Package pl.poznan.put.structure

Class DotBracketSymbol

java.lang.Object

pl.poznan.put.structure.DotBracketSymbol

All Implemented Interfaces:

Serializable, Comparable<DotBracketSymbol>

Direct Known Subclasses:

ImmutableDotBracketSymbol

@Immutable
public abstract class DotBracketSymbol
extends Object
implements Comparable<DotBracketSymbol>, Serializable

A single symbol in a dot-bracket structure.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DotBracketSymbol()

Method Summary

Modifier and Type	Method	Description
int	compareTo(DotBracketSymbol t)
abstract int	index()
boolean	isClosing()
static boolean	isClosing(char c)	Checks if the given character is a closing character in dot-bracket format.
boolean	isMissing()
boolean	isOpening()
static boolean	isOpening(char c)	Checks if the given character is an opening character in dot-bracket format.
boolean	isPairing()
static boolean	isPairing(char c)	Checks if the given character is a pairing character in dot-bracket format.
static char	matchingBracket(char c)	Finds a matching bracket (closing for opening and vice versa) of the same level.
int	order()
abstract char	sequence()
abstract char	structure()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

DotBracketSymbol

public DotBracketSymbol()

Method Detail

isPairing

public static boolean isPairing(char c)

Checks if the given character is a pairing character in dot-bracket format.

Parameters:

c - The character to check.

Returns:

True if c is either an opening or closing symbol.

isOpening

public static boolean isOpening(char c)

Checks if the given character is an opening character in dot-bracket format.

Parameters:

c - The character to check

Returns:

True if c is one of: ([{<ABCDEFGHIJKLMNOPQRSTUVWXYZ.

isClosing

public static boolean isClosing(char c)

Checks if the given character is a closing character in dot-bracket format.

Parameters:

c - The character to check

Returns:

True if c is one of: )]}>abcdefghijklmnopqrstuvwxyz.

matchingBracket

public static char matchingBracket(char c)

Finds a matching bracket (closing for opening and vice versa) of the same level.

Parameters:

c - The character to find a matching bracket for.

Returns:

A matching bracket or a dot if the input is also a dot.

sequence

@Parameter(order=1)
public abstract char sequence()

Returns:

The sequence character.

structure

@Parameter(order=2)
public abstract char structure()

Returns:

The structure character (dot or bracket).

index

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

Returns:

The index of this symbol.

isMissing

public final boolean isMissing()

Returns:

True if this symbol is a minus '-'.

isPairing

public final boolean isPairing()

Returns:

True if this symbol is either opening or closing.

isOpening

public final boolean isOpening()

Returns:

True if this symbol is opening (see isOpening(char)).

isClosing

public final boolean isClosing()

Returns:

True if this symbol is closing (see isClosing(char)).

order

public final int order()

Returns:

The pseudoknot order of this symbol.

toString

public final String toString()

Overrides:

toString in class Object

compareTo

public final int compareTo(DotBracketSymbol t)

Specified by:

compareTo in interface Comparable<DotBracketSymbol>