Package org.intermine.bio.web.logic

Class SequenceFeatureExportUtil

  • public final class SequenceFeatureExportUtil
extends java.lang.Object
    Utility methods for LocatedSequenceFeature exporting.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.List<org.intermine.pathquery.Path> getExportClassPaths​(org.intermine.pathquery.PathQuery pathQuery)
      From the view elements of a PathQuery, return a List of the Paths that this exporter will use to find sequences to export.
      static java.util.Set<java.lang.String> getOrganisms​(org.intermine.pathquery.PathQuery pathQuery, javax.servlet.http.HttpSession session)
      Get organism info from PathQuery
      static java.util.Set<java.lang.String> getOrganisms​(org.intermine.pathquery.PathQuery pathQuery, org.intermine.api.InterMineAPI im, org.intermine.api.profile.Profile profile)  
      static java.util.Set<java.lang.String> getTaxonIds​(org.intermine.pathquery.PathQuery pathQuery, javax.servlet.http.HttpSession session)
      Get organism taxon ids info from PathQuery
      static java.util.Set<java.lang.String> getTaxonIds​(org.intermine.pathquery.PathQuery pathQuery, org.intermine.api.InterMineAPI im, org.intermine.api.profile.Profile profile)  
      static void isValidFastaQuery​(org.intermine.pathquery.PathQuery pq)  
      static void isValidSequenceFeatureQuery​(org.intermine.pathquery.PathQuery pq)
      true if valid feature

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • getExportClassPaths

        public static java.util.List<org.intermine.pathquery.Path> getExportClassPaths​(org.intermine.pathquery.PathQuery pathQuery)
        From the view elements of a PathQuery, return a List of the Paths that this exporter will use to find sequences to export. The returned Paths are a subset of the prefixes of the column paths. eg. if the columns are ("Gene.primaryIdentifier", "Gene.secondaryIdentifier", "Gene.proteins.primaryIdentifier") return ("Gene", "Gene.proteins").
        Parameters:
        pathQuery - the query to look for paths in
        Returns:
        a list of Paths that have sequence

      • getOrganisms

        public static java.util.Set<java.lang.String> getOrganisms​(org.intermine.pathquery.PathQuery pathQuery,
                                                           javax.servlet.http.HttpSession session)
        Get organism info from PathQuery
        Parameters:
        pathQuery - PathQuery
        session - http session
        Returns:
        set of organisms

      • getOrganisms

        public static java.util.Set<java.lang.String> getOrganisms​(org.intermine.pathquery.PathQuery pathQuery,
                                                           org.intermine.api.InterMineAPI im,
                                                           org.intermine.api.profile.Profile profile)
        Parameters:
        pathQuery - query
        im - API
        profile - userprofile
        Returns:
        set of organism short names

      • isValidFastaQuery

        public static void isValidFastaQuery​(org.intermine.pathquery.PathQuery pq)
        Parameters:
        pq - pathquery

      • isValidSequenceFeatureQuery

        public static void isValidSequenceFeatureQuery​(org.intermine.pathquery.PathQuery pq)
        true if valid feature
        Parameters:
        pq - pathquery

      • getTaxonIds

        public static java.util.Set<java.lang.String> getTaxonIds​(org.intermine.pathquery.PathQuery pathQuery,
                                                          javax.servlet.http.HttpSession session)
        Get organism taxon ids info from PathQuery
        Parameters:
        pathQuery - PathQuery
        session - http session
        Returns:
        set of organism taxon ids

      • getTaxonIds

        public static java.util.Set<java.lang.String> getTaxonIds​(org.intermine.pathquery.PathQuery pathQuery,
                                                          org.intermine.api.InterMineAPI im,
                                                          org.intermine.api.profile.Profile profile)
        Parameters:
        pathQuery - query
        im - API
        profile - userprofile
        Returns:
        set of taxon IDs