public class HELM2NotationUtils extends Object
| Modifier and Type | Field and Description |
|---|---|
static String |
DEFAULT_BASE_PAIR_CHAR |
static String |
DEFAULT_PADDING_CHAR |
| 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
|
public static final String DEFAULT_PADDING_CHAR
public static final String DEFAULT_BASE_PAIR_CHAR
public static final String toJSON(org.helm.notation2.parser.notation.HELM2Notation helm2notation) throws com.fasterxml.jackson.core.JsonProcessingException
helm2notation - HELM2Notation objectcom.fasterxml.jackson.core.JsonProcessingException - json could not producedpublic static final List<org.helm.notation2.parser.notation.connection.ConnectionNotation> getAllEdgeConnections(List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections)
connections - List of ConnectionNotation objectspublic static final List<org.helm.notation2.parser.notation.connection.ConnectionNotation> getAllBasePairConnections(List<org.helm.notation2.parser.notation.connection.ConnectionNotation> connections)
connections - List of ConnectionNotation objectspublic static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getRNAPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
polymers - List of PolymerNotationpublic static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getPeptidePolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
polymers - List of PolymerNotation objectspublic static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getCHEMPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
polymers - List of PolymerNotation objectspublic static final List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getBLOBPolymers(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
polymers - List of PolymerNotation objectspublic 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
helm2notation - HELM2NotationnewHELM2Notation - new HELMNotationorg.helm.notation2.parser.exceptionparser.NotationException - if the HELMNotation is not validpublic static final int getTotalMonomerCount(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
helm2notation - given HELM2Notationpublic static boolean hasNucleotideModification(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) throws org.helm.notation2.parser.exceptionparser.NotationException
polymers - list of PolymerNotationorg.helm.notation2.parser.exceptionparser.NotationException - if notation is not validpublic static String[] getFormatedSirnaSequences(org.helm.notation2.parser.notation.HELM2Notation helm2notation) throws org.helm.notation2.parser.exceptionparser.NotationException, RNAUtilsException, HELM2HandledException, NotationException, ChemistryException
helm2notation - HELM2Notationorg.helm.notation2.parser.exceptionparser.NotationException - if notation is not validRNAUtilsException - if the polymer is not a RNA/DNAHELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 FormatNotationException - if notation is not validChemistryException - if the Chemistry Engine can not be initializedpublic 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
helm2notation - HELM2NotationpaddingChar - padding characterbasePairChar - base pair characterorg.helm.notation2.parser.exceptionparser.NotationException - if notation is not validRNAUtilsException - if the polymer is not a RNA/DNAHELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 FormatNotationException - if notation is not validChemistryException - if the Chemistry Engine can not be initializedpublic List<org.helm.notation2.parser.notation.HELM2Notation> decompose(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
helm2notation - HELM2 objectpublic static org.helm.notation2.parser.notation.HELM2Notation readNotation(String notation) throws ParserException, org.jdom2.JDOMException
ParserExceptionorg.jdom2.JDOMExceptionpublic static List<org.helm.notation2.parser.notation.polymer.PolymerNotation> getListOfPolymersSpecificType(String str, List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
str - specific polymer typepolymers - List of PolymerNotationCopyright © 2017. All rights reserved.