Class ProfeatPropertiesImpl
- java.lang.Object
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- org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl
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- All Implemented Interfaces:
IProfeatProperties
public class ProfeatPropertiesImpl extends java.lang.Object implements IProfeatProperties
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
IProfeatProperties.ATTRIBUTE, IProfeatProperties.DISTRIBUTION, IProfeatProperties.GROUPING, IProfeatProperties.TRANSITION
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Constructor Summary
Constructors Constructor Description ProfeatPropertiesImpl()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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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Method Detail
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getComposition
public double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
Description copied from interface:IProfeatProperties
Returns the composition of the specific grouping for the given attribute.- Specified by:
getComposition
in interfaceIProfeatProperties
- Parameters:
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 computed- Returns:
- returns the composition of the specific grouping for the given attribute
- Throws:
java.lang.Exception
- throws Exception if attribute or group are unknown
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getTransition
public double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
Description copied from interface:IProfeatProperties
Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.- Specified by:
getTransition
in interfaceIProfeatProperties
- Parameters:
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 groups- Returns:
- returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
- Throws:
java.lang.Exception
- throws Exception if attribute or group are unknown
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getDistributionPosition
public double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
Description copied from interface:IProfeatProperties
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)- Specified by:
getDistributionPosition
in interfaceIProfeatProperties
- Parameters:
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 grouping- Returns:
- the position with respect to the length of sequence where the given distribution of the grouping can be found.
- Throws:
java.lang.Exception
- throws Exception if attribute or group are unknown
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getComposition
public java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Specified by:
getComposition
in interfaceIProfeatProperties
- Throws:
java.lang.Exception
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getComposition
public java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> getComposition(ProteinSequence sequence) throws java.lang.Exception
- Specified by:
getComposition
in interfaceIProfeatProperties
- Throws:
java.lang.Exception
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getTransition
public java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Specified by:
getTransition
in interfaceIProfeatProperties
- Throws:
java.lang.Exception
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getTransition
public java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> getTransition(ProteinSequence sequence) throws java.lang.Exception
- Specified by:
getTransition
in interfaceIProfeatProperties
- Throws:
java.lang.Exception
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getDistributionPosition
public java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
- Specified by:
getDistributionPosition
in interfaceIProfeatProperties
- Throws:
java.lang.Exception
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getDistributionPosition
public java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Specified by:
getDistributionPosition
in interfaceIProfeatProperties
- Throws:
java.lang.Exception
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getDistributionPosition
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
- Specified by:
getDistributionPosition
in interfaceIProfeatProperties
- Throws:
java.lang.Exception
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