lib/ensembl/variation/activerecord.rb in ensembl-0.0.4 vs lib/ensembl/variation/activerecord.rb in ensembl-0.0.5

@@ -45,11 +45,10 @@
       belongs_to :attrib_type
     end
 
     class AttribSet < ModelBase
       belongs_to :attrib
-
     end
 
     class AttribType < ModelBase
       has_many :attribs, class_name: 'Attrib'
       has_many :pheotype_feature_attrib
@@ -64,10 +63,36 @@
 
     class CompressedGenotypeVar < Connection
       belongs_to :variation
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
 
+      def individual_genotypes
+        nil if genotypes.nil?
+
+        # To decrease number of DB queries needed
+        # FIXME: Should be in GenotypeCodes class or should use caching
+        genotype_codes=genotype_code_ids.uniq.inject({}) { |hsh, gc_id | hsh[gc_id]=GenotypeCode.find gc_id;hsh  }
+
+        @igs||=unpacked_genotypes.map{|s| IndividualGenotype.new({ individual_id:  s[0],genotype_code_id:s[1]})}
+      end
+
+      def unpacked_genotypes
+        unpack_genotypes.each_slice(2).map{|sl| sl }
+      end
+
+      def individual_ids
+        unpack_genotypes.select.each_with_index{|str,i| i.even?}
+      end
+
+      def genotype_code_ids
+        unpack_genotypes.select.each_with_index{|str,i| i.odd?}
+      end
+
+      protected
+      def unpack_genotypes
+        @g_unpacked||=genotypes.unpack('ww*') unless genotypes.nil?
+      end
     end
 
     class CoordSystem < ModelBase
     end
 
@@ -93,12 +118,12 @@
       has_one :failed_description
 
     end
 
     class GenotypeCode < ModelBase
+
       belongs_to :allele_code
-      belongs_to :genotype_code
 
     end
 
     class Individual < ModelBase
       belongs_to :individual_type
@@ -175,33 +200,30 @@
     end
 
     class PhenotypeFeatureAttrib < Connection
       belongs_to :attrib_type
       belongs_to :phenotype_feature
-
     end
 
     class Population < ModelBase
       self.extend Ensembl::SearchByName
 
-      has_many :population_synonyms
-      #has_many :synonyms, through: :population_synonyms, source: :synonym
       has_many :alleles
+      has_many :population_synonyms
 
       has_many :individual_populations
       has_many :individuals, through: :individual_populations
 
-      has_many :population_structures, foreign_key: 'super_population_id'
+      has_many :sub_population_structures, foreign_key: 'super_population_id', class_name: 'PopulationStructure'
       has_many :sub_populations, through: :population_structures, source: :sub_population
-      has_many :parents, through: :population_structures, source: :super_populaton#, foreign_key: 'sub_population_id'
 
+      has_many :super_population_structures, foreign_key: 'sub_population_id', class_name: 'PopulationStructure'
+      has_many :super_populations, through: :population_structures, source: :super_populaton
+
       has_many :population_genotypes
 
-      def parent
-        ps=PopulationStructure.find_by(sub_population: id)
-        ps.super_population unless ps.nil?
-      end
+      scope :displayable, -> { where(display:'LD')}
 
       def all_individual_populations
         IndividualPopulation.where(population_id: sub_population_ids(self)<<id)
       end
 
@@ -231,12 +253,12 @@
 
     class PopulationGenotype < ModelBase
       belongs_to :variation
       belongs_to :population
       belongs_to :subsnp_handle, foreign_key: 'subsnp_id'
-
       belongs_to :genotype_code
+
       has_one :allele_code, through: :genotype_code
     end
 
     class PopulationStructure < Connection
       belongs_to :super_population, foreign_key: 'super_population_id', class_name: 'Population'
@@ -307,14 +329,14 @@
     end
 
     class StructuralVariationSample < ModelBase
       belongs_to :structural_variation
       belongs_to :individual
+      belongs_to :strain, foreign_key: 'strain_id', class_name: 'Individual'
     end
 
     class Source < ModelBase
-
     end
 
     class Study < ModelBase
       has_many :associate_studies, foreign_key: 'study1_id'
       has_many :associated_studies, through: :associate_studies, source: :associated_study
@@ -447,10 +469,9 @@
       self.extend Ensembl::SearchByName
 
       belongs_to :short_name, foreign_key: 'short_name_attrib_id', class_name: 'Attrib'
       has_many :structural_variations
 
-      #has_many :variation_set_structures, foreign_key: 'variation_set_super'
       has_many :sub_variation_set_structures, foreign_key: 'variation_set_super', class_name: 'VariationSetStructure'
       has_many :sub_variation_sets, through: :sub_variation_set_structures , source: :sub_variation_set
 
       has_many :super_variation_set_structures, foreign_key: 'variation_set_sub', class_name: 'VariationSetStructure'
       has_many :super_variation_sets, through: :super_variation_set_structures , source: :super_variation_set
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