Package org.intermine.bio.web.model

Class GeneModel

  • public class GeneModel
extends java.lang.Object
    Representation of a gene model - being one transcript of a gene and including exons, introns, UTRs and CDSs where data are available. On construction for a particular transcript this will fetch additional information from the database.

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected static org.apache.log4j.Logger LOG  
      static java.util.Set<java.lang.String> TYPES
      The unqualified class names of types that comprise a gene model.

    • Constructor Summary

      Constructors 
      Constructor Description
      GeneModel​(org.intermine.metadata.Model model, org.intermine.model.bio.Gene gene, org.intermine.model.InterMineObject transcript)
      Construct a new gene model for the given transcript and gene.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.List<org.intermine.model.InterMineObject> getCDSs()
      Get the CDSs if present.
      java.util.List<org.intermine.model.InterMineObject> getExons()
      Get the exons if present.
      org.intermine.model.InterMineObject getFivePrimeUTR()
      Get the fivePrimeUTR if present.
      org.intermine.model.bio.Gene getGene()
      The parent gene for this gene model.
      java.util.Set<java.lang.Integer> getIds()
      Return the ids of all objects represented in this gene model including the gene itself.
      java.util.List<org.intermine.model.InterMineObject> getIntrons()
      Get the introns if present.
      org.intermine.model.InterMineObject getThreePrimeUTR()
      Get the threePrimeUTR if present.
      org.intermine.model.InterMineObject getTranscript()
      Get the transcript this gene model represents

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • TYPES

        public static final java.util.Set<java.lang.String> TYPES
        The unqualified class names of types that comprise a gene model.

      • LOG

        protected static final org.apache.log4j.Logger LOG

    • Constructor Detail

      • GeneModel

        public GeneModel​(org.intermine.metadata.Model model,
                 org.intermine.model.bio.Gene gene,
                 org.intermine.model.InterMineObject transcript)
        Construct a new gene model for the given transcript and gene. This will run queries for exons, introns, UTRs, etc. Note that model classes other than Gene can't be referred to by name as they may not be in all models.
        Parameters:
        model - the data model
        gene - the parent gene
        transcript - the transcript to construct a gene model for

    • Method Detail

      • getGene

        public org.intermine.model.bio.Gene getGene()
        The parent gene for this gene model.
        Returns:
        the gene

      • getTranscript

        public org.intermine.model.InterMineObject getTranscript()
        Get the transcript this gene model represents
        Returns:
        the transcript

      • getExons

        public java.util.List<org.intermine.model.InterMineObject> getExons()
        Get the exons if present.
        Returns:
        the exons

      • getIntrons

        public java.util.List<org.intermine.model.InterMineObject> getIntrons()
        Get the introns if present.
        Returns:
        the introns

      • getCDSs

        public java.util.List<org.intermine.model.InterMineObject> getCDSs()
        Get the CDSs if present.
        Returns:
        the CDSs

      • getThreePrimeUTR

        public org.intermine.model.InterMineObject getThreePrimeUTR()
        Get the threePrimeUTR if present.
        Returns:
        the threePrimeUTR

      • getFivePrimeUTR

        public org.intermine.model.InterMineObject getFivePrimeUTR()
        Get the fivePrimeUTR if present.
        Returns:
        the fivePrimeUTR

      • getIds

        public java.util.Set<java.lang.Integer> getIds()
        Return the ids of all objects represented in this gene model including the gene itself.
        Returns:
        the ids of all objects represented in this gene model