edu.rit.compbio.seq

Interface AlignmentStats

All Known Implementing Classes:

DefaultAlignmentStats

public interface AlignmentStats

Interface AlignmentStats specifies the interface for an object that computes statistics of an Alignment. Methods are provided to compute the raw score, the bit score, and the E-value. The formulas for these statistics depend on the procedure used to produce the alignment.

Method Summary

Modifier and Type	Method and Description
double	bitScore(Alignment alignment) Returns the bit score for the given alignment.
double	eValue(Alignment alignment) Returns the E-value (expect value) for the given alignment.
void	print(java.io.PrintStream out) Print information about this alignment statistics object on the given print stream.
double	rawScore(Alignment alignment) Returns the raw score for the given alignment.

Method Detail

rawScore

double rawScore(Alignment alignment)

Returns the raw score for the given alignment. A larger raw score signifies a greater degree of similarity between the query sequence and subject sequence that were aligned.

Parameters:

alignment - Alignment.

Returns:

Raw score.

bitScore

double bitScore(Alignment alignment)

Returns the bit score for the given alignment. A larger bit score signifies a greater degree of similarity between the query sequence and subject sequence that were aligned.

The bit score is the raw score normalized to units of "bits." Bit scores for different alignment procedures may be compared, whereas raw (unnormalized) scores for different alignment procedures may not be compared.

Parameters:

alignment - Alignment.

Returns:

Bit score.

eValue

double eValue(Alignment alignment)

Returns the E-value (expect value) for the given alignment. A smaller E-value signifies a more statistically significant degree of similarity between the query sequence and subject sequence that were aligned.

The E-value is the expected number of alignments with a score greater than or equal to the alignment's score when a randomly-chosen query of the same length as the query that produced the alignment is matched against the database.

Parameters:

alignment - Alignment.

Returns:

Bit score.

print

void print(java.io.PrintStream out)

Print information about this alignment statistics object on the given print stream.

Parameters:

out - Print stream.