public class ProfeatProperties
extends java.lang.Object
IProfeatProperties
,
ProfeatPropertiesImpl
Constructor and Description |
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ProfeatProperties() |
Modifier and Type | Method and Description |
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static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> |
getComposition(ProteinSequence sequence) |
static java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> |
getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute) |
static double |
getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
An adaptor method which returns the composition of the specific grouping for the given attribute.
|
static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> |
getComposition(java.lang.String sequence) |
static java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> |
getComposition(java.lang.String sequence,
IProfeatProperties.ATTRIBUTE attribute) |
static double |
getComposition(java.lang.String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group) |
static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>> |
getDistributionPosition(ProteinSequence sequence) |
static java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute) |
static java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group) |
static double |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group,
IProfeatProperties.DISTRIBUTION distribution)
An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222" For the above example, position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0) position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4) |
static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>> |
getDistributionPosition(java.lang.String sequence) |
static java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> |
getDistributionPosition(java.lang.String sequence,
IProfeatProperties.ATTRIBUTE attribute) |
static java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> |
getDistributionPosition(java.lang.String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group) |
static double |
getDistributionPosition(java.lang.String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group,
IProfeatProperties.DISTRIBUTION distribution) |
static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> |
getTransition(ProteinSequence sequence) |
static java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> |
getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute) |
static double |
getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.TRANSITION transition)
An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
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static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> |
getTransition(java.lang.String sequence) |
static java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> |
getTransition(java.lang.String sequence,
IProfeatProperties.ATTRIBUTE attribute) |
static double |
getTransition(java.lang.String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.TRANSITION transition) |
public static double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
sequence
- a protein sequence consisting of non-ambiguous characters onlyattribute
- one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)group
- the grouping to be computedjava.lang.Exception
- throws Exception if attribute or group are unknownpublic static java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> getComposition(ProteinSequence sequence) throws java.lang.Exception
java.lang.Exception
public static double getComposition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> getComposition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> getComposition(java.lang.String sequence) throws java.lang.Exception
java.lang.Exception
public static double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
sequence
- a protein sequence consisting of non-ambiguous characters onlyattribute
- one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)transition
- the interested transition between the groupsjava.lang.Exception
- throws Exception if attribute or group are unknownpublic static java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> getTransition(ProteinSequence sequence) throws java.lang.Exception
java.lang.Exception
public static double getTransition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> getTransition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> getTransition(java.lang.String sequence) throws java.lang.Exception
java.lang.Exception
public static double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
sequence
- a protein sequence consisting of non-ambiguous characters onlyattribute
- one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)group
- one the three groups for the attributedistribution
- the distribution of the groupingjava.lang.Exception
- throws Exception if attribute or group are unknownpublic static java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>> getDistributionPosition(ProteinSequence sequence) throws java.lang.Exception
java.lang.Exception
public static double getDistributionPosition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> getDistributionPosition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> getDistributionPosition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>> getDistributionPosition(java.lang.String sequence) throws java.lang.Exception
java.lang.Exception