public interface IProfeatProperties
Modifier and Type | Interface and Description |
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static class |
IProfeatProperties.ATTRIBUTE
Enumeration of the seven different attributes
|
static class |
IProfeatProperties.DISTRIBUTION
Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
|
static class |
IProfeatProperties.GROUPING
Enumeration of the three different groupings for each attributes
|
static class |
IProfeatProperties.TRANSITION
Enumeration of the transition between groupA and groupB
|
Modifier and Type | Method and 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.
|
double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
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 unknownjava.util.Map<IProfeatProperties.GROUPING,java.lang.Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.GROUPING,java.lang.Double>> getComposition(ProteinSequence sequence) throws java.lang.Exception
java.lang.Exception
double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws java.lang.Exception
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 unknownjava.util.Map<IProfeatProperties.TRANSITION,java.lang.Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
java.util.Map<IProfeatProperties.ATTRIBUTE,java.util.Map<IProfeatProperties.TRANSITION,java.lang.Double>> getTransition(ProteinSequence sequence) throws java.lang.Exception
java.lang.Exception
double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws java.lang.Exception
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 unknownjava.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws java.lang.Exception
java.lang.Exception
java.util.Map<IProfeatProperties.GROUPING,java.util.Map<IProfeatProperties.DISTRIBUTION,java.lang.Double>> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws java.lang.Exception
java.lang.Exception
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
java.lang.Exception