@@ -0,0 +1,1805 @@
+/**%0A * Copyright %C2%A9 2011-2013 EMBL - European Bioinformatics Institute%0A * %0A * Licensed under the Apache License, Version 2.0 (the %22License%22); %0A * you may not use this file except in compliance with the License.  %0A * You may obtain a copy of the License at%0A *%0A *     http://www.apache.org/licenses/LICENSE-2.0%0A *%0A * Unless required by applicable law or agreed to in writing, software%0A * distributed under the License is distributed on an %22AS IS%22 BASIS,%0A * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.%0A * See the License for the specific language governing permissions and%0A * limitations under the License.%0A */%0Apackage uk.ac.ebi.phenotype.dao;%0A%0Aimport java.util.List;%0A%0Aimport uk.ac.ebi.phenotype.pojo.BiologicalModel;%0Aimport uk.ac.ebi.phenotype.pojo.CategoricalResult;%0Aimport uk.ac.ebi.phenotype.pojo.Organisation;%0Aimport uk.ac.ebi.phenotype.pojo.Parameter;%0Aimport uk.ac.ebi.phenotype.pojo.SexType;%0Aimport uk.ac.ebi.phenotype.pojo.ZygosityType;%0A%0Apublic interface CategoricalStatisticsDAO %7B%0A%0A%09public List%3CString%3E getCategories(Parameter parameter);%0A%0A%09public Long countControl(SexType sex, Parameter parameter, String category, Integer populationId);%0A%09public Long countMutant(SexType sex, ZygosityType zygosity, Parameter parameter, String category, Integer populationId);%0A%09%0A%09public BiologicalModel getControlBiologicalModelByPopulation(Integer populationId);%0A%09public BiologicalModel getMutantBiologicalModelByPopulation(Integer populationId);%0A%0A%09public Organisation getOrganisationByPopulation(Integer populationId);%0A%09public List%3CInteger%3E getPopulationIdsByParameter(Parameter parameter);%0A%0A%09public void saveCategoricalResult(CategoricalResult result);%0A%0A%09public SexType getSexByPopulation(Integer populationId);%0A%09public ZygosityType getZygosityByPopulation(Integer populationId);%0A%0A%7D%0A

add methods to get gender and zygosity from population id updates required for the new categorical database schema clean up app config a little update control (don't use zygosity) make DAO methods more general; use biological model instead of genomic feature to query mutants add more general methods for passing in the correct values rather than a method for every combination add classes and test for pulling out categorical data by parameter