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java.lang.Objectmethods.scores.ComplexScoreCalculator
public class ComplexScoreCalculator
Contains static methods to calculate scores of complexes using a given scores network. The score of a single complex is calculated by averaging the weight of all protein-protein edges within a complex. For a complex containing n proteins this means n*(n-1)/2 edges are read from the network and averaged. Missing edges in the network are generally treated as having a weight of zero.
This class is not instantiatable.
Method Summary | |
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static float |
averageComplexScore(ProteinNetwork scoreNetwork,
Complex complex)
Calculates the score of a complex using a given scores network. |
static float |
averageComplexScore(ProteinNetwork scoreNetwork,
Complex complex,
boolean ignoreMissingScores)
Calculates the score of a complex using a given scores network. |
static float |
averageComplexScore(ScoresCalculator scoreCalc,
Complex complex)
Calculates the score of a complex using a given scores calculator. |
static float |
averageComplexScore(ScoresCalculator scoreCalc,
Complex complex,
boolean ignoreMissingScores)
Calculates the score of a complex using a given scores calculator. |
static float |
averageComplexSetScore(ProteinNetwork scoreNetwork,
ComplexSet complexSet,
boolean weighted)
Calculates the average complex score of a given complex set. |
static float |
averageComplexSetScore(ProteinNetwork scoreNetwork,
ComplexSet complexSet,
boolean weighted,
boolean ignoreMissingScores)
Calculates the average complex score of a given complex set. |
static float |
averageComplexSetScore(ScoresCalculator scoreCalc,
ComplexSet complexSet,
boolean weighted)
Calculates the average complex score of a given complex set. |
static float |
averageComplexSetScore(ScoresCalculator scoreCalc,
ComplexSet complexSet,
boolean weighted,
boolean ignoreMissingScores)
Calculates the average complex score of a given complex set. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static float averageComplexScore(ProteinNetwork scoreNetwork, Complex complex)
scoreNetwork
- scores network to be usedcomplex
- complex for which the score will be calculated
public static float averageComplexScore(ScoresCalculator scoreCalc, Complex complex)
scoreCalc
- scores calculator to be usedcomplex
- complex for which the score will be calculated
public static float averageComplexScore(ProteinNetwork scoreNetwork, Complex complex, boolean ignoreMissingScores)
scoreNetwork
- scores network to be usedcomplex
- complex for which the score will be calculatedignoreMissingScores
- If true
then missing scores in the
network will not get an implicit weight of zero, but will be
completely ignored in the calculation. Note: When
missing scores are ignored the method will return NaN if none
of the edges in the complex has a weight in the network.
public static float averageComplexScore(ScoresCalculator scoreCalc, Complex complex, boolean ignoreMissingScores)
scoreCalc
- scores calculator to be usedcomplex
- complex for which the score will be calculatedignoreMissingScores
- If true
then missing scores in the
network will not get an implicit weight of zero, but will be
completely ignored in the calculation. Note: When
missing scores are ignored the method will return NaN if none
of the edges in the complex has a weight in the network.
public static float averageComplexSetScore(ProteinNetwork scoreNetwork, ComplexSet complexSet, boolean weighted)
scoreNetwork
- scores network to be usedcomplexSet
- complex set for which the average is calculatedweighted
- weight scores by complex size?
public static float averageComplexSetScore(ScoresCalculator scoreCalc, ComplexSet complexSet, boolean weighted)
scoreCalcs
- scores calculator to be usedcomplexSet
- complex set for which the average is calculatedweighted
- weight scores by complex size?
public static float averageComplexSetScore(ProteinNetwork scoreNetwork, ComplexSet complexSet, boolean weighted, boolean ignoreMissingScores)
scoreNetwork
- scores calculator to be usedcomplexSet
- complex set for which the average is calculatedweighted
- weight scores by complex size?ignoreMissingScores
- Ignore missing scores in the complex score
calculation? NaNs will be treated as zero. (see also:
averageComplexScore(ProteinNetwork, Complex, boolean)
)
public static float averageComplexSetScore(ScoresCalculator scoreCalc, ComplexSet complexSet, boolean weighted, boolean ignoreMissingScores)
scoreCalc
- scores calculator to be usedcomplexSet
- complex set for which the average is calculatedweighted
- weight scores by complex size?ignoreMissingScorescalculator
- Ignore missing scores in the complex score
calculation? NaNs will be treated as zero. (see also:
averageComplexScore(ProteinNetwork, Complex, boolean)
)
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