Package com.biomatters.geneious.publicapi.documents.sequence

Class SequenceListSummary.Coverage

java.lang.Object

com.biomatters.geneious.publicapi.documents.sequence.SequenceListSummary.Coverage

Enclosing class:

SequenceListSummary

public static class SequenceListSummary.Coverage
extends java.lang.Object

Represents the coverage (number of sequences covering a column in an alignment)

Constructor Summary

Constructors

Constructor	Description
Coverage(double meanCoverage, double minCoverage, double maxCoverage, boolean bothStrandsCovered)
Coverage(double meanCoverage, int minCoverage, int maxCoverage, boolean bothStrandsCovered)

Method Summary

Modifier and Type	Method	Description
int	getMaximumCoverage()
double	getMaximumCoverageAsDouble()
double	getMeanCoverage()
int	getMinimumCoverage()
double	getMinimumCoverageAsDouble()
boolean	isBothStrandsCovered()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Coverage

public Coverage(double meanCoverage,
                int minCoverage,
                int maxCoverage,
                boolean bothStrandsCovered)

Parameters:

meanCoverage - the mean coverage

minCoverage - the minimum coverage

maxCoverage - the maximum coverage

bothStrandsCovered - true if there is at least one sequence in each direction covering this position.

Coverage

public Coverage(double meanCoverage,
                double minCoverage,
                double maxCoverage,
                boolean bothStrandsCovered)

Parameters:

meanCoverage - the mean coverage

minCoverage - the minimum coverage

maxCoverage - the maximum coverage

bothStrandsCovered - true if there is at least one sequence in each direction covering this position.

Since:

API 4.600 (Geneious 6.0.0)

Method Detail

getMeanCoverage

public double getMeanCoverage()

Returns:

the mean coverage

getMinimumCoverage

public int getMinimumCoverage()

Returns:

the minimum coverage

getMaximumCoverage

public int getMaximumCoverage()

Returns:

the maximum coverage

getMinimumCoverageAsDouble

public double getMinimumCoverageAsDouble()

Returns:

the minimum coverage. In most cases this will be an integer, except when there are reads with DocumentField.NUMBER_OF_MAPPED_LOCATIONS in which case the read contributes a fractional value towards the coverage

Since:

API 4.600 (Geneious 6.0.0)

getMaximumCoverageAsDouble

public double getMaximumCoverageAsDouble()

Returns:

the maximum coverage. In most cases this will be an integer, except when there are reads with DocumentField.NUMBER_OF_MAPPED_LOCATIONS in which case the read contributes a fractional value towards the coverage

Since:

API 4.600 (Geneious 6.0.0)

isBothStrandsCovered

public boolean isBothStrandsCovered()

Returns:

true if there is at least one sequence in each direction covering this position