Package org.intermine.webservice.server.jbrowse

Class Config

  • public class Config
extends JSONService
    Provide standard JBrowse configuration files (trackList.json and refSeqs.json) that are required to run a JBrowse instance. This service automatically generates the configuration required to run JBrowse for a given domain (usually an Organism), exposing all the reference sequences for which there are data, and providing a description of all the feature tracks. This service requires appropriate values to be configured in the web-properties of a mine. For most biological genomic webservices, the default configuration will suffice, but this can be altered on a per installation basis. See the JBrowse wiki for a guide to the formats of the files generated here.
    Author:
    Alex Kalderimis

    • Constructor Detail

      • Config

        public Config​(InterMineAPI im)
        Build a new instance with the injected API
        Parameters:
        im - InterMine API

    • Method Detail

      • initState

        protected void initState()
        Description copied from class: WebService
        Subclasses can put initialisation here.
        Overrides:
        initState in class WebService

      • makeJSONOutput

        protected Output makeJSONOutput​(java.io.PrintWriter out,
                                java.lang.String separator)
        Description copied from class: WebService
        Make the default JSON output given the HttpResponse's PrintWriter.
        Overrides:
        makeJSONOutput in class WebService
        Parameters:
        out - The PrintWriter from the HttpResponse.
        separator - The line-separator for the client's platform.
        Returns:
        An Output that produces good JSON.

      • execute

        protected void execute()
                throws ServiceException
        Description copied from class: WebService
        Runs service. This is abstract method, that must be defined in subclasses and so performs something useful. Standard procedure is overwrite this method in subclasses and let this method to be called from WebService.doGet method that encapsulates logic common for all web services else you can overwrite doGet method in your web service class and manage all the things alone.
        Specified by:
        execute in class WebService
        Throws:
        ServiceException