Package pl.poznan.put.structure.formats

Class DefaultDotBracket

java.lang.Object

pl.poznan.put.structure.formats.DefaultDotBracket

All Implemented Interfaces:

Serializable, DotBracket

Direct Known Subclasses:

ImmutableDefaultDotBracket

@Immutable
public abstract class DefaultDotBracket
extends Object
implements Serializable

A default implementation of a dot-bracket.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DefaultDotBracket()

Method Summary

Modifier and Type	Method	Description
protected List<List<Strand>>	candidatesToCombine()
List<DotBracket>	combineStrands()	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
static DotBracket	copyWithStrands(DotBracket input, Ct ct)	Creates a copy of existing instance and applies the information in CT format to divide strands accordingly.
static DefaultDotBracket	fromString(String data)	Parses a string into an instance of this class.
Map<DotBracketSymbol,DotBracketSymbol>	pairs()
abstract String	sequence()
List<Strand>	strands()
abstract String	structure()
List<DotBracketSymbol>	symbols()
String	toString()
protected void	validate()

Methods inherited from class java.lang.Object

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

Methods inherited from interface pl.poznan.put.structure.formats.DotBracket

containsMissing, findStrand, length, missingInternal, missingTerminal, originalIndex, pseudoknotOrder, sequence, structure, toStringWithStrands

Constructor Detail

DefaultDotBracket

public DefaultDotBracket()

Method Detail

copyWithStrands

public static DotBracket copyWithStrands(DotBracket input,
                                         Ct ct)

Creates a copy of existing instance and applies the information in CT format to divide strands accordingly.

Parameters:

input - The input dot-bracket structure.

ct - The CT data to take strand information from.

Returns:

An instance of this class.

fromString

public static DefaultDotBracket fromString(String data)

Parses a string into an instance of this class. The string must be in format:

     >strand_name
     ACGU
     .().
 

The first line (strand name) is optional. The three lines might appear multiple times.

Parameters:

data - The string to parse.

Returns:

An instance of this class.

combineStrands

public final List<DotBracket> combineStrands()

Description copied from interface: DotBracket

Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.

Specified by:

combineStrands in interface DotBracket

Returns:

The list of dot-bracket instances, each containing strands which only pair with each other.

strands

@Auxiliary
@Default
public List<Strand> strands()

Specified by:

strands in interface DotBracket

Returns:

The list of strands.

sequence

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

Specified by:

sequence in interface DotBracket

Returns:

The sequence of nucleotides.

structure

@Parameter(order=2)
public abstract String structure()

Specified by:

structure in interface DotBracket

Returns:

The sequence of dots and brackets representing paired and unpaired residues.

pairs

@Lazy
@Auxiliary
public Map<DotBracketSymbol,DotBracketSymbol> pairs()

Specified by:

pairs in interface DotBracket

toString

public final String toString()

Overrides:

toString in class Object

validate

@Check
protected void validate()

symbols

public List<DotBracketSymbol> symbols()

Specified by:

symbols in interface DotBracket

Returns:

The list of dot-bracket symbols.

candidatesToCombine

protected final List<List<Strand>> candidatesToCombine()