Interface IProfeatProperties
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- All Known Implementing Classes:
ProfeatPropertiesImpl
public interface IProfeatProperties
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
IProfeatProperties.ATTRIBUTE
Enumeration of the seven different attributesstatic class
IProfeatProperties.DISTRIBUTION
Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the groupingstatic class
IProfeatProperties.GROUPING
Enumeration of the three different groupings for each attributesstatic class
IProfeatProperties.TRANSITION
Enumeration of the transition between groupA and groupB
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Method Summary
All Methods Instance Methods Abstract 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
double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
Returns the composition of the specific grouping for the given attribute.- 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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getComposition
java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Throws:
java.lang.Exception
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getComposition
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> getComposition(ProteinSequence sequence) throws java.lang.Exception
- Throws:
java.lang.Exception
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getTransition
double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.- 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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getTransition
java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Throws:
java.lang.Exception
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getTransition
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> getTransition(ProteinSequence sequence) throws java.lang.Exception
- Throws:
java.lang.Exception
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getDistributionPosition
double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
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)- 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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getDistributionPosition
java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
- Throws:
java.lang.Exception
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getDistributionPosition
java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Throws:
java.lang.Exception
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getDistributionPosition
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
- Throws:
java.lang.Exception
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