org.expasy.jpl.core.mol
Class AbstractMolecularSymbolManager<T extends Molecule>

java.lang.Object
  org.expasy.jpl.core.mol.AbstractMolecularSymbolManager<T>

All Implemented Interfaces:

Serializable, org.expasy.jpl.commons.collection.symbol.AlphabetView<T>, org.expasy.jpl.commons.collection.symbol.DataSymbolRegister<T>

Direct Known Subclasses:

AAManager, AATermManager, CTermManager, DeoxyRiboNucManager, NTermManager, RiboNucManager

public abstract class AbstractMolecularSymbolManager<T extends Molecule>
extends Object
implements org.expasy.jpl.commons.collection.symbol.DataSymbolRegister<T>

This abstract class proposes a mechanism to map a Symbol to its Molecule by coupling a table of molecular symbols with the molecular pool. Each subclasses symbol manager will have to implement 3 methods:

• createSymbols() where a tree of symbols will be defined.
• loadMolecularMap() where all molecules linked to their symbol character representation are loaded.
• getMolecule(char symChar) to access the Molecule mapped by symChar.

Version:

1.0

Author:

nikitin

See Also:

ChemicalFacade, Serialized Form

Field Summary

protected Map<Character,T>	molecularMap data molecular map
protected static org.expasy.jpl.commons.collection.symbol.SymbolTable	SYMBOL_TABLE the table of molecular symbols
protected Map<org.expasy.jpl.commons.collection.symbol.Symbol<T>,T>	symbol2molecules map molecular symbols to their (pooled) molecule instance

Constructor Summary

protected

AbstractMolecularSymbolManager(org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType<T> type) Sole constructor.

Method Summary

Set<Character>	getLetters()
String	getRegEx()
int	getSymbolNumber()
static <T extends Molecule> org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType<T>	getSymbolType(String name)
boolean	hasSymbol(char name)
void	link(org.expasy.jpl.commons.collection.symbol.Symbol<T> symbol, T molecule)
T	lookupData(char name)
T	lookupData(org.expasy.jpl.commons.collection.symbol.Symbol<T> symbol) Get the T-data linked to terminal symbol.
Set<T>	lookUpDataFromSymbols(Set<org.expasy.jpl.commons.collection.symbol.Symbol<T>> symbols)
String	lookUpRegex(char name)
org.expasy.jpl.commons.collection.symbol.Symbol<T>	lookupSymbol(char name)
org.expasy.jpl.commons.collection.tree.TreeView<? extends org.expasy.jpl.commons.collection.symbol.Symbol<T>>	lookupSymbolNode(char name)
protected static byte	toByte(char c)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister

createDataMap

Field Detail

SYMBOL_TABLE

protected static org.expasy.jpl.commons.collection.symbol.SymbolTable SYMBOL_TABLE

the table of molecular symbols

symbol2molecules

protected Map<org.expasy.jpl.commons.collection.symbol.Symbol<T extends Molecule>,T extends Molecule> symbol2molecules

map molecular symbols to their (pooled) molecule instance

molecularMap

protected Map<Character,T extends Molecule> molecularMap

data molecular map

Constructor Detail

AbstractMolecularSymbolManager

protected AbstractMolecularSymbolManager(org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType<T> type)

Sole constructor. Create and register symbols in table of molecular symbols for invocation by subclass constructors.)

Parameters:

type - the type of molecular symbol.

Method Detail

getSymbolType

public static <T extends Molecule> org.expasy.jpl.commons.collection.symbol.Symbol.SymbolType<T> getSymbolType(String name)

getLetters

public Set<Character> getLetters()

Specified by:

getLetters in interface org.expasy.jpl.commons.collection.symbol.AlphabetView<T extends Molecule>

link

public final void link(org.expasy.jpl.commons.collection.symbol.Symbol<T> symbol,
                       T molecule)

Specified by:

link in interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister<T extends Molecule>

lookupData

public final T lookupData(org.expasy.jpl.commons.collection.symbol.Symbol<T> symbol)

Get the T-data linked to terminal symbol.

Specified by:

lookupData in interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister<T extends Molecule>

Parameters:

symbol - the terminal symbol.

lookUpDataFromSymbols

public final Set<T> lookUpDataFromSymbols(Set<org.expasy.jpl.commons.collection.symbol.Symbol<T>> symbols)

lookupData

public final T lookupData(char name)

Specified by:

lookupData in interface org.expasy.jpl.commons.collection.symbol.DataSymbolRegister<T extends Molecule>

lookupSymbolNode

public final org.expasy.jpl.commons.collection.tree.TreeView<? extends org.expasy.jpl.commons.collection.symbol.Symbol<T>> lookupSymbolNode(char name)

Specified by:

lookupSymbolNode in interface org.expasy.jpl.commons.collection.symbol.AlphabetView<T extends Molecule>

getRegEx

public String getRegEx()

Specified by:

getRegEx in interface org.expasy.jpl.commons.collection.symbol.AlphabetView<T extends Molecule>

lookUpRegex

public final String lookUpRegex(char name)

Returns:

the regular expression defining the symbol

lookupSymbol

public final org.expasy.jpl.commons.collection.symbol.Symbol<T> lookupSymbol(char name)

Specified by:

lookupSymbol in interface org.expasy.jpl.commons.collection.symbol.AlphabetView<T extends Molecule>

hasSymbol

public final boolean hasSymbol(char name)

Specified by:

hasSymbol in interface org.expasy.jpl.commons.collection.symbol.AlphabetView<T extends Molecule>

getSymbolNumber

public final int getSymbolNumber()

Specified by:

getSymbolNumber in interface org.expasy.jpl.commons.collection.symbol.AlphabetView<T extends Molecule>

toByte

protected static final byte toByte(char c)

toString

public String toString()

Overrides:

toString in class Object