org.biojava3.aaproperties.profeat
Class ProfeatProperties
java.lang.Object
org.biojava3.aaproperties.profeat.ProfeatProperties
public class ProfeatProperties
- extends 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
Method Summary |
static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> |
getComposition(ProteinSequence sequence)
|
static Map<IProfeatProperties.GROUPING,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 Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> |
getComposition(String sequence)
|
static Map<IProfeatProperties.GROUPING,Double> |
getComposition(String sequence,
IProfeatProperties.ATTRIBUTE attribute)
|
static double |
getComposition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
|
static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> |
getDistributionPosition(ProteinSequence sequence)
|
static Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> |
getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
|
static Map<IProfeatProperties.DISTRIBUTION,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 Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> |
getDistributionPosition(String sequence)
|
static Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> |
getDistributionPosition(String sequence,
IProfeatProperties.ATTRIBUTE attribute)
|
static Map<IProfeatProperties.DISTRIBUTION,Double> |
getDistributionPosition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
|
static double |
getDistributionPosition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group,
IProfeatProperties.DISTRIBUTION distribution)
|
static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> |
getTransition(ProteinSequence sequence)
|
static Map<IProfeatProperties.TRANSITION,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. |
static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> |
getTransition(String sequence)
|
static Map<IProfeatProperties.TRANSITION,Double> |
getTransition(String sequence,
IProfeatProperties.ATTRIBUTE attribute)
|
static double |
getTransition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.TRANSITION transition)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ProfeatProperties
public ProfeatProperties()
getComposition
public static double getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
throws 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:
Exception
- throws Exception if attribute or group are unknown
getComposition
public static Map<IProfeatProperties.GROUPING,Double> getComposition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Throws:
Exception
getComposition
public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(ProteinSequence sequence)
throws Exception
- Throws:
Exception
getComposition
public static double getComposition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
throws Exception
- Throws:
Exception
getComposition
public static Map<IProfeatProperties.GROUPING,Double> getComposition(String sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Throws:
Exception
getComposition
public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(String sequence)
throws Exception
- Throws:
Exception
getTransition
public static double getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.TRANSITION transition)
throws 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:
Exception
- throws Exception if attribute or group are unknown
getTransition
public static Map<IProfeatProperties.TRANSITION,Double> getTransition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Throws:
Exception
getTransition
public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(ProteinSequence sequence)
throws Exception
- Throws:
Exception
getTransition
public static double getTransition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.TRANSITION transition)
throws Exception
- Throws:
Exception
getTransition
public static Map<IProfeatProperties.TRANSITION,Double> getTransition(String sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Throws:
Exception
getTransition
public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(String sequence)
throws Exception
- Throws:
Exception
getDistributionPosition
public static double getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group,
IProfeatProperties.DISTRIBUTION distribution)
throws 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:
Exception
- throws Exception if attribute or group are unknown
getDistributionPosition
public static Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
throws Exception
- Throws:
Exception
getDistributionPosition
public static Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(ProteinSequence sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Throws:
Exception
getDistributionPosition
public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(ProteinSequence sequence)
throws Exception
- Throws:
Exception
getDistributionPosition
public static double getDistributionPosition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group,
IProfeatProperties.DISTRIBUTION distribution)
throws Exception
- Throws:
Exception
getDistributionPosition
public static Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(String sequence,
IProfeatProperties.ATTRIBUTE attribute,
IProfeatProperties.GROUPING group)
throws Exception
- Throws:
Exception
getDistributionPosition
public static Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(String sequence,
IProfeatProperties.ATTRIBUTE attribute)
throws Exception
- Throws:
Exception
getDistributionPosition
public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(String sequence)
throws Exception
- Throws:
Exception