Package pl.poznan.put.structure.formats

Class MultiLineDotBracket

java.lang.Object

pl.poznan.put.structure.formats.MultiLineDotBracket

Direct Known Subclasses:

ImmutableMultiLineDotBracket

@Immutable
public abstract class MultiLineDotBracket
extends Object

An extended secondary structure, which contains also non-canonical base pairs.

Constructor Summary

Constructors

Constructor	Description
MultiLineDotBracket()

Method Summary

Modifier and Type	Method	Description
abstract Collection<? extends ClassifiedBasePair>	basePairs()
protected Collection<ClassifiedBasePair>	basePairs5to3()
static MultiLineDotBracket	fromString(String input)	Creates an instance by reading a set of lines in dot-bracket notation.
abstract String	sequence()
final String	toString()

Methods inherited from class java.lang.Object

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

Constructor Details

MultiLineDotBracket

public MultiLineDotBracket()

Method Details

fromString

public static MultiLineDotBracket fromString(String input)

Creates an instance by reading a set of lines in dot-bracket notation. Each line begins with a Leontis-Westhof notation shortand (e.g. cWW, tSH, etc.), a whitespace, and a dot-bracket. One line contains 'seq' instead of LW notation and it is followed by the sequence. For example:

 seq AGGGCGGGU
 cWW (.......)
 cWH .([{.}]).
 

Parameters:

input - A string containing input in the format specified above.

Returns:

An instance of this class.

sequence

@Parameter(order=1)
public abstract String sequence()

Returns:

The sequence of nucleotides.

basePairs

@Parameter(order=2)
public abstract Collection<? extends ClassifiedBasePair> basePairs()

Returns:

The list of base pairs.

toString

public final String toString()

Overrides:

toString in class Object

basePairs5to3

@Lazy
protected Collection<ClassifiedBasePair> basePairs5to3()