org.nmdp.ngs.reads.coverage

Class MinimumCoverageStrategy

java.lang.Object

org.nmdp.ngs.reads.coverage.MinimumCoverageStrategy

All Implemented Interfaces:

CoverageStrategy

public final class MinimumCoverageStrategy
extends Object

Minimum coverage strategy.

Constructor Summary

Constructors

Constructor and Description
MinimumCoverageStrategy(int minimumCoverage) Create a new minimum coverage strategy with the specified minimum coverage.

Method Summary

Methods

Modifier and Type	Method and Description
void	add(org.biojava.bio.seq.Sequence reference, int start, int end) Add coverage for the specified reference sequence for the region defined by [start, end] inclusive.
boolean	evaluate(org.biojava.bio.seq.Sequence reference) Return true if the specified reference sequence has enough coverage.
protected boolean	evaluate(org.biojava.bio.seq.Sequence reference, org.biojava.bio.symbol.SymbolList coverage) Return true if the specified reference sequence has enough coverage given the specified coverage scores.

Methods inherited from class java.lang.Object

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

Constructor Detail

MinimumCoverageStrategy

public MinimumCoverageStrategy(int minimumCoverage)

Create a new minimum coverage strategy with the specified minimum coverage.

Parameters:

minimumCoverage - minimum coverage, must be at least 0

Method Detail

evaluate

protected boolean evaluate(org.biojava.bio.seq.Sequence reference,
               org.biojava.bio.symbol.SymbolList coverage)

Return true if the specified reference sequence has enough coverage given the specified coverage scores.

Parameters:

reference - reference sequence to evaluate

coverage - coverage scores

Returns:

true if the specified reference sequence has enough coverage given the specified coverage scores

evaluate

public final boolean evaluate(org.biojava.bio.seq.Sequence reference)

Description copied from interface: CoverageStrategy

Return true if the specified reference sequence has enough coverage.

Specified by:

evaluate in interface CoverageStrategy

Parameters:

reference - reference sequence to evaluate

Returns:

true if the specified reference sequence has enough coverage

add

public final void add(org.biojava.bio.seq.Sequence reference,
       int start,
       int end)

Description copied from interface: CoverageStrategy

Add coverage for the specified reference sequence for the region defined by [start, end] inclusive.

Specified by:

add in interface CoverageStrategy

Parameters:

reference - reference sequence

start - region start, 1-based coordinate

end - region end, 1-based coordinate