org.biojava3.aaproperties.profeat
Class ProfeatPropertiesImpl
java.lang.Object
org.biojava3.aaproperties.profeat.ProfeatPropertiesImpl
- All Implemented Interfaces:
- IProfeatProperties
public class ProfeatPropertiesImpl
- extends Object
- implements IProfeatProperties
Method Summary |
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> |
getComposition(ProteinSequence sequence)
|
Map<IProfeatProperties.GROUPING,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. |
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> |
getDistributionPosition(ProteinSequence sequence)
|
Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
|
Map<IProfeatProperties.DISTRIBUTION,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)
|
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> |
getTransition(ProteinSequence sequence)
|
Map<IProfeatProperties.TRANSITION,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. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ProfeatPropertiesImpl
public ProfeatPropertiesImpl()
getComposition
public double getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
throws Exception
- Description copied from interface:
IProfeatProperties
- Returns the composition of the specific grouping for the given attribute.
- Specified by:
getComposition
in interface IProfeatProperties
- 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
getTransition
public double getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.TRANSITION transition)
throws 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 interface IProfeatProperties
- 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
getDistributionPosition
public double getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group,
IProfeatProperties.DISTRIBUTION distribution)
throws 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 interface IProfeatProperties
- 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
getComposition
public Map<IProfeatProperties.GROUPING,Double> getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Specified by:
getComposition
in interface IProfeatProperties
- Throws:
Exception
getComposition
public Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(ProteinSequence sequence)
throws Exception
- Specified by:
getComposition
in interface IProfeatProperties
- Throws:
Exception
getTransition
public Map<IProfeatProperties.TRANSITION,Double> getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Specified by:
getTransition
in interface IProfeatProperties
- Throws:
Exception
getTransition
public Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(ProteinSequence sequence)
throws Exception
- Specified by:
getTransition
in interface IProfeatProperties
- Throws:
Exception
getDistributionPosition
public Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
throws Exception
- Specified by:
getDistributionPosition
in interface IProfeatProperties
- Throws:
Exception
getDistributionPosition
public Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Specified by:
getDistributionPosition
in interface IProfeatProperties
- Throws:
Exception
getDistributionPosition
public Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(ProteinSequence sequence)
throws Exception
- Specified by:
getDistributionPosition
in interface IProfeatProperties
- Throws:
Exception