Package pl.poznan.put.structure.formats

Class AbstractCombinedStrand

java.lang.Object

pl.poznan.put.structure.formats.AbstractCombinedStrand

All Implemented Interfaces:

DotBracket

Direct Known Subclasses:

CombinedStrand, CombinedStrandFromPdb

public abstract class AbstractCombinedStrand
extends Object
implements DotBracket

Constructor Summary

Constructors

Constructor	Description
AbstractCombinedStrand()

Method Summary

Modifier and Type	Method	Description
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()
List<Strand>	strands()
List<DotBracketSymbol>	symbols()

Methods inherited from class java.lang.Object

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

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

containsMissing, findStrand, isIsolated, isolatedSymbols, length, missingInternal, missingTerminal, originalIndex, pairs, pseudoknotOrder, sequence, sequence, structure, structure, toStringWithStrands

Constructor Details

AbstractCombinedStrand

public AbstractCombinedStrand()

Method Details

inputStrands

protected abstract List<Strand> inputStrands()

combineStrands

public 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.

symbols

public List<DotBracketSymbol> symbols()

Specified by:

symbols in interface DotBracket

Returns:

The list of dot-bracket symbols.

strands

public List<Strand> strands()

Specified by:

strands in interface DotBracket

Returns:

The list of strands.