Package pl.poznan.put.structure.formats

Class BpSeq

java.lang.Object

pl.poznan.put.structure.formats.BpSeq

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

ImmutableBpSeq

@Immutable
public abstract class BpSeq
extends Object
implements Serializable

RNA secondary structure in BPSEQ format.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BpSeq.Entry	An entry of a BPSEQ data.

Constructor Summary

Constructors

Constructor	Description
BpSeq()

Method Summary

Modifier and Type	Method	Description
abstract SortedSet<BpSeq.Entry>	entries()
static BpSeq	fromBasePairs(List<PdbNamedResidueIdentifier> residues, Collection<? extends ClassifiedBasePair> basePairs)	Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs.
static BpSeq	fromCt(Ct ct)	Converts RNA secondary structure in CT format to BPSEQ format.
static BpSeq	fromDotBracket(DotBracket db)	Converts RNA secondary structure in dot-bracket format to BPSEQ format.
static BpSeq	fromString(String data)	Parses string into an instance of this class.
boolean	hasAnyPair()
SortedSet<BpSeq.Entry>	paired()
String	sequence()
int	size()
String	toString()
protected void	validate()
BpSeq	withoutIsolatedPairs()	Finds all isolated base pairs and creates a copy of this instance without them.
BpSeq	withoutPair(BpSeq.Entry entry)	Creates a copy of this instance, but with the given pair removed.

Methods inherited from class java.lang.Object

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

Constructor Detail

BpSeq

public BpSeq()

Method Detail

fromString

public static BpSeq fromString(String data)

Parses string into an instance of this class.

Parameters:

data - The string with BPSEQ data.

Returns:

An instance of this class with parsed data.

fromCt

public static BpSeq fromCt(Ct ct)

Converts RNA secondary structure in CT format to BPSEQ format.

Parameters:

ct - The data in CT format.

Returns:

An instance of this class with converted data.

fromDotBracket

public static BpSeq fromDotBracket(DotBracket db)

Converts RNA secondary structure in dot-bracket format to BPSEQ format.

Parameters:

db - The data in dot-bracket format.

Returns:

An instance of this class with converted data.

fromBasePairs

public static BpSeq fromBasePairs(List<PdbNamedResidueIdentifier> residues,
                                  Collection<? extends ClassifiedBasePair> basePairs)

Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs. The PDB chains are automatically reordered so that connecting ones are next to each other.

Parameters:

residues - The list of residue identifiers with names.

basePairs - The list of base pairs.

Returns:

An instance of this class.

entries

@Parameter(order=1)
@NaturalOrder
public abstract SortedSet<BpSeq.Entry> entries()

Returns:

The list of BPSEQ entries.

sequence

public final String sequence()

Returns:

The sequence of nucleotides stored in this object.

paired

public final SortedSet<BpSeq.Entry> paired()

Returns:

The set of paired BPSEQ entries without duplicates. For example, pair (4, 15) will not be repeated as (15, 4).

size

public final int size()

Returns:

The number of BPSEQ entries.

hasAnyPair

public final boolean hasAnyPair()

Returns:

True if at least one BPSEQ entry stands for a pair.

withoutIsolatedPairs

public final BpSeq withoutIsolatedPairs()

Finds all isolated base pairs and creates a copy of this instance without them.

Returns:

A copy of this instance, but with all isolated base pairs removed.

withoutPair

public final BpSeq withoutPair(BpSeq.Entry entry)

Creates a copy of this instance, but with the given pair removed.

Parameters:

entry - The pair to remove.

Returns:

A copy of this instance without the given pair.

toString

public final String toString()

Overrides:

toString in class Object

validate

@Check
protected void validate()