edu.rit.compbio.seq

Class AlignmentPrinter

java.lang.Object

edu.rit.compbio.seq.AlignmentPrinter

public class AlignmentPrinter
extends java.lang.Object

Class AlignmentPrinter provides an object that prints an Alignment.

Constructor Summary

Constructors

Constructor and Description
AlignmentPrinter(java.io.PrintStream out, AlignmentStats stats) Construct a new alignment printer.

Method Summary

Modifier and Type	Method and Description
void	printDetails(Alignment alignment, Sequence query, Sequence subject) Print details of the given alignment.
void	printSummary(Alignment alignment, Sequence subject) Print a summary of the given alignment.
void	setSubstitutionMatrix(int[][] matrix) Set the substitution matrix.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentPrinter

public AlignmentPrinter(java.io.PrintStream out,
                        AlignmentStats stats)

Construct a new alignment printer.

Parameters:

out - Print stream on which to print (e.g., System.out).

stats - Object for calculating alignment statistics.

Method Detail

setSubstitutionMatrix

public void setSubstitutionMatrix(int[][] matrix)

Set the substitution matrix. If not set, the default is the BLOSUM-62 substitution matrix.

The expression matrix[x][y] is the score when sequence element x is aligned with sequence element y.

Parameters:

matrix - Substition matrix.

printSummary

public void printSummary(Alignment alignment,
                         Sequence subject)

Print a summary of the given alignment. The printout consists of:

• Subject sequence description (columns 1-60).
• Bit score (columns 63-67).
• E-value (columns 70-75).

Parameters:

alignment - Alignment.

subject - Subject sequence.

printDetails

public void printDetails(Alignment alignment,
                         Sequence query,
                         Sequence subject)

Print details of the given alignment. The printout consists of:

• Subject sequence description and length.
• Bit score, raw score, and E-value.
• Number and percent of identities, positives, and gaps.
• The aligned query and subject sequences.

Parameters:

alignment - Alignment.

query - Query sequence.

subject - Subject sequence.