Package de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg

Class KeggAPIServiceHelper

java.lang.Object

de.ipk_gatersleben.ag_nw.graffiti.plugins.databases.kegg.KeggAPIServiceHelper

All Implemented Interfaces:

FileDownloadStatusInformationProvider, HelperClass

public class KeggAPIServiceHelper
extends Object
implements HelperClass, FileDownloadStatusInformationProvider

This Kegg API Service helper will retrieve and cache results looked up from the Kegg public REST webservice. The cache will be implemented using the MapDB database library. The service helper will return KoEntry objects (single or Lists) given on of the following commonly used inputs - KO Ids - EC number - Gene ID

Author:

matthiak

Method Summary

Modifier and Type	Method	Description
void	finishedNewDownload()
String	getDescription()
List<KoEntry>	getEntriesByEC(String ecId)	Retrieves an array of KO entries for a given EC number
List<KoEntry>	getEntriesByEC(List<String> listEC)	Algorithm to retrieve KO entries from EC numbers 2 step process 1.
List<KoEntry>	getEntriesByKO(String koId)	Retrieves an array of KO entries for a given KO id
List<KoEntry>	getEntriesByKO(List<String> listKOids)	returns List of koEntry objects matching the given KO ids (K numbers)
static KeggAPIServiceHelper	getInstance()
JComponent	getStatusPane(boolean showEmpty)

Methods inherited from class java.lang.Object

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

Method Details

getInstance

public static KeggAPIServiceHelper getInstance()

getEntriesByEC

public List<KoEntry> getEntriesByEC(String ecId)

Retrieves an array of KO entries for a given EC number

Parameters:

ecId -

Returns:

getEntriesByEC

public List<KoEntry> getEntriesByEC(List<String> listEC)

Algorithm to retrieve KO entries from EC numbers 2 step process 1. find KO id to EC number in cache OR 1. if not in cache find KO entry online 2. download KO entry -create KoEntry object and put it in the cache returns List of koEntry objects matching the given EC numbers

getEntriesByKO

public List<KoEntry> getEntriesByKO(String koId)

Retrieves an array of KO entries for a given KO id

Parameters:

KO - id (K number)

Returns:

getEntriesByKO

public List<KoEntry> getEntriesByKO(List<String> listKOids)

returns List of koEntry objects matching the given KO ids (K numbers)

getStatusPane

public JComponent getStatusPane(boolean showEmpty)

Specified by:

getStatusPane in interface FileDownloadStatusInformationProvider

getDescription

public String getDescription()

Specified by:

getDescription in interface FileDownloadStatusInformationProvider

finishedNewDownload

public void finishedNewDownload()

Specified by:

finishedNewDownload in interface FileDownloadStatusInformationProvider