DefaultConverter (BioCommons 3.0.4 API)

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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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 Detail
  - DefaultConverter
```
public DefaultConverter()
```
- Method Detail
  - 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.