com.hfg.bio.seq

Class SeqMappingCoverage

java.lang.Object

com.hfg.bio.seq.SeqMappingCoverage

public class SeqMappingCoverage
extends java.lang.Object

Simple container for sequence mapping stats.

See Also:

Gene2D

Constructor Summary

Constructors

Constructor and Description
SeqMappingCoverage()

Method Summary

Modifier and Type	Method and Description
java.lang.Integer	getMappedLength() Returns the summed length of the query sequence that was successfully mapped.
java.lang.Float	getPercentIdentity() Returns the percent identity of the query sequence to the mapping target for the region(s) mapped.
java.lang.Integer	getQueryLength() Returns the length of the query sequence that was mapped.
SeqMappingCoverage	setMappedLength(java.lang.Integer inValue) Sets the summed length of the query sequence that was successfully mapped.
SeqMappingCoverage	setPercentIdentity(java.lang.Float inValue) Sets the percent identity of the query sequence to the mapping target for the region(s) mapped.
SeqMappingCoverage	setQueryLength(java.lang.Integer inValue) Sets the length of the query sequence that was mapped.

Methods inherited from class java.lang.Object

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

Constructor Detail

SeqMappingCoverage

public SeqMappingCoverage()

Method Detail

setMappedLength

public SeqMappingCoverage setMappedLength(java.lang.Integer inValue)

Sets the summed length of the query sequence that was successfully mapped.

Parameters:

inValue - the length of the query seq portions that were covered by mapping

Returns:

this SeqMappingCoverage object (for potential method chaining)

getMappedLength

public java.lang.Integer getMappedLength()

Returns the summed length of the query sequence that was successfully mapped.

Returns:

the summed length of the query sequence that was successfully mapped

setQueryLength

public SeqMappingCoverage setQueryLength(java.lang.Integer inValue)

Sets the length of the query sequence that was mapped.

Parameters:

inValue - the query seq length

Returns:

this SeqMappingCoverage object (for potential method chaining)

getQueryLength

public java.lang.Integer getQueryLength()

Returns the length of the query sequence that was mapped.

Returns:

the query length

setPercentIdentity

public SeqMappingCoverage setPercentIdentity(java.lang.Float inValue)

Sets the percent identity of the query sequence to the mapping target for the region(s) mapped.

Parameters:

inValue - the pct. identity of the query seq to the mapping target

Returns:

this SeqMappingCoverage object (for potential method chaining)

getPercentIdentity

public java.lang.Float getPercentIdentity()

Returns the percent identity of the query sequence to the mapping target for the region(s) mapped.

Returns:

the pct. identity of the query sequence to the mapping target sequence for the mapped region(s)