Package org.intermine.bio.web.logic

Class OrthologueConverter

  • public class OrthologueConverter
extends org.intermine.web.logic.bag.BagConverter

    • Field Summary

      • Fields inherited from class org.intermine.web.logic.bag.BagConverter

        im, webConfig

    • Constructor Summary

      Constructors 
      Constructor Description
      OrthologueConverter​(org.intermine.api.InterMineAPI im, org.intermine.web.logic.config.WebConfig webConfig)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      org.apache.struts.action.ActionMessage getActionMessage​(java.lang.String externalids, int convertedSize, java.lang.String type, java.lang.String parameter)
      java.util.List<java.lang.Integer> getConvertedObjectIds​(org.intermine.api.profile.Profile profile, java.lang.String bagType, java.util.List<java.lang.Integer> bagList, java.lang.String organismName)
      runs the orthologue conversion pathquery and returns list of intermine IDs used in the portal
      java.util.Map<java.lang.String,​java.lang.String> getCounts​(org.intermine.api.profile.Profile profile, org.intermine.api.profile.InterMineBag bag)

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • OrthologueConverter

        public OrthologueConverter​(org.intermine.api.InterMineAPI im,
                           org.intermine.web.logic.config.WebConfig webConfig)
        Parameters:
        im - intermine api
        webConfig - the webconfig

    • Method Detail

      • getConvertedObjectIds

        public java.util.List<java.lang.Integer> getConvertedObjectIds​(org.intermine.api.profile.Profile profile,
                                                               java.lang.String bagType,
                                                               java.util.List<java.lang.Integer> bagList,
                                                               java.lang.String organismName)
                                                        throws org.intermine.objectstore.ObjectStoreException
        runs the orthologue conversion pathquery and returns list of intermine IDs used in the portal
        Specified by:
        getConvertedObjectIds in class org.intermine.web.logic.bag.BagConverter
        Parameters:
        profile - the user's profile
        bagType - not used, always gene
        bagList - list of intermine object IDs
        organismName - name of homologue's organism
        Returns:
        list of intermine IDs
        Throws:
        org.intermine.objectstore.ObjectStoreException - if can't store to database

      • getCounts

        public java.util.Map<java.lang.String,​java.lang.String> getCounts​(org.intermine.api.profile.Profile profile,
                                                                        org.intermine.api.profile.InterMineBag bag)
                                                                 throws org.intermine.objectstore.ObjectStoreException
        Specified by:
        getCounts in class org.intermine.web.logic.bag.BagConverter
        Throws:
        org.intermine.objectstore.ObjectStoreException - if the query cannot be run.

      • getActionMessage

        public org.apache.struts.action.ActionMessage getActionMessage​(java.lang.String externalids,
                                                               int convertedSize,
                                                               java.lang.String type,
                                                               java.lang.String parameter)
                                                        throws java.io.UnsupportedEncodingException
        Specified by:
        getActionMessage in class org.intermine.web.logic.bag.BagConverter
        Throws:
        java.io.UnsupportedEncodingException