org.sbolstandard.core2

Class Sequence

java.lang.Object

org.sbolstandard.core2.Identified

org.sbolstandard.core2.TopLevel

org.sbolstandard.core2.Sequence

public class Sequence
extends TopLevel

Represents a Sequence object in the SBOL data model.

Version:

2.1

Author:

Zhen Zhang, Nicholas Roehner, Chris Myers

Field Summary

Fields

Modifier and Type	Field and Description
static URI	IUPAC_DNA Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC_DNA).
static URI	IUPAC_PROTEIN Nomenclature and Symbolism for Amino Acids and Peptides (IUPAC_PROTEIN).
static URI	IUPAC_RNA Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC_RNA).
static URI	SMILES SMILES was originally developed as a proprietary specification by Daylight Chemical Information Systems Since the introduction of SMILES in the late 1980’s, it has become widely accepted as a defacto standard for exchange of molecular structures (SMILES).

Fields inherited from class org.sbolstandard.core2.TopLevel

ACTIVITY, AGENT, ANNOTATION, ATTACHMENT, COLLECTION, COMBINATORIAL_DERIVATION, COMPONENT_DEFINITION, EXPERIMENT, EXPERIMENTAL_DATA, GENERIC_TOP_LEVEL, IMPLEMENTATION, MODEL, MODULE_DEFINITION, PLAN, SEQUENCE

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
String	getElements() Returns the elements property of this sequence.
URI	getEncoding() Returns the encoding property of this sequence.
int	hashCode()
static String	reverseComplement(String elements, URI type) Perform the reverse complement of a sequence encoded using IUPAC_DNA
void	setElements(String elements) Sets the elements property to the given argument.
void	setEncoding(URI encoding) Sets the encoding property to the given argument.
String	toString()

Methods inherited from class org.sbolstandard.core2.TopLevel

addAttachment, addAttachment, addAttachment, clearAttachments, containsAttachment, getAttachments, getAttachmentURIs, removeAttachment, setAttachments

Methods inherited from class org.sbolstandard.core2.Identified

addWasDerivedFrom, addWasGeneratedBy, clearAnnotations, clearWasDerivedFroms, clearWasGeneratedBys, containsWasDerivedFrom, containsWasGeneratedBy, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, createAnnotation, getAnnotation, getAnnotations, getDescription, getDisplayId, getIdentity, getName, getPersistentIdentity, getVersion, getWasDerivedFrom, getWasDerivedFroms, getWasGeneratedBys, hasAnnotations, isSetDescription, isSetDisplayId, isSetName, isSetPersistentIdentity, isSetVersion, isSetWasDerivedFrom, removeAnnotation, removeWasDerivedFrom, removeWasGeneratedBy, setDescription, setName, setWasDerivedFrom, setWasDerivedFroms, setWasGeneratedBys, unsetDescription, unsetName, unsetWasDerivedFrom

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

IUPAC_DNA

public static final URI IUPAC_DNA

Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC_DNA).

IUPAC_RNA

public static final URI IUPAC_RNA

Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC_RNA).

IUPAC_PROTEIN

public static final URI IUPAC_PROTEIN

Nomenclature and Symbolism for Amino Acids and Peptides (IUPAC_PROTEIN).

SMILES

public static final URI SMILES

SMILES was originally developed as a proprietary specification by Daylight Chemical Information Systems Since the introduction of SMILES in the late 1980’s, it has become widely accepted as a defacto standard for exchange of molecular structures (SMILES). Many independent SMILES software packages have been written in C, C++, Java, Python, LISP, and probably even FORTRAN.

Method Detail

getElements

public String getElements()

Returns the elements property of this sequence.

Returns:

the elements property of this sequence.

setElements

public void setElements(String elements)
                 throws SBOLValidationException

Sets the elements property to the given argument.

Parameters:

elements - the given elements property

Throws:

SBOLValidationException - if either of the following SBOL validation rule was violated: 10402, 10405.

getEncoding

public URI getEncoding()

Returns the encoding property of this sequence.

Returns:

the encoding property of this sequence

setEncoding

public void setEncoding(URI encoding)
                 throws SBOLValidationException

Sets the encoding property to the given argument.

Parameters:

encoding - the given encoding property

Throws:

SBOLValidationException - if the following SBOL validation rule was violated: 10403.

hashCode

public int hashCode()

Overrides:

hashCode in class TopLevel

equals

public boolean equals(Object obj)

Overrides:

equals in class TopLevel

reverseComplement

public static String reverseComplement(String elements,
                                       URI type)

Perform the reverse complement of a sequence encoded using IUPAC_DNA

Parameters:

elements - sequence to reverse complement

type - DNA or RNA type

Returns:

the reverse complement of a sequence encoded using IUPAC_DNA

toString

public String toString()

Overrides:

toString in class Identified