Class ProfeatProperties
- java.lang.Object
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- org.biojava.nbio.aaproperties.profeat.ProfeatProperties
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public class ProfeatProperties extends java.lang.Object
This is an adaptor class which enable the ease of generating profeat properties. At least one adaptor method is written for each available properties provided in IProfeatProperties.- Since:
- 3.0.2
- Version:
- 2011.06.16
- Author:
- kohchuanhock
- See Also:
IProfeatProperties
,ProfeatPropertiesImpl
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Constructor Summary
Constructors Constructor Description ProfeatProperties()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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.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.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.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.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)
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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Method Detail
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getComposition
public static double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
An adaptor method which 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
public static 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
public static 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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getComposition
public static double getComposition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
- Throws:
java.lang.Exception
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getComposition
public static java.util.Map<IProfeatProperties.GROUPING,java.lang.Double> getComposition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Throws:
java.lang.Exception
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getComposition
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> getComposition(java.lang.String sequence) throws java.lang.Exception
- Throws:
java.lang.Exception
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getTransition
public static double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
An adaptor method which 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
public static 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
public static 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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getTransition
public static double getTransition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
- Throws:
java.lang.Exception
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getTransition
public static java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> getTransition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
- Throws:
java.lang.Exception
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getTransition
public static java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> getTransition(java.lang.String sequence) throws java.lang.Exception
- Throws:
java.lang.Exception
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getDistributionPosition
public static double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
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)- 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
public static 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
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
- Throws:
java.lang.Exception
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getDistributionPosition
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
- Throws:
java.lang.Exception
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getDistributionPosition
public static double getDistributionPosition(java.lang.String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
- Throws:
java.lang.Exception
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getDistributionPosition
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
- Throws:
java.lang.Exception
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getDistributionPosition
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
- Throws:
java.lang.Exception
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getDistributionPosition
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
- Throws:
java.lang.Exception
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