Package org.helm.notation2.wsadapter

Class MonomerWSLoader

java.lang.Object

org.helm.notation2.wsadapter.MonomerWSLoader

public class MonomerWSLoader
extends Object

MonomerWSLoader loads monomers from the webservice configured in MonomerStoreConfiguration.

Version:

$Id$

Author:

Marco Lanig

Constructor Summary

Constructors

Constructor	Description
MonomerWSLoader(String polymerType)	Constructor using polymerType as parameter.

Method Summary

Modifier and Type	Method	Description
static List<CategorizedMonomer>	loadMonomerCategorization()	Loads the monomer categories using the URL configured in MonomerStoreConfiguration.
Map<String,Monomer>	loadMonomerStore(Map<String,Attachment> attachmentDB)	Loads the monomer store using the URL configured in MonomerStoreConfiguration and the polymerType that was given to constructor.

Methods inherited from class java.lang.Object

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

Constructor Details

MonomerWSLoader

public MonomerWSLoader(String polymerType) throws IOException

Constructor using polymerType as parameter. This will be one of PEPTIDE, RNA, or CHEM.

Parameters:

polymerType - given polymer type

Throws:

IOException - if polymer type is unknown

Method Details

loadMonomerStore

public Map<String,Monomer> loadMonomerStore(Map<String,Attachment> attachmentDB) throws IOException, URISyntaxException, EncoderException

Loads the monomer store using the URL configured in MonomerStoreConfiguration and the polymerType that was given to constructor.

Parameters:

attachmentDB - the attachments stored in Toolkit.

Returns:

Map containing monomers

Throws:

IOException - IO Error

URISyntaxException - string could not be parsed as URI

EncoderException - monomer store could be not encoded

loadMonomerCategorization

public static List<CategorizedMonomer> loadMonomerCategorization() throws IOException, URISyntaxException

Loads the monomer categories using the URL configured in MonomerStoreConfiguration.

Returns:

List containing monomer categories

Throws:

IOException - IO error

URISyntaxException - url is not valid