org.nmdp.ngs.align

Class HighScoringPair

java.lang.Object

org.nmdp.ngs.align.HighScoringPair

@Immutable
public final class HighScoringPair
extends Object

High-scoring segment pair (HSP).

Method Summary

Methods

Modifier and Type	Method and Description
long	alignmentLength() Return the alignment length for this high-scoring segment pair (HSP).
double	bitScore() Return the bit score for this high-scoring segment pair (HSP).
double	evalue() Return the evalue for this high-scoring segment pair (HSP).
int	gapOpens() Return the gap opens for this high-scoring segment pair (HSP).
int	mismatches() Return the mismatches for this high-scoring segment pair (HSP).
double	percentIdentity() Return the percent identity for this high-scoring segment pair (HSP).
String	source() Return the source for this high-scoring segment pair (HSP).
long	sourceEnd() Return the source end for this high-scoring segment pair (HSP).
long	sourceStart() Return the source start for this high-scoring segment pair (HSP).
String	target() Return the target for this high-scoring segment pair (HSP).
long	targetEnd() Return the target end for this high-scoring segment pair (HSP).
long	targetStart() Return the target start for this high-scoring segment pair (HSP).
String	toString()
static HighScoringPair	valueOf(String value) Return a new high scoring pair parsed from the specified value.

Methods inherited from class java.lang.Object

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

Method Detail

source

public String source()

Return the source for this high-scoring segment pair (HSP).

Returns:

the source for this high-scoring segment pair (HSP)

target

public String target()

Return the target for this high-scoring segment pair (HSP).

Returns:

the target for this high-scoring segment pair (HSP)

percentIdentity

public double percentIdentity()

Return the percent identity for this high-scoring segment pair (HSP).

Returns:

the percent identity for this high-scoring segment pair (HSP)

alignmentLength

public long alignmentLength()

Return the alignment length for this high-scoring segment pair (HSP).

Returns:

the alignment length for this high-scoring segment pair (HSP)

mismatches

public int mismatches()

Return the mismatches for this high-scoring segment pair (HSP).

Returns:

the mismatches for this high-scoring segment pair (HSP)

gapOpens

public int gapOpens()

Return the gap opens for this high-scoring segment pair (HSP).

Returns:

the gap opens for this high-scoring segment pair (HSP)

sourceStart

public long sourceStart()

Return the source start for this high-scoring segment pair (HSP).

Returns:

the source start for this high-scoring segment pair (HSP)

sourceEnd

public long sourceEnd()

Return the source end for this high-scoring segment pair (HSP).

Returns:

the source end for this high-scoring segment pair (HSP)

targetStart

public long targetStart()

Return the target start for this high-scoring segment pair (HSP).

Returns:

the target start for this high-scoring segment pair (HSP)

targetEnd

public long targetEnd()

Return the target end for this high-scoring segment pair (HSP).

Returns:

the target end for this high-scoring segment pair (HSP)

evalue

public double evalue()

Return the evalue for this high-scoring segment pair (HSP).

Returns:

the evalue for this high-scoring segment pair (HSP)

bitScore

public double bitScore()

Return the bit score for this high-scoring segment pair (HSP).

Returns:

the bit score for this high-scoring segment pair (HSP)

toString

public String toString()

Overrides:

toString in class Object

valueOf

public static HighScoringPair valueOf(String value)

Return a new high scoring pair parsed from the specified value.

Parameters:

value - value to parse, must not be null

Returns:

a new high scoring pair parsed from the specified value

Throws:

IllegalArgumentException - if the value is not valid high scoring pair format

NumberFormatException - if a number valued field cannot be parsed as a number