public enum DinucleotideProperty extends Enum<DinucleotideProperty>
enum
defines physicochemical, conformational, and letter-based dinucleotide properties of nucleotide sequences.
All dinucleotide parameters are obtained from http://diprodb.fli-leibniz.de/.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.
|
Modifier and Type | Field and Description |
---|---|
static AlphabetContainer |
continuousAlphabet |
static DinucleotideProperty.Smoothing |
NO_SMOOTHING |
Modifier and Type | Method and Description |
---|---|
static DinucleotideProperty[] |
filterProperties(String nucleicAcid,
Boolean doubleStrand,
DinucleotideProperty.HowCreated howCreated,
DinucleotideProperty.Type type,
String dimension)
Filters all
DinucleotideProperty s 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 DinucleotideProperty s 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 DinucleotideProperty s 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)
|
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 dimers 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 dimers 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.
|
public static final DinucleotideProperty TWIST_KARAS
public static final DinucleotideProperty STACKING_ENERGY_SPONER
public static final DinucleotideProperty RISE_KARAS
public static final DinucleotideProperty BEND
public static final DinucleotideProperty TIP
public static final DinucleotideProperty INCLINATION
public static final DinucleotideProperty MAJOR_GROOVE_WIDTH
public static final DinucleotideProperty MAJOR_GROOVE_DEPTH
public static final DinucleotideProperty MAJOR_GROOVE_SIZE
public static final DinucleotideProperty MAJOR_GROOVE_DISTANCE
public static final DinucleotideProperty MINOR_GROOVE_WIDTH
public static final DinucleotideProperty MINOR_GROOVE_DEPTH
public static final DinucleotideProperty MINOR_GROOVE_SIZE
public static final DinucleotideProperty MINOR_GROOVE_DISTANCE
public static final DinucleotideProperty PERSISTANCE_LENGTH
public static final DinucleotideProperty MELTING_TEMPERATURE_GOTOH
public static final DinucleotideProperty PROBABILITY_CONTACTING_NUCLEOSOME_CORE
public static final DinucleotideProperty MOBILITY_TO_BEND_TOWARDS_MAJOR_GROOVE
public static final DinucleotideProperty MOBILITY_TO_BEND_TOWARDS_MINOR_GROOVE
public static final DinucleotideProperty PROPELLER_TWIST
public static final DinucleotideProperty CLASH_STRENGTH
public static final DinucleotideProperty ENTHALPY_SUGIMOTO
public static final DinucleotideProperty ENTROPY_SUGIMOTO
public static final DinucleotideProperty SHIFT_RNA
public static final DinucleotideProperty ROLL_DNA_PROTEIN_COMPLEX_SUZUKI
public static final DinucleotideProperty TWIST_DNA_PROTEIN_COMPLEX_SUZUKI
public static final DinucleotideProperty TILT_DNA_PROTEIN_COMPLEX_SUZUKI
public static final DinucleotideProperty SLIDE_DNA_PROTEIN_COMPLEX_SUZUKI
public static final DinucleotideProperty HYDROPHILICITY_RNA_WEBER
public static final DinucleotideProperty SHIFT_DNA_PROTEIN_COMPLEX_SUZUKI
public static final DinucleotideProperty HYDROPHILICITY_RNA_BARZILAY
public static final DinucleotideProperty RISE_DNA_PROTEIN_COMPLEX_SUZUKI
public static final DinucleotideProperty STACKING_ENERGY_USSERY
public static final DinucleotideProperty FREE_ENERGY_DELCOURT
public static final DinucleotideProperty FREE_ENERGY_BRESLAUER
public static final DinucleotideProperty FREE_ENERGY_VOLOGODSKII
public static final DinucleotideProperty TWIST_DNA_PROTEIN_COMPLEX_OLSON
public static final DinucleotideProperty FREE_ENERGY_GOTOH
public static final DinucleotideProperty TWIST_TWIST
public static final DinucleotideProperty TILT_TILT
public static final DinucleotideProperty ROLL_ROLL
public static final DinucleotideProperty TWIST_TILT
public static final DinucleotideProperty TWIST_ROLL
public static final DinucleotideProperty TILT_ROLL
public static final DinucleotideProperty SHIFT_SHIFT
public static final DinucleotideProperty SLIDE_SLIDE
public static final DinucleotideProperty RISE_RISE
public static final DinucleotideProperty SHIFT_SLIDE
public static final DinucleotideProperty SHIFT_RISE
public static final DinucleotideProperty SLIDE_RISE
public static final DinucleotideProperty TWIST_SHIFT
public static final DinucleotideProperty TWIST_SLIDE
public static final DinucleotideProperty TWIST_RISE
public static final DinucleotideProperty TILT_SHIFT
public static final DinucleotideProperty TILT_SLIDE
public static final DinucleotideProperty TILT_RISE
public static final DinucleotideProperty ROLL_SHIFT
public static final DinucleotideProperty ROLL_SLIDE
public static final DinucleotideProperty ROLL_RISE
public static final DinucleotideProperty STACKING_ENERGY_PEREZ
public static final DinucleotideProperty TWIST_PEREZ
public static final DinucleotideProperty TILT_PEREZ
public static final DinucleotideProperty ROLL_PEREZ
public static final DinucleotideProperty SHIFT_PEREZ
public static final DinucleotideProperty SLIDE_PEREZ
public static final DinucleotideProperty RISE_PEREZ
public static final DinucleotideProperty SLIDE_STIFFNESS
public static final DinucleotideProperty SHIFT_STIFFNESS
public static final DinucleotideProperty ROLL_STIFFNESS
public static final DinucleotideProperty TILT_STIFFNESS
public static final DinucleotideProperty TWIST_STIFFNESS
public static final DinucleotideProperty FREE_ENERGY_SUGIMOTO
public static final DinucleotideProperty FREE_ENERGY_ALLAWI
public static final DinucleotideProperty FREE_ENERGY_SANTALUCIA_1996
public static final DinucleotideProperty FREE_ENERGY_OWCZARZY
public static final DinucleotideProperty GC_CONTENT
public static final DinucleotideProperty PURINE_AG_CONTENT
public static final DinucleotideProperty KETO_GT_CONTENT
public static final DinucleotideProperty ADENINE_CONTENT
public static final DinucleotideProperty GUANINE_CONTENT
public static final DinucleotideProperty CYTOSINE_CONTENT
public static final DinucleotideProperty THYMINE_CONTENT
public static final DinucleotideProperty TILT_DNA_PROTEIN_COMPLEX_OLSON
public static final DinucleotideProperty ROLL_DNA_PROTEIN_COMPLEX_OLSON
public static final DinucleotideProperty SHIFT_DNA_PROTEIN_COMPLEX_OLSON
public static final DinucleotideProperty SLIDE_DNA_PROTEIN_COMPLEX_OLSON
public static final DinucleotideProperty RISE_DNA_PROTEIN_COMPLEX_OLSON
public static final DinucleotideProperty TWIST_GORIN
public static final DinucleotideProperty TILT_GORIN
public static final DinucleotideProperty ROLL_GORIN
public static final DinucleotideProperty SLIDE_GORIN
public static final DinucleotideProperty TWIST_SUZUKI
public static final DinucleotideProperty TILT_SUZUKI
public static final DinucleotideProperty ROLL_SUZUKI
public static final DinucleotideProperty SHIFT_SUZUKI
public static final DinucleotideProperty SLIDE_SUZUKI
public static final DinucleotideProperty RISE_SUZUKI
public static final DinucleotideProperty TWIST_SHPIGELMAN
public static final DinucleotideProperty WEDGE
public static final DinucleotideProperty DIRECTION
public static final DinucleotideProperty SLIDE_RNA
public static final DinucleotideProperty RISE_RNA
public static final DinucleotideProperty TILT_RNA
public static final DinucleotideProperty ROLL_RNA
public static final DinucleotideProperty TWIST_RNA
public static final DinucleotideProperty STACKING_ENERGY_RNA
public static final DinucleotideProperty RISE_STIFFNESS
public static final DinucleotideProperty MELTING_TEMPERATURE_ANSELMI
public static final DinucleotideProperty STACKING_ENERGY_ANSELMI
public static final DinucleotideProperty ENTHALPY_RNA_FREIER
public static final DinucleotideProperty ENTROPY_RNA_FREIER
public static final DinucleotideProperty FREE_ENERGY_RNA_FREIER
public static final DinucleotideProperty FREE_ENERGY_RNA_XIA
public static final DinucleotideProperty ENTHALPY_RNA_XIA
public static final DinucleotideProperty ENTROPY_RNA_XIA
public static final DinucleotideProperty ROLL_ANSELMI
public static final DinucleotideProperty TILT_ANSELMI
public static final DinucleotideProperty TWIST_ANSELMI
public static final DinucleotideProperty ROLL_PACKER
public static final DinucleotideProperty TWIST_PACKER
public static final DinucleotideProperty FLEXIBILITY_SLIDE
public static final DinucleotideProperty FLEXIBILITY_SHIFT
public static final DinucleotideProperty ENTHALPY_SANTALUCIA
public static final DinucleotideProperty ENTROPY_SANTALUCIA
public static final DinucleotideProperty FREE_ENERGY_SANTALUCIA_2004
public static final DinucleotideProperty.Smoothing NO_SMOOTHING
public static final AlphabetContainer continuousAlphabet
public static DinucleotideProperty[] values()
for (DinucleotideProperty c : DinucleotideProperty.values()) System.out.println(c);
public static DinucleotideProperty valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is nullpublic double[] getProperty(Sequence original, DinucleotideProperty.Smoothing smoothing) throws WrongSequenceTypeException
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.original
- the original nucleotide sequencesmoothing
- the smoothing applied to the property valuesWrongSequenceTypeException
- if original
is not a DNA sequencepublic double getProperty(Sequence seq, int start)
public double[] getProperty(Sequence original) throws WrongSequenceTypeException
original
and returns the result as a double
array of length original.getLength()-1
original
- the original nucleotide sequenceWrongSequenceTypeException
- if original
is not a DNA sequencepublic ArbitrarySequence getPropertyAsSequence(Sequence original) throws WrongAlphabetException, WrongSequenceTypeException
original
and returns the result as a Sequence
of length original.getLength()-1
original
- the original nucleotide sequenceWrongAlphabetException
- if the new sequence could not be createdWrongSequenceTypeException
- if original
is not a DNA sequencepublic ArbitrarySequence getPropertyAsSequence(Sequence original, DinucleotideProperty.Smoothing smoothing) throws WrongSequenceTypeException
original
, smoothes the result using smoothing
,
and returns the smoothed property as a Sequence
. The length of this Sequence
depends on the smoothing applied.original
- the original nucleotide sequencesmoothing
- the smoothing applied to the property valuesWrongSequenceTypeException
- if original
is not a DNA sequencepublic double[][] getDinucleotideParameters()
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.public String getNucleicAcid()
public boolean isDoubleStrand()
true
if this property has been determined for a double-stranded nucleic acid.true
if this property has been determined for a double-stranded nucleic acidpublic String getReference()
public String getPubMedID()
public DinucleotideProperty.HowCreated getHowCreated()
DinucleotideProperty.HowCreated
public DinucleotideProperty.Type getType()
DinucleotideProperty.Type
public String getDimension()
public String getComments()
public static DinucleotideProperty[] filterProperties(String nucleicAcid, Boolean doubleStrand, DinucleotideProperty.HowCreated howCreated, DinucleotideProperty.Type type, String dimension)
DinucleotideProperty
s by some of their annotations.nucleicAcid
- the kind of the nucleic acid or null
if no filter shall be applieddoubleStrand
- the strandedness or null
if no filter shall be appliedhowCreated
- the kind of creation or null
if no filter shall be appliedtype
- the type of the property or null
if no filter shall be applieddimension
- the dimension of the property or null
if no filter shall be appliedDinucleotideProperty
spublic static DataSet getDataSetForProperty(DataSet original, DinucleotideProperty property) throws WrongSequenceTypeException
original
- DataSet
containing the original Sequence
sproperty
- the propertySequence
s as a DataSet
WrongSequenceTypeException
- if original
contains non-DNA sequencespublic static DataSet getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean originalAsAnnotation, DinucleotideProperty property) throws WrongSequenceTypeException
DataSet
by converting each Sequence
in original
to the DinucleotideProperty
property
using the DinucleotideProperty.Smoothing
smoothing.original
- DataSet
containing the original Sequence
ssmoothing
- the smoothingoriginalAsAnnotation
- if true
, the original Sequence
is added as a ReferenceSequenceAnnotation
to each converted Sequence
property
- the propertySequence
s as a DataSet
WrongSequenceTypeException
- if original
contains non-DNA sequencespublic static DataSet getDataSetForProperty(DataSet original, DinucleotideProperty... properties) throws WrongSequenceTypeException
DataSet
by converting each Sequence
in original
to the DinucleotideProperty
s properties
and setting these as ReferenceSequenceAnnotation
of each original sequence.original
- DataSet
containing the original Sequence
sproperties
- the propertiesSequence
s as a DataSet
WrongSequenceTypeException
- if original
contains non-DNA sequencespublic static DataSet getDataSetForProperty(DataSet original, DinucleotideProperty.Smoothing smoothing, boolean addToAnnotation, DinucleotideProperty... properties) throws WrongSequenceTypeException
DataSet
by converting each Sequence
in original
to the DinucleotideProperty
s properties
and adding or setting these as ReferenceSequenceAnnotation
of each original sequence.original
- DataSet
containing the original Sequence
ssmoothing
- the smoothingaddToAnnotation
- if true
the converted Sequence
s are added to the current annotation, otherwise the current annotation is replacedproperties
- the propertiesDataSet
of property sequencesWrongSequenceTypeException
- if original
contains non-DNA sequencespublic static ImageResult getPropertyImage(Sequence original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height) throws Exception
Exception
public static ImageResult getPropertyImage(DataSet original, DinucleotideProperty prop, DinucleotideProperty.Smoothing smoothing, REnvironment re, int xLeft, String pltOptions, int width, int height) throws Exception
Exception