IProfeatProperties
public class ProfeatPropertiesImpl extends java.lang.Object implements IProfeatProperties
IProfeatProperties.ATTRIBUTE, IProfeatProperties.DISTRIBUTION, IProfeatProperties.GROUPING, IProfeatProperties.TRANSITION
Constructor | Description |
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ProfeatPropertiesImpl() |
Modifier and Type | Method | Description |
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java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> |
getComposition(ProteinSequence sequence) |
|
java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> |
getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute) |
|
double |
getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group) |
Returns the composition of the specific grouping for the given attribute.
|
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>>> |
getDistributionPosition(ProteinSequence sequence) |
|
java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute) |
|
java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group) |
|
double |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group,
IProfeatProperties.DISTRIBUTION distribution) |
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) |
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> |
getTransition(ProteinSequence sequence) |
|
java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> |
getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute) |
|
double |
getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.TRANSITION transition) |
Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
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public double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
IProfeatProperties
getComposition
in interface IProfeatProperties
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 double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
IProfeatProperties
getTransition
in interface IProfeatProperties
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 double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
IProfeatProperties
getDistributionPosition
in interface IProfeatProperties
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 java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
getComposition
in interface IProfeatProperties
java.lang.Exception
public java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> getComposition(ProteinSequence sequence) throws java.lang.Exception
getComposition
in interface IProfeatProperties
java.lang.Exception
public java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
getTransition
in interface IProfeatProperties
java.lang.Exception
public java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> getTransition(ProteinSequence sequence) throws java.lang.Exception
getTransition
in interface IProfeatProperties
java.lang.Exception
public java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
getDistributionPosition
in interface IProfeatProperties
java.lang.Exception
public java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
getDistributionPosition
in interface IProfeatProperties
java.lang.Exception
public 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
getDistributionPosition
in interface IProfeatProperties
java.lang.Exception