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	Description
`static String`	`ATTACHMENT_LIST_ELEMENT`
`static String`	`ATTACHMENTS_RESOURCE`
`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

Modifier and Type	Method	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 Details
- NOTATION_DIRECTORY
  
  public static final String NOTATION_DIRECTORY
- MONOMER_CACHE_FILE_NAME
  
  public static final String MONOMER_CACHE_FILE_NAME
  
  See Also:
  
  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
  
  See Also:
  
  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
  
  See Also:
  
  Constant Field Values
- MONOMER_DB_SCHEMA_RESOURCE
  
  public static final String MONOMER_DB_SCHEMA_RESOURCE
  
  See Also:
  
  Constant Field Values
- ATTACHMENTS_RESOURCE
  
  public static final String ATTACHMENTS_RESOURCE
  
  See Also:
  
  Constant Field Values
- XML_SCHEMA_VALIDATION_FEATURE
  
  public static final String XML_SCHEMA_VALIDATION_FEATURE
  
  See Also:
  
  Constant Field Values
- EXTERNAL_SCHEMA_LOCATION_KEY
  
  public static final String EXTERNAL_SCHEMA_LOCATION_KEY
  
  See Also:
  
  Constant Field Values
- DEFAULT_NAME_SPACE
  
  public static final String DEFAULT_NAME_SPACE
  
  See Also:
  
  Constant Field Values
- POLYMER_LIST_ELEMENT
  
  public static final String POLYMER_LIST_ELEMENT
  
  See Also:
  
  Constant Field Values
- POLYMER_ELEMENT
  
  public static final String POLYMER_ELEMENT
  
  See Also:
  
  Constant Field Values
- POLYMER_TYPE_ATTRIBUTE
  
  public static final String POLYMER_TYPE_ATTRIBUTE
  
  See Also:
  
  Constant Field Values
- ATTACHMENT_LIST_ELEMENT
  
  public static final String ATTACHMENT_LIST_ELEMENT
  
  See Also:
  
  Constant Field Values
- monomerStore
  
  protected MonomerStore monomerStore
Method Details
- 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()

Class MonomerFactory

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

Method Details