Package pl.poznan.put.structure.formats

Class DefaultConverter

java.lang.Object

pl.poznan.put.structure.formats.DefaultConverter

All Implemented Interfaces:

Converter

Direct Known Subclasses:

ImmutableDefaultConverter

@Immutable(singleton=true)
public abstract class DefaultConverter
extends Object
implements Converter

A default converter from BPSEQ to dot-bracket which iteratively (1) finds non-pseudoknots and assigns the current lowest level, then (2) increases level and (3) treats pseudoknots as the next input to (1) until there are base pairs without level assigned.

Constructor Summary

Constructors

Constructor	Description
DefaultConverter()

Method Summary

Modifier and Type	Method	Description
final DotBracket	convert(BpSeq bpSeq)	Converts the secondary structure in BPSEQ format to dot-bracket.
int	maxSolutions()
PseudoknotFinder	pseudoknotFinder()

Methods inherited from class java.lang.Object

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

Constructor Details

DefaultConverter

public DefaultConverter()

Method Details

pseudoknotFinder

@Default
public PseudoknotFinder pseudoknotFinder()

Returns:

The finder of pseudoknots (MinGain by default).

maxSolutions

@Default
public int maxSolutions()

Returns:

The number of solutions to return (1 by default).

convert

public final DotBracket convert(BpSeq bpSeq)

Converts the secondary structure in BPSEQ format to dot-bracket. Works level-by-level, see class description.

Specified by:

convert in interface Converter

Parameters:

bpSeq - The data in BPSEQ format.

Returns:

The converted dot-bracket.