Package pl.poznan.put.structure.formats

Class Ct

java.lang.Object

pl.poznan.put.structure.formats.Ct

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

ImmutableCt

@Immutable
public abstract class Ct
extends Object
implements Serializable

An RNA secondary structure encoded in CT (connect) format.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Ct.ExtendedEntry	A single entry in the CT formatted structure.

Constructor Summary

Constructors

Constructor	Description
Ct()

Method Summary

Modifier and Type	Method	Description
abstract SortedSet<Ct.ExtendedEntry>	entries()
static Ct	fromBpSeq(BpSeq bpSeq)	Converts RNA secondary structure in BPSEQ format to CT format.
static Ct	fromBpSeqAndPdbModel(BpSeq bpSeq, PdbModel model)	Converts RNA secondary structure in BPSEQ format to CT format, taking into account information from 3D coordinates (residue numbering, chain sizes).
static Ct	fromDotBracket(DotBracket dotBracket)	Converts RNA secondary structure in dot-bracket format to CT format.
static Ct	fromString(String data)	Parses string into an instance of this class.
int	strandCount()
String	toString()
protected Ct	validate()
Ct	withoutIsolatedPairs()	Finds all isolated base pairs and creates a copy of this instance without them.
Ct	withoutPair(Ct.ExtendedEntry 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

Ct

public Ct()

Method Detail

fromString

public static Ct fromString(String data)

Parses string into an instance of this class.

Parameters:

data - The string with CT data.

Returns:

An instance of this class with parsed data.

fromBpSeq

public static Ct fromBpSeq(BpSeq bpSeq)

Converts RNA secondary structure in BPSEQ format to CT format.

Parameters:

bpSeq - The data in BPSEQ format.

Returns:

An instance of this class with converted data.

fromBpSeqAndPdbModel

public static Ct fromBpSeqAndPdbModel(BpSeq bpSeq,
                                      PdbModel model)

Converts RNA secondary structure in BPSEQ format to CT format, taking into account information from 3D coordinates (residue numbering, chain sizes).

Parameters:

bpSeq - The data in BPSEQ format.

model - The 3D data.

Returns:

An instance of this class with converted data.

fromDotBracket

public static Ct fromDotBracket(DotBracket dotBracket)

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

Parameters:

dotBracket - The data in dot-bracket format.

Returns:

An instance of this class with converted data.

entries

@Parameter(order=1)
@NaturalOrder
public abstract SortedSet<Ct.ExtendedEntry> entries()

Returns:

The list of CT entries.

strandCount

public final int strandCount()

Returns:

The number of strands.

withoutPair

public final Ct withoutPair(Ct.ExtendedEntry 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.

withoutIsolatedPairs

public final Ct 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.

toString

public final String toString()

Overrides:

toString in class Object

validate

@Check
protected Ct validate()