Package pl.poznan.put.structure.formats

Class StrandView

java.lang.Object

pl.poznan.put.structure.formats.StrandView

All Implemented Interfaces:

DotBracket, Strand

Direct Known Subclasses:

ImmutableStrandView

@Immutable
public abstract class StrandView
extends Object
implements Strand

A strand which is defined as a fragment of a dot-bracket structure.

Constructor Summary

Constructors

Constructor	Description
StrandView()

Method Summary

Modifier and Type	Method	Description
abstract int	begin()
final String	description()	Prepares description of strand in RNAComposer format.
abstract int	end()
abstract String	name()
abstract DotBracket	parent()
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

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

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

isSingleStrand, missingBegin, missingEnd, sequenceRY

Constructor Details

StrandView

public StrandView()

Method Details

name

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

Specified by:

name in interface Strand

Returns:

The name of the strand.

description

public final String description()

Description copied from interface: Strand

Prepares description of strand in RNAComposer format. The format has 5 elements: index-from, index-to, sequence, structure, RY-sequence.

Specified by:

description in interface Strand

Returns:

A description of strand in RNAComposer format.

begin

@Parameter(order=3)
public abstract int begin()

Specified by:

begin in interface Strand

Returns:

The index of the first residue in this strand.

end

@Parameter(order=4)
public abstract int end()

Specified by:

end in interface Strand

Returns:

The index of the last residue in this strand.

parent

@Parameter(order=2)
public abstract DotBracket parent()

Returns:

The parent dot-bracket structure of this strand.

symbols

@Lazy
public List<DotBracketSymbol> symbols()

Specified by:

symbols in interface DotBracket

Returns:

The list of dot-bracket symbols.

toString

public final String toString()

Overrides:

toString in class Object