org.helm.notation2

Class MonomerStore

java.lang.Object

org.helm.notation2.MonomerStore

public class MonomerStore
extends Object

This class represents a store for monomers. It is mainly used to seperate the monomers coming from a single (XHELM) file from the monomers within the local database.

Author:

maisel

Constructor Summary

Constructors

Constructor and Description
MonomerStore() Constructs empty MonomerStore
MonomerStore(Map<String,Map<String,Monomer>> monomerDB, Map<String,Monomer> smilesMonomerDB) Constructor with Monomer- and SmilesDB

Method Summary

Modifier and Type	Method and Description
void	addMonomer(Monomer monomer) Adds a monomer to the store
void	addMonomer(Monomer monomer, boolean dbChanged) Adds a monomer to the store and optionally sets the dbChanged flag
void	addNewMonomer(Monomer monomer) Adds a monomer to the store and makes it a temporary new monomer
void	clearMonomers() Clears the MonomerStore
List<Monomer>	getAllMonomersList() This method returns all monomers of the store as list sorted by polymer type
Monomer	getMonomer(String smiles) Returns the monomer by smiles string
Monomer	getMonomer(String polymerType, String alternateId) Returns the monomer specified by polymerType and alternatId
Map<String,Map<String,Monomer>>	getMonomerDB() returns MonomerDB
Map<String,Monomer>	getMonomers(String polymerType) Returns all monomers by polymerType
Set<String>	getPolymerTypeSet() Returns the polymer type set
Map<String,Monomer>	getSmilesMonomerDB() returns SmilesMonomerDB
boolean	hasMonomer(String polymerType, String alternateId) Checks if a specific monomer exists in the store
boolean	isMonomerStoreEmpty() Checks for the empty store
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

MonomerStore

public MonomerStore(Map<String,Map<String,Monomer>> monomerDB,
                    Map<String,Monomer> smilesMonomerDB)

Constructor with Monomer- and SmilesDB

Parameters:

monomerDB - given monomerDB

smilesMonomerDB - given smiles DB

MonomerStore

public MonomerStore()

Constructs empty MonomerStore

Method Detail

getMonomerDB

public Map<String,Map<String,Monomer>> getMonomerDB()

returns MonomerDB

Returns:

MonomerDB as Map<String, Map<String, Monomer>>

getSmilesMonomerDB

public Map<String,Monomer> getSmilesMonomerDB()

returns SmilesMonomerDB

Returns:

SmilesMonomerDB as Map<String, Monomer>

addMonomer

public void addMonomer(Monomer monomer)
                throws IOException,
                       MonomerException

Adds a monomer to the store

Parameters:

monomer - given monomer

Throws:

IOException - if the monomer store can not be saved

MonomerException - if the monomer is not valid

addMonomer

public void addMonomer(Monomer monomer,
                       boolean dbChanged)
                throws IOException,
                       MonomerException

Adds a monomer to the store and optionally sets the dbChanged flag

Parameters:

monomer - given monomer

dbChanged - if db was changed

Throws:

IOException - if the monomer store can not be saved

MonomerException - if the monomer is not valid

hasMonomer

public boolean hasMonomer(String polymerType,
                          String alternateId)

Checks if a specific monomer exists in the store

Parameters:

polymerType - polymer type of monomer

alternateId - alternateId of monomer

Returns:

true if monomer exists, false if not

getMonomer

public Monomer getMonomer(String polymerType,
                          String alternateId)

Returns the monomer specified by polymerType and alternatId

Parameters:

polymerType - polymer type of monomer

alternateId - alternateId of monomer

Returns:

the matching monomer

getMonomer

public Monomer getMonomer(String smiles)

Returns the monomer by smiles string

Parameters:

smiles - given smiles

Returns:

the matching monomer

getMonomers

public Map<String,Monomer> getMonomers(String polymerType)

Returns all monomers by polymerType

Parameters:

polymerType - given polymer type

Returns:

All monomers with polymerType

addNewMonomer

public void addNewMonomer(Monomer monomer)
                   throws IOException,
                          MonomerException

Adds a monomer to the store and makes it a temporary new monomer

Parameters:

monomer - given monomer

Throws:

IOException - if the monomer can not be saved

MonomerException - if the monomer is not valid

isMonomerStoreEmpty

public boolean isMonomerStoreEmpty()

Checks for the empty store

Returns:

true if the store is empty, false if not

clearMonomers

public void clearMonomers()

Clears the MonomerStore

toString

public String toString()

Overrides:

toString in class Object

getPolymerTypeSet

public Set<String> getPolymerTypeSet()

Returns the polymer type set

Returns:

the polymer type set as Set<String>

getAllMonomersList

public List<Monomer> getAllMonomersList()

This method returns all monomers of the store as list sorted by polymer type

Returns:

all monomers of store as List<{@link Monomer}>