Package org.intermine.webservice.server.jbrowse.genomic

Class Engine

  • public class Engine
extends org.intermine.webservice.server.jbrowse.CommandRunner
    An adaptor for running JBrowse queries against a genomic database.

    This engine is written in such a way that it does not need reference to the compiled model classes to be deployed; in order to do that it makes a number of assumptions about the shape of the core model, namely it expects that:

    • SequenceFeatures have a chromosomeLocation reference, which can be used in range queries
    • SequenceFeatures have an organism reference which has a taxonId :: integer field.
    • SequenceFeatures have name, symbol, primaryIdentifer, and score fields.

    • Constructor Summary

      Constructors 
      Constructor Description
      Engine​(org.intermine.api.InterMineAPI api)
      constructor

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void densities​(org.intermine.webservice.server.jbrowse.Command command)  
      void features​(org.intermine.webservice.server.jbrowse.Command command)  
      void reference​(org.intermine.webservice.server.jbrowse.Command command)  
      void stats​(org.intermine.webservice.server.jbrowse.Command command)  

      • Methods inherited from class org.intermine.webservice.server.jbrowse.CommandRunner

        addListener, getAPI, getIntro, getOutro, getRunner, onData, onData, run

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • Engine

        public Engine​(org.intermine.api.InterMineAPI api)
        constructor
        Parameters:
        api - The API

    • Method Detail

      • stats

        public void stats​(org.intermine.webservice.server.jbrowse.Command command)
        Specified by:
        stats in class org.intermine.webservice.server.jbrowse.CommandRunner

      • reference

        public void reference​(org.intermine.webservice.server.jbrowse.Command command)
        Specified by:
        reference in class org.intermine.webservice.server.jbrowse.CommandRunner

      • features

        public void features​(org.intermine.webservice.server.jbrowse.Command command)
        Specified by:
        features in class org.intermine.webservice.server.jbrowse.CommandRunner

      • densities

        public void densities​(org.intermine.webservice.server.jbrowse.Command command)
        Specified by:
        densities in class org.intermine.webservice.server.jbrowse.CommandRunner
        Parameters:
        command - command to run