Notation will be merged to the first HELM2Notation

Parameters:

helm2notation - HELM2Notation

newHELM2Notation - new HELMNotation

Throws:

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

getTotalMonomerCount

public static final int getTotalMonomerCount(org.helm.notation2.parser.notation.HELM2Notation helm2notation)

method to get the total number of MonomerNotationUnits in a HELMNotation object

Parameters:

helm2notation - given HELM2Notation

Returns:

number of MonomerNotationUnits

hasNucleotideModification

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

method to check if any of the rna polymers have a modified nucleotide

Parameters:

polymers - list of PolymerNotation

Returns:

true if at least one rna polymer has a modified nucleotide

Throws:

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

getFormatedSirnaSequences

public static String[] getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                                          throws org.helm.notation2.parser.exceptionparser.NotationException,
                                                 RNAUtilsException,
                                                 HELM2HandledException,
                                                 NotationException,
                                                 ChemistryException

generate formated siRNA sequence with default padding char " " and base-pair char "|"

Parameters:

helm2notation - HELM2Notation

Returns:

string array of formated nucloeotide 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

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

getFormatedSirnaSequences

public static String[] getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation,
                                 String paddingChar,
                                 String basePairChar)
                                          throws org.helm.notation2.parser.exceptionparser.NotationException,
                                                 RNAUtilsException,
                                                 HELM2HandledException,
                                                 NotationException,
                                                 ChemistryException

Parameters:

helm2notation - HELM2Notation

paddingChar - padding character

basePairChar - base pair character

Returns:

string array of formated 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

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

decompose

public List<org.helm.notation2.parser.notation.HELM2Notation> decompose(org.helm.notation2.parser.notation.HELM2Notation helm2notation)

decompose the HELM2 into smaller HELM2 objects

Parameters:

helm2notation - HELM2 object

Returns:

list of ContainerHELM2 objects

readNotation

public static org.helm.notation2.parser.notation.HELM2Notation readNotation(String notation)
                                                                     throws ParserException,
                                                                            org.jdom2.JDOMException

Throws:

ParserException

org.jdom2.JDOMException

getListOfPolymersSpecificType

public static List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getListOfPolymersSpecificType(String str,
                                                                                             List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)

method to get all polymers for one specific polymer type

Parameters:

str - specific polymer type

polymers - List of PolymerNotation

Returns:

List of PolymerNotation with the specific type