Package pl.poznan.put.structure.formats

Class CombinedStrand

java.lang.Object

pl.poznan.put.structure.formats.AbstractCombinedStrand

pl.poznan.put.structure.formats.CombinedStrand

All Implemented Interfaces:

DotBracket

Direct Known Subclasses:

ImmutableCombinedStrand

@Immutable
public abstract class CombinedStrand
extends AbstractCombinedStrand

A dot-bracket encoded structure made from combining one or more strands.

Constructor Summary

Constructors

Constructor	Description
CombinedStrand()

Method Summary

Modifier and Type	Method	Description
final List<DotBracket>	combineStrands()	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
protected abstract List<Strand>	inputStrands()
Map<DotBracketSymbol,DotBracketSymbol>	pairs()
List<Strand>	strands()
List<DotBracketSymbol>	symbols()
final String	toString()

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, isIsolated, isolatedSymbols, length, missingInternal, missingTerminal, originalIndex, pseudoknotOrder, sequence, sequence, structure, structure, toStringWithStrands

Constructor Details

CombinedStrand

public CombinedStrand()

Method Details

inputStrands

@Parameter(order=1)
protected abstract List<Strand> inputStrands()

Specified by:

inputStrands in class AbstractCombinedStrand

Returns:

The list of input strands.

symbols

@Lazy
@Auxiliary
public List<DotBracketSymbol> symbols()

Specified by:

symbols in interface DotBracket

Overrides:

symbols in class AbstractCombinedStrand

Returns:

The list of dot-bracket symbols.

strands

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

Specified by:

strands in interface DotBracket

Overrides:

strands in class AbstractCombinedStrand

Returns:

The list of strands.

toString

public final String toString()

Overrides:

toString in class Object

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

Overrides:

combineStrands in class AbstractCombinedStrand

Returns:

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

pairs

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