de.jstacs.data

Enum DinucleotideProperty

java.lang.Object

java.lang.Enum<DinucleotideProperty>

de.jstacs.data.DinucleotideProperty

All Implemented Interfaces:

Serializable, Comparable<DinucleotideProperty>

public enum DinucleotideProperty
extends Enum<DinucleotideProperty>

This enum defines physicochemical, conformational, and letter-based dinucleotide properties of nucleotide sequences. All dinucleotide parameters are obtained from http://diprodb.fli-leibniz.de/.

Author:

Jens Keilwagen, Jan Grau

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DinucleotideProperty.HowCreated This enum defines the origins of nucleotide properties
static class	DinucleotideProperty.MeanSmoothing Smoothing by mean using a pre-defined window width.
static class	DinucleotideProperty.MedianSmoothing Smoothing by median using a pre-defined window width.
static class	DinucleotideProperty.NoSmoothing Implementation of DinucleotideProperty.Smoothing that conducts no smoothing.
static class	DinucleotideProperty.Smoothing Abstract class for methods that smooth a series of real values.
static class	DinucleotideProperty.Type This enum defines the types of dinucleotide properties.

Enum Constant Summary

Enum Constants

Enum Constant and Description
ADENINE_CONTENT
BEND
CLASH_STRENGTH
CYTOSINE_CONTENT
DIRECTION
ENTHALPY_RNA_FREIER
ENTHALPY_RNA_XIA
ENTHALPY_SANTALUCIA
ENTHALPY_SUGIMOTO
ENTROPY_RNA_FREIER
ENTROPY_RNA_XIA
ENTROPY_SANTALUCIA
ENTROPY_SUGIMOTO
FLEXIBILITY_SHIFT
FLEXIBILITY_SLIDE
FREE_ENERGY_ALLAWI
FREE_ENERGY_BRESLAUER
FREE_ENERGY_DELCOURT
FREE_ENERGY_GOTOH
FREE_ENERGY_OWCZARZY
FREE_ENERGY_RNA_FREIER
FREE_ENERGY_RNA_XIA
FREE_ENERGY_SANTALUCIA_1996
FREE_ENERGY_SANTALUCIA_2004
FREE_ENERGY_SUGIMOTO
FREE_ENERGY_VOLOGODSKII
GC_CONTENT
GUANINE_CONTENT
HYDROPHILICITY_RNA_BARZILAY
HYDROPHILICITY_RNA_WEBER
INCLINATION
KETO_GT_CONTENT
MAJOR_GROOVE_DEPTH
MAJOR_GROOVE_DISTANCE
MAJOR_GROOVE_SIZE
MAJOR_GROOVE_WIDTH
MELTING_TEMPERATURE_ANSELMI
MELTING_TEMPERATURE_GOTOH
MINOR_GROOVE_DEPTH
MINOR_GROOVE_DISTANCE
MINOR_GROOVE_SIZE
MINOR_GROOVE_WIDTH
MOBILITY_TO_BEND_TOWARDS_MAJOR_GROOVE
MOBILITY_TO_BEND_TOWARDS_MINOR_GROOVE
PERSISTANCE_LENGTH
PROBABILITY_CONTACTING_NUCLEOSOME_CORE
PROPELLER_TWIST
PURINE_AG_CONTENT
RISE_DNA_PROTEIN_COMPLEX_OLSON
RISE_DNA_PROTEIN_COMPLEX_SUZUKI
RISE_KARAS
RISE_PEREZ
RISE_RISE
RISE_RNA
RISE_STIFFNESS
RISE_SUZUKI
ROLL_ANSELMI
ROLL_DNA_PROTEIN_COMPLEX_OLSON
ROLL_DNA_PROTEIN_COMPLEX_SUZUKI
ROLL_GORIN
ROLL_PACKER
ROLL_PEREZ
ROLL_RISE
ROLL_RNA
ROLL_ROLL
ROLL_SHIFT
ROLL_SLIDE
ROLL_STIFFNESS
ROLL_SUZUKI
SHIFT_DNA_PROTEIN_COMPLEX_OLSON
SHIFT_DNA_PROTEIN_COMPLEX_SUZUKI
SHIFT_PEREZ
SHIFT_RISE
SHIFT_RNA
SHIFT_SHIFT
SHIFT_SLIDE
SHIFT_STIFFNESS
SHIFT_SUZUKI
SLIDE_DNA_PROTEIN_COMPLEX_OLSON
SLIDE_DNA_PROTEIN_COMPLEX_SUZUKI
SLIDE_GORIN
SLIDE_PEREZ
SLIDE_RISE
SLIDE_RNA
SLIDE_SLIDE
SLIDE_STIFFNESS
SLIDE_SUZUKI
STACKING_ENERGY_ANSELMI
STACKING_ENERGY_PEREZ
STACKING_ENERGY_RNA
STACKING_ENERGY_SPONER
STACKING_ENERGY_USSERY
THYMINE_CONTENT
TILT_ANSELMI
TILT_DNA_PROTEIN_COMPLEX_OLSON
TILT_DNA_PROTEIN_COMPLEX_SUZUKI
TILT_GORIN
TILT_PEREZ
TILT_RISE
TILT_RNA
TILT_ROLL
TILT_SHIFT
TILT_SLIDE
TILT_STIFFNESS
TILT_SUZUKI
TILT_TILT
TIP
TWIST_ANSELMI
TWIST_DNA_PROTEIN_COMPLEX_OLSON
TWIST_DNA_PROTEIN_COMPLEX_SUZUKI
TWIST_GORIN
TWIST_KARAS
TWIST_PACKER
TWIST_PEREZ
TWIST_RISE
TWIST_RNA
TWIST_ROLL
TWIST_SHIFT
TWIST_SHPIGELMAN
TWIST_SLIDE
TWIST_STIFFNESS
TWIST_SUZUKI
TWIST_TILT
TWIST_TWIST
WEDGE

Field Summary

Fields

Modifier and Type	Field and Description
static AlphabetContainer	continuousAlphabet
static DinucleotideProperty.Smoothing	NO_SMOOTHING

Method Summary

Methods

Modifier and Type	Method and Description
static DinucleotideProperty[]	filterProperties(String nucleicAcid, Boolean doubleStrand, DinucleotideProperty.HowCreated howCreated, DinucleotideProperty.Type type, String dimension) Filters all DinucleotidePropertys by some of their annotations.
String	getComments() Returns additional comments on this property.
static DataSet	getDataSetForProperty(DataSet original, DinucleotideProperty... properties) Creates a new DataSet by converting each Sequence in original to the DinucleotidePropertys properties and setting these as ReferenceSequenceAnnotation of each original sequence.
static DataSet	getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean addToAnnotation, DinucleotideProperty... properties) Creates a new DataSet by converting each Sequence in original to the DinucleotidePropertys properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence.
static DataSet	getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean originalAsAnnotation, DinucleotideProperty property) Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing.
static DataSet	getDataSetForProperty(DataSet original, DinucleotideProperty property) Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property.
String	getDimension() Returns the dimension of this property, e.g.
double[][]	getDinucleotideParameters() Returns the dinucleotide parameters of this DinucleotideProperty as a two-dimensional double array, where the rows correspond to the first nucleotide and the columns correspond to the second nucleotide in the dinucleotide in order A, C, G, and T.
DinucleotideProperty.HowCreated	getHowCreated() Returns how this property has been determined.
String	getNucleicAcid() Returns the kind of nucleic acid, e.g.
double[]	getProperty(Sequence original) Computes this dinucleotide property for all overlapping twomers in original and returns the result as a double array of length original.getLength()-1
double[]	getProperty(Sequence original, DinucleotideProperty.Smoothing smoothing) Computes this dinucleotide property for all overlapping twomers in original, smoothes the result using smoothing, and returns the smoothed property as a double array.
double	getProperty(Sequence seq, int start)
ArbitrarySequence	getPropertyAsSequence(Sequence original) Computes this dinucleotide property for all overlapping twomers in original and returns the result as a Sequence of length original.getLength()-1
ArbitrarySequence	getPropertyAsSequence(Sequence original, DinucleotideProperty.Smoothing smoothing) Computes this dinucleotide property for all overlapping twomers in original, smoothes the result using smoothing, and returns the smoothed property as a Sequence.
static ImageResult	getPropertyImage(DataSet original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height)
static ImageResult	getPropertyImage(Sequence original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height)
String	getPubMedID() Returns the PubMed ID of the publication where the parameters of this property has been published.
String	getReference() Returns the reference of the publication where the parameters of this property has been published.
DinucleotideProperty.Type	getType() Returns the type of this property.
boolean	isDoubleStrand() Returns true if this property has been determined for a double-stranded nucleic acid.
static DinucleotideProperty	valueOf(String name) Returns the enum constant of this type with the specified name.
static DinucleotideProperty[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

TWIST_KARAS

public static final DinucleotideProperty TWIST_KARAS

STACKING_ENERGY_SPONER

public static final DinucleotideProperty STACKING_ENERGY_SPONER

RISE_KARAS

public static final DinucleotideProperty RISE_KARAS

BEND

public static final DinucleotideProperty BEND

TIP

public static final DinucleotideProperty TIP

INCLINATION

public static final DinucleotideProperty INCLINATION

MAJOR_GROOVE_WIDTH

public static final DinucleotideProperty MAJOR_GROOVE_WIDTH

MAJOR_GROOVE_DEPTH

public static final DinucleotideProperty MAJOR_GROOVE_DEPTH

MAJOR_GROOVE_SIZE

public static final DinucleotideProperty MAJOR_GROOVE_SIZE

MAJOR_GROOVE_DISTANCE

public static final DinucleotideProperty MAJOR_GROOVE_DISTANCE

MINOR_GROOVE_WIDTH

public static final DinucleotideProperty MINOR_GROOVE_WIDTH

MINOR_GROOVE_DEPTH

public static final DinucleotideProperty MINOR_GROOVE_DEPTH

MINOR_GROOVE_SIZE

public static final DinucleotideProperty MINOR_GROOVE_SIZE

MINOR_GROOVE_DISTANCE

public static final DinucleotideProperty MINOR_GROOVE_DISTANCE

PERSISTANCE_LENGTH

public static final DinucleotideProperty PERSISTANCE_LENGTH

MELTING_TEMPERATURE_GOTOH

public static final DinucleotideProperty MELTING_TEMPERATURE_GOTOH

PROBABILITY_CONTACTING_NUCLEOSOME_CORE

public static final DinucleotideProperty PROBABILITY_CONTACTING_NUCLEOSOME_CORE

MOBILITY_TO_BEND_TOWARDS_MAJOR_GROOVE

public static final DinucleotideProperty MOBILITY_TO_BEND_TOWARDS_MAJOR_GROOVE

MOBILITY_TO_BEND_TOWARDS_MINOR_GROOVE

public static final DinucleotideProperty MOBILITY_TO_BEND_TOWARDS_MINOR_GROOVE

PROPELLER_TWIST

public static final DinucleotideProperty PROPELLER_TWIST

CLASH_STRENGTH

public static final DinucleotideProperty CLASH_STRENGTH

ENTHALPY_SUGIMOTO

public static final DinucleotideProperty ENTHALPY_SUGIMOTO

ENTROPY_SUGIMOTO

public static final DinucleotideProperty ENTROPY_SUGIMOTO

SHIFT_RNA

public static final DinucleotideProperty SHIFT_RNA

ROLL_DNA_PROTEIN_COMPLEX_SUZUKI

public static final DinucleotideProperty ROLL_DNA_PROTEIN_COMPLEX_SUZUKI

TWIST_DNA_PROTEIN_COMPLEX_SUZUKI

public static final DinucleotideProperty TWIST_DNA_PROTEIN_COMPLEX_SUZUKI

TILT_DNA_PROTEIN_COMPLEX_SUZUKI

public static final DinucleotideProperty TILT_DNA_PROTEIN_COMPLEX_SUZUKI

SLIDE_DNA_PROTEIN_COMPLEX_SUZUKI

public static final DinucleotideProperty SLIDE_DNA_PROTEIN_COMPLEX_SUZUKI

HYDROPHILICITY_RNA_WEBER

public static final DinucleotideProperty HYDROPHILICITY_RNA_WEBER

SHIFT_DNA_PROTEIN_COMPLEX_SUZUKI

public static final DinucleotideProperty SHIFT_DNA_PROTEIN_COMPLEX_SUZUKI

HYDROPHILICITY_RNA_BARZILAY

public static final DinucleotideProperty HYDROPHILICITY_RNA_BARZILAY

RISE_DNA_PROTEIN_COMPLEX_SUZUKI

public static final DinucleotideProperty RISE_DNA_PROTEIN_COMPLEX_SUZUKI

STACKING_ENERGY_USSERY

public static final DinucleotideProperty STACKING_ENERGY_USSERY

FREE_ENERGY_DELCOURT

public static final DinucleotideProperty FREE_ENERGY_DELCOURT

FREE_ENERGY_BRESLAUER

public static final DinucleotideProperty FREE_ENERGY_BRESLAUER

FREE_ENERGY_VOLOGODSKII

public static final DinucleotideProperty FREE_ENERGY_VOLOGODSKII

TWIST_DNA_PROTEIN_COMPLEX_OLSON

public static final DinucleotideProperty TWIST_DNA_PROTEIN_COMPLEX_OLSON

FREE_ENERGY_GOTOH

public static final DinucleotideProperty FREE_ENERGY_GOTOH

TWIST_TWIST

public static final DinucleotideProperty TWIST_TWIST

TILT_TILT

public static final DinucleotideProperty TILT_TILT

ROLL_ROLL

public static final DinucleotideProperty ROLL_ROLL

TWIST_TILT

public static final DinucleotideProperty TWIST_TILT

TWIST_ROLL

public static final DinucleotideProperty TWIST_ROLL

TILT_ROLL

public static final DinucleotideProperty TILT_ROLL

SHIFT_SHIFT

public static final DinucleotideProperty SHIFT_SHIFT

SLIDE_SLIDE

public static final DinucleotideProperty SLIDE_SLIDE

RISE_RISE

public static final DinucleotideProperty RISE_RISE

SHIFT_SLIDE

public static final DinucleotideProperty SHIFT_SLIDE

SHIFT_RISE

public static final DinucleotideProperty SHIFT_RISE

SLIDE_RISE

public static final DinucleotideProperty SLIDE_RISE

TWIST_SHIFT

public static final DinucleotideProperty TWIST_SHIFT

TWIST_SLIDE

public static final DinucleotideProperty TWIST_SLIDE

TWIST_RISE

public static final DinucleotideProperty TWIST_RISE

TILT_SHIFT

public static final DinucleotideProperty TILT_SHIFT

TILT_SLIDE

public static final DinucleotideProperty TILT_SLIDE

TILT_RISE

public static final DinucleotideProperty TILT_RISE

ROLL_SHIFT

public static final DinucleotideProperty ROLL_SHIFT

ROLL_SLIDE

public static final DinucleotideProperty ROLL_SLIDE

ROLL_RISE

public static final DinucleotideProperty ROLL_RISE

STACKING_ENERGY_PEREZ

public static final DinucleotideProperty STACKING_ENERGY_PEREZ

TWIST_PEREZ

public static final DinucleotideProperty TWIST_PEREZ

TILT_PEREZ

public static final DinucleotideProperty TILT_PEREZ

ROLL_PEREZ

public static final DinucleotideProperty ROLL_PEREZ

SHIFT_PEREZ

public static final DinucleotideProperty SHIFT_PEREZ

SLIDE_PEREZ

public static final DinucleotideProperty SLIDE_PEREZ

RISE_PEREZ

public static final DinucleotideProperty RISE_PEREZ

SLIDE_STIFFNESS

public static final DinucleotideProperty SLIDE_STIFFNESS

SHIFT_STIFFNESS

public static final DinucleotideProperty SHIFT_STIFFNESS

ROLL_STIFFNESS

public static final DinucleotideProperty ROLL_STIFFNESS

TILT_STIFFNESS

public static final DinucleotideProperty TILT_STIFFNESS

TWIST_STIFFNESS

public static final DinucleotideProperty TWIST_STIFFNESS

FREE_ENERGY_SUGIMOTO

public static final DinucleotideProperty FREE_ENERGY_SUGIMOTO

FREE_ENERGY_ALLAWI

public static final DinucleotideProperty FREE_ENERGY_ALLAWI

FREE_ENERGY_SANTALUCIA_1996

public static final DinucleotideProperty FREE_ENERGY_SANTALUCIA_1996

FREE_ENERGY_OWCZARZY

public static final DinucleotideProperty FREE_ENERGY_OWCZARZY

GC_CONTENT

public static final DinucleotideProperty GC_CONTENT

PURINE_AG_CONTENT

public static final DinucleotideProperty PURINE_AG_CONTENT

KETO_GT_CONTENT

public static final DinucleotideProperty KETO_GT_CONTENT

ADENINE_CONTENT

public static final DinucleotideProperty ADENINE_CONTENT

GUANINE_CONTENT

public static final DinucleotideProperty GUANINE_CONTENT

CYTOSINE_CONTENT

public static final DinucleotideProperty CYTOSINE_CONTENT

THYMINE_CONTENT

public static final DinucleotideProperty THYMINE_CONTENT

TILT_DNA_PROTEIN_COMPLEX_OLSON

public static final DinucleotideProperty TILT_DNA_PROTEIN_COMPLEX_OLSON

ROLL_DNA_PROTEIN_COMPLEX_OLSON

public static final DinucleotideProperty ROLL_DNA_PROTEIN_COMPLEX_OLSON

SHIFT_DNA_PROTEIN_COMPLEX_OLSON

public static final DinucleotideProperty SHIFT_DNA_PROTEIN_COMPLEX_OLSON

SLIDE_DNA_PROTEIN_COMPLEX_OLSON

public static final DinucleotideProperty SLIDE_DNA_PROTEIN_COMPLEX_OLSON

RISE_DNA_PROTEIN_COMPLEX_OLSON

public static final DinucleotideProperty RISE_DNA_PROTEIN_COMPLEX_OLSON

TWIST_GORIN

public static final DinucleotideProperty TWIST_GORIN

TILT_GORIN

public static final DinucleotideProperty TILT_GORIN

ROLL_GORIN

public static final DinucleotideProperty ROLL_GORIN

SLIDE_GORIN

public static final DinucleotideProperty SLIDE_GORIN

TWIST_SUZUKI

public static final DinucleotideProperty TWIST_SUZUKI

TILT_SUZUKI

public static final DinucleotideProperty TILT_SUZUKI

ROLL_SUZUKI

public static final DinucleotideProperty ROLL_SUZUKI

SHIFT_SUZUKI

public static final DinucleotideProperty SHIFT_SUZUKI

SLIDE_SUZUKI

public static final DinucleotideProperty SLIDE_SUZUKI

RISE_SUZUKI

public static final DinucleotideProperty RISE_SUZUKI

TWIST_SHPIGELMAN

public static final DinucleotideProperty TWIST_SHPIGELMAN

WEDGE

public static final DinucleotideProperty WEDGE

DIRECTION

public static final DinucleotideProperty DIRECTION

SLIDE_RNA

public static final DinucleotideProperty SLIDE_RNA

RISE_RNA

public static final DinucleotideProperty RISE_RNA

TILT_RNA

public static final DinucleotideProperty TILT_RNA

ROLL_RNA

public static final DinucleotideProperty ROLL_RNA

TWIST_RNA

public static final DinucleotideProperty TWIST_RNA

STACKING_ENERGY_RNA

public static final DinucleotideProperty STACKING_ENERGY_RNA

RISE_STIFFNESS

public static final DinucleotideProperty RISE_STIFFNESS

MELTING_TEMPERATURE_ANSELMI

public static final DinucleotideProperty MELTING_TEMPERATURE_ANSELMI

STACKING_ENERGY_ANSELMI

public static final DinucleotideProperty STACKING_ENERGY_ANSELMI

ENTHALPY_RNA_FREIER

public static final DinucleotideProperty ENTHALPY_RNA_FREIER

ENTROPY_RNA_FREIER

public static final DinucleotideProperty ENTROPY_RNA_FREIER

FREE_ENERGY_RNA_FREIER

public static final DinucleotideProperty FREE_ENERGY_RNA_FREIER

FREE_ENERGY_RNA_XIA

public static final DinucleotideProperty FREE_ENERGY_RNA_XIA

ENTHALPY_RNA_XIA

public static final DinucleotideProperty ENTHALPY_RNA_XIA

ENTROPY_RNA_XIA

public static final DinucleotideProperty ENTROPY_RNA_XIA

ROLL_ANSELMI

public static final DinucleotideProperty ROLL_ANSELMI

TILT_ANSELMI

public static final DinucleotideProperty TILT_ANSELMI

TWIST_ANSELMI

public static final DinucleotideProperty TWIST_ANSELMI

ROLL_PACKER

public static final DinucleotideProperty ROLL_PACKER

TWIST_PACKER

public static final DinucleotideProperty TWIST_PACKER

FLEXIBILITY_SLIDE

public static final DinucleotideProperty FLEXIBILITY_SLIDE

FLEXIBILITY_SHIFT

public static final DinucleotideProperty FLEXIBILITY_SHIFT

ENTHALPY_SANTALUCIA

public static final DinucleotideProperty ENTHALPY_SANTALUCIA

ENTROPY_SANTALUCIA

public static final DinucleotideProperty ENTROPY_SANTALUCIA

FREE_ENERGY_SANTALUCIA_2004

public static final DinucleotideProperty FREE_ENERGY_SANTALUCIA_2004

Field Detail

NO_SMOOTHING

public static final DinucleotideProperty.Smoothing NO_SMOOTHING

continuousAlphabet

public static final AlphabetContainer continuousAlphabet

Method Detail

values

public static DinucleotideProperty[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (DinucleotideProperty c : DinucleotideProperty.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static DinucleotideProperty valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum type has no constant with the specified name

NullPointerException - if the argument is null

getProperty

public double[] getProperty(Sequence original,
                   DinucleotideProperty.Smoothing smoothing)
                     throws WrongSequenceTypeException

Computes this dinucleotide property for all overlapping twomers in original, smoothes the result using smoothing, and returns the smoothed property as a double array. The length of this double array depends on the smoothing applied.

Parameters:

original - the original nucleotide sequence

smoothing - the smoothing applied to the property values

Returns:

the smoothed property for all overlapping twomers

Throws:

WrongSequenceTypeException - if original is not a DNA sequence

getProperty

public double getProperty(Sequence seq,
                 int start)

getProperty

public double[] getProperty(Sequence original)
                     throws WrongSequenceTypeException

Computes this dinucleotide property for all overlapping twomers in original and returns the result as a double array of length original.getLength()-1

Parameters:

original - the original nucleotide sequence

Returns:

the property for all overlapping twomers

Throws:

WrongSequenceTypeException - if original is not a DNA sequence

getPropertyAsSequence

public ArbitrarySequence getPropertyAsSequence(Sequence original)
                                        throws WrongAlphabetException,
                                               WrongSequenceTypeException

Computes this dinucleotide property for all overlapping twomers in original and returns the result as a Sequence of length original.getLength()-1

Parameters:

original - the original nucleotide sequence

Returns:

the property for all overlapping twomers

Throws:

WrongSequenceTypeException - if original is not a DNA sequence

WrongAlphabetException

getPropertyAsSequence

public ArbitrarySequence getPropertyAsSequence(Sequence original,
                                      DinucleotideProperty.Smoothing smoothing)
                                        throws WrongSequenceTypeException

Computes this dinucleotide property for all overlapping twomers in original, smoothes the result using smoothing, and returns the smoothed property as a Sequence. The length of this Sequence depends on the smoothing applied.

Parameters:

original - the original nucleotide sequence

smoothing - the smoothing applied to the property values

Returns:

the smoothed property for all overlapping twomers

Throws:

WrongSequenceTypeException - if original is not a DNA sequence

getDinucleotideParameters

public double[][] getDinucleotideParameters()

Returns the dinucleotide parameters of this DinucleotideProperty as a two-dimensional double array, where the rows correspond to the first nucleotide and the columns correspond to the second nucleotide in the dinucleotide in order A, C, G, and T.

Returns:

the dinucleotide parameters

getNucleicAcid

public String getNucleicAcid()

Returns the kind of nucleic acid, e.g. RNA, DNA, this property has been determined for.

Returns:

the kind of nucleic acid

isDoubleStrand

public boolean isDoubleStrand()

Returns true if this property has been determined for a double-stranded nucleic acid.

Returns:

true if this property has been determined for a double-stranded nucleic acid

getReference

public String getReference()

Returns the reference of the publication where the parameters of this property has been published.

Returns:

the reference

getPubMedID

public String getPubMedID()

Returns the PubMed ID of the publication where the parameters of this property has been published.

Returns:

the PubMed ID

getHowCreated

public DinucleotideProperty.HowCreated getHowCreated()

Returns how this property has been determined.

Returns:

one of DinucleotideProperty.HowCreated

getType

public DinucleotideProperty.Type getType()

Returns the type of this property.

Returns:

one of DinucleotideProperty.Type

getDimension

public String getDimension()

Returns the dimension of this property, e.g. kcal/mol or angstroem.

Returns:

the dimension

getComments

public String getComments()

Returns additional comments on this property.

Returns:

the comments

filterProperties

public static DinucleotideProperty[] filterProperties(String nucleicAcid,
                                      Boolean doubleStrand,
                                      DinucleotideProperty.HowCreated howCreated,
                                      DinucleotideProperty.Type type,
                                      String dimension)

Filters all DinucleotidePropertys by some of their annotations.

Parameters:

nucleicAcid - the kind of the nucleic acid or null if no filter shall be applied

doubleStrand - the strandedness or null if no filter shall be applied

howCreated - the kind of creation or null if no filter shall be applied

type - the type of the property or null if no filter shall be applied

dimension - the dimension of the property or null if no filter shall be applied

Returns:

a filtered subset of DinucleotidePropertys

getDataSetForProperty

public static DataSet getDataSetForProperty(DataSet original,
                            DinucleotideProperty property)
                                     throws WrongSequenceTypeException

Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property.

Parameters:

original - DataSet containing the original Sequences

property - the property

Returns:

the converted Sequences as a DataSet

Throws:

WrongSequenceTypeException - if original contains non-DNA sequences

getDataSetForProperty

public static DataSet getDataSetForProperty(DataSet original,
                            DinucleotideProperty.Smoothing smoothing,
                            boolean originalAsAnnotation,
                            DinucleotideProperty property)
                                     throws WrongSequenceTypeException

Creates a new DataSet by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing.

Parameters:

original - DataSet containing the original Sequences

smoothing - the smoothing

originalAsAnnotation - if true, the original Sequence is added as a ReferenceSequenceAnnotation to each converted Sequence

property - the property

Returns:

the converted Sequences as a DataSet

Throws:

WrongSequenceTypeException - if original contains non-DNA sequences

getDataSetForProperty

public static DataSet getDataSetForProperty(DataSet original,
                            DinucleotideProperty... properties)
                                     throws WrongSequenceTypeException

Creates a new DataSet by converting each Sequence in original to the DinucleotidePropertys properties and setting these as ReferenceSequenceAnnotation of each original sequence.

Parameters:

original - DataSet containing the original Sequences

properties - the properties

Returns:

the annotated Sequences as a DataSet

Throws:

WrongSequenceTypeException - if original contains non-DNA sequences

getDataSetForProperty

public static DataSet getDataSetForProperty(DataSet original,
                            DinucleotideProperty.Smoothing smoothing,
                            boolean addToAnnotation,
                            DinucleotideProperty... properties)
                                     throws WrongSequenceTypeException

Creates a new DataSet by converting each Sequence in original to the DinucleotidePropertys properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence.

Parameters:

original - DataSet containing the original Sequences

smoothing - the smoothing

addToAnnotation - if true the converted Sequences are added to the current annotation, otherwise the current annotation is replaced

properties - the properties

Throws:

WrongSequenceTypeException - if original contains non-DNA sequences

getPropertyImage

public static ImageResult getPropertyImage(Sequence original,
                           DinucleotideProperty prop,
                           DinucleotideProperty.Smoothing smoothing,
                           REnvironment re,
                           int xLeft,
                           String pltOptions,
                           int width,
                           int height)
                                    throws Exception

Throws:

Exception

getPropertyImage

public static ImageResult getPropertyImage(DataSet original,
                           DinucleotideProperty prop,
                           DinucleotideProperty.Smoothing smoothing,
                           REnvironment re,
                           int xLeft,
                           String pltOptions,
                           int width,
                           int height)
                                    throws Exception

Throws:

Exception