Interface IProfeatProperties
- All Known Implementing Classes:
ProfeatPropertiesImpl
public interface IProfeatProperties
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic enumEnumeration of the seven different attributesstatic enumEnumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the groupingstatic enumEnumeration of the three different groupings for each attributesstatic enumEnumeration of the transition between groupA and groupB -
Method Summary
Modifier and TypeMethodDescriptiongetComposition(ProteinSequence sequence) getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) doublegetComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) Returns the composition of the specific grouping for the given attribute.Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING, Map<IProfeatProperties.DISTRIBUTION, Double>>> getDistributionPosition(ProteinSequence sequence) getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) doublegetDistributionPosition(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)getTransition(ProteinSequence sequence) getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) doublegetTransition(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 Details
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getComposition
double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws 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:
Exception- throws Exception if attribute or group are unknown
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getComposition
Map<IProfeatProperties.GROUPING,Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception - Throws:
Exception
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getComposition
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING, getCompositionDouble>> (ProteinSequence sequence) throws Exception - Throws:
Exception
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getTransition
double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws 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:
Exception- throws Exception if attribute or group are unknown
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getTransition
Map<IProfeatProperties.TRANSITION,Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception - Throws:
Exception
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getTransition
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION, getTransitionDouble>> (ProteinSequence sequence) throws Exception - Throws:
Exception
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getDistributionPosition
double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws 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:
Exception- throws Exception if attribute or group are unknown
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getDistributionPosition
Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws Exception - Throws:
Exception
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getDistributionPosition
Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION, getDistributionPositionDouble>> (ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception - Throws:
Exception
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getDistributionPosition
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING, getDistributionPositionMap<IProfeatProperties.DISTRIBUTION, Double>>> (ProteinSequence sequence) throws Exception - Throws:
Exception
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