org.helm.notation2

Class MonomerFactory

java.lang.Object

org.helm.notation2.MonomerFactory

public class MonomerFactory
extends Object

This is a factory class to build monomer database from MonomerDBGZEnconded.xml document

Author:

zhangtianhong

Field Summary

Fields

Modifier and Type	Field and Description
static String	ATTACHMENT_LIST_ELEMENT
static String	DEFAULT_NAME_SPACE
static String	EXTERNAL_SCHEMA_LOCATION_KEY
static String	MONOMER_CACHE_FILE_NAME
static String	MONOMER_CACHE_FILE_PATH
static String	MONOMER_DB_FILE_NAME
static String	MONOMER_DB_FILE_PATH
static String	MONOMER_DB_SCHEMA_RESOURCE
static String	MONOMER_DB_XML_RESOURCE
protected MonomerStore	monomerStore
static String	NOTATION_DIRECTORY
static String	POLYMER_ELEMENT
static String	POLYMER_LIST_ELEMENT
static String	POLYMER_TYPE_ATTRIBUTE
static String	XML_SCHEMA_VALIDATION_FEATURE

Method Summary

Methods

Modifier and Type	Method and Description
void	addNewMonomer(Monomer monomer) To add new monomer into monomerCache
MonomerCache	buildMonomerCacheFromXML(String monomerDBXML) Build an MonomerCache object with monomerDBXML String
static void	finalizeMonomerCache()
Map<String,Attachment>	getAttachmentDB()
Map<String,List<String>>	getAttachmentLabelIDs()
Map<Monomer,Monomer>	getConflictedMonomerMap(MonomerCache remoteMonomerCache)
static MonomerFactory	getInstance() Initialize MonomerCache and returns the singleton Factory class
Map<String,Map<String,Monomer>>	getMonomerDB() retruns the monomer database
Map<String,Map<String,Monomer>>	getMonomerDB(boolean includeNewMonomers) returns the monomer database including monomers that where temporary marked as new, else without those monomers
MonomerStore	getMonomerStore() create a MonomerStore instance based on MonomerFactory's monomerDB and smilesMonomerDB
List<String>	getMonomerTypes()
List<String>	getPolymerTypes()
Map<String,Monomer>	getSmilesMonomerDB()
Map<String,Monomer>	getSmilesMonomerDB(boolean includeNewMonomers)
static boolean	hasDBChanged() Returns whether one of the stored databases has changed, for example by adding or removing monomers.
void	merge(MonomerCache remoteMonomerCache) merge remote monomerCache with local monomerCache, will throw exception if conflicts found.
static void	refreshMonomerCache()
static void	resetDBChanged()
void	saveMonomerCache() save monomerCache to disk file
static void	setDBChanged(boolean isChanged)
void	setMonomerCache(MonomerCache remoteMonomerCache) replace local cache with remote one completely, may cause loss of data
static void	setupBuilder()

Methods inherited from class java.lang.Object

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

Field Detail

NOTATION_DIRECTORY

public static final String NOTATION_DIRECTORY

MONOMER_CACHE_FILE_NAME

public static final String MONOMER_CACHE_FILE_NAME

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Constant Field Values

MONOMER_CACHE_FILE_PATH

public static final String MONOMER_CACHE_FILE_PATH

MONOMER_DB_FILE_NAME

public static final String MONOMER_DB_FILE_NAME

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Constant Field Values

MONOMER_DB_FILE_PATH

public static final String MONOMER_DB_FILE_PATH

MONOMER_DB_XML_RESOURCE

public static final String MONOMER_DB_XML_RESOURCE

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Constant Field Values

MONOMER_DB_SCHEMA_RESOURCE

public static final String MONOMER_DB_SCHEMA_RESOURCE

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Constant Field Values

XML_SCHEMA_VALIDATION_FEATURE

public static final String XML_SCHEMA_VALIDATION_FEATURE

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Constant Field Values

EXTERNAL_SCHEMA_LOCATION_KEY

public static final String EXTERNAL_SCHEMA_LOCATION_KEY

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Constant Field Values

DEFAULT_NAME_SPACE

public static final String DEFAULT_NAME_SPACE

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Constant Field Values

POLYMER_LIST_ELEMENT

public static final String POLYMER_LIST_ELEMENT

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Constant Field Values

POLYMER_ELEMENT

public static final String POLYMER_ELEMENT

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Constant Field Values

POLYMER_TYPE_ATTRIBUTE

public static final String POLYMER_TYPE_ATTRIBUTE

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Constant Field Values

ATTACHMENT_LIST_ELEMENT

public static final String ATTACHMENT_LIST_ELEMENT

See Also:

Constant Field Values

monomerStore

protected MonomerStore monomerStore

Method Detail

getMonomerDB

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

retruns the monomer database

Returns:

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

getMonomerDB

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

returns the monomer database including monomers that where temporary marked as new, else without those monomers

Parameters:

includeNewMonomers - if true, then the new monomers will be added to the monomer db

Returns:

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

getMonomerStore

public MonomerStore getMonomerStore()

create a MonomerStore instance based on MonomerFactory's monomerDB and smilesMonomerDB

Returns:

MonomerStore

getAttachmentDB

public Map<String,Attachment> getAttachmentDB()

getSmilesMonomerDB

public Map<String,Monomer> getSmilesMonomerDB()

getSmilesMonomerDB

public Map<String,Monomer> getSmilesMonomerDB(boolean includeNewMonomers)

getPolymerTypes

public List<String> getPolymerTypes()

getMonomerTypes

public List<String> getMonomerTypes()

getAttachmentLabelIDs

public Map<String,List<String>> getAttachmentLabelIDs()

setupBuilder

public static void setupBuilder()

getInstance

public static MonomerFactory getInstance()
                                  throws MonomerLoadingException,
                                         ChemistryException

Initialize MonomerCache and returns the singleton Factory class

Returns:

MonomerFactory current monomerfactory

Throws:

MonomerLoadingException - if the monomer could not be loaded from the source

ChemistryException - if the chemistry could not be initialized

refreshMonomerCache

public static void refreshMonomerCache()
                                throws MonomerLoadingException,
                                       ChemistryException

Throws:

MonomerLoadingException

ChemistryException

setDBChanged

public static void setDBChanged(boolean isChanged)

hasDBChanged

public static boolean hasDBChanged()

Returns whether one of the stored databases has changed, for example by adding or removing monomers.

Returns:

true when database has changed else false

resetDBChanged

public static void resetDBChanged()

addNewMonomer

public void addNewMonomer(Monomer monomer)
                   throws IOException,
                          MonomerException

To add new monomer into monomerCache

Parameters:

monomer - given Monomer

Throws:

IOException - if monomer store can not be read

MonomerException - if monomer is not valid

buildMonomerCacheFromXML

public MonomerCache buildMonomerCacheFromXML(String monomerDBXML)
                                      throws MonomerException,
                                             IOException,
                                             org.jdom2.JDOMException,
                                             ChemistryException,
                                             org.helm.chemtoolkit.CTKException

Build an MonomerCache object with monomerDBXML String

Parameters:

monomerDBXML - monomer db in xml format as string

Returns:

MonomerCache

Throws:

MonomerException - if monomer is not valid

IOException - if string can not be read

org.jdom2.JDOMException - if xml file is not valid

ChemistryException - if chemistry could not be initialized

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

merge

public void merge(MonomerCache remoteMonomerCache)
           throws IOException,
                  MonomerException

merge remote monomerCache with local monomerCache, will throw exception if conflicts found. Client needs to resolve conflicts prior to calling merge

Parameters:

remoteMonomerCache - remote monomer cache

Throws:

IOException - if monomer store can not be read

MonomerException - if monomer is not valid

setMonomerCache

public void setMonomerCache(MonomerCache remoteMonomerCache)
                     throws IOException,
                            MonomerException

replace local cache with remote one completely, may cause loss of data

Parameters:

remoteMonomerCache - remote monomer cache

Throws:

IOException - if monomer store can not be read

MonomerException - if monomer is not valid

getConflictedMonomerMap

public Map<Monomer,Monomer> getConflictedMonomerMap(MonomerCache remoteMonomerCache)
                                             throws IOException,
                                                    MonomerException

Parameters:

remoteMonomerCache - remoteMonomerCache

Returns:

localMonomer and remoteMonomer mismatch, key is local, value is remote

Throws:

IOException - if monomer store can not be read

MonomerException - if monomer is not valid

saveMonomerCache

public void saveMonomerCache()
                      throws IOException,
                             MonomerException

save monomerCache to disk file

Throws:

IOException - if the monomer can not be saved to disk file

MonomerException - if monomer is not valid

finalizeMonomerCache

public static void finalizeMonomerCache()