Examples of com.compomics.util.experiment.annotation.gene.GeneFactory

                genePreferences.loadSpeciesAndGoDomains();
                genePreferences.setCurrentSpecies(cliInputBean.getSpecies());
                genePreferences.setCurrentSpeciesType(cliInputBean.getSpeciesType());


                // try to download gene and go information
                GeneFactory geneFactory = GeneFactory.getInstance();


                String currentEnsemblSpeciesType = cliInputBean.getSpeciesType().toLowerCase();
                if (currentEnsemblSpeciesType.equalsIgnoreCase("Vertebrates")) {
                    currentEnsemblSpeciesType = "ensembl";
                }


                Integer latestEnsemblVersion = geneFactory.getCurrentEnsemblVersion(currentEnsemblSpeciesType);


                String selectedSpecies = cliInputBean.getSpecies();
                String selectedDb = genePreferences.getEnsemblDatabaseName(cliInputBean.getSpeciesType(), selectedSpecies);
                String currentEnsemblVersionAsString = genePreferences.getEnsemblVersion(selectedDb);

                return proteinMatch.getMainMatch();
            case protein_description:
                return SequenceFactory.getInstance().getHeader(proteinMatch.getMainMatch()).getSimpleProteinDescription();
            case ensembl_gene_id:
                if (!proteinMatch.isDecoy()) {
                    GeneFactory geneFactory = GeneFactory.getInstance();
                    String geneName = geneFactory.getGeneNameForUniProtProtein(proteinMatch.getMainMatch());
                    if (geneName != null) {
                        String ensemblId = geneFactory.getGeneEnsemblId(geneName);
                        if (ensemblId != null) {
                            return ensemblId;
                        }
                    }
                }
                return "";
            case gene_name:
                if (!proteinMatch.isDecoy()) {
                    GeneFactory geneFactory = GeneFactory.getInstance();
                    String geneName = geneFactory.getGeneNameForUniProtProtein(proteinMatch.getMainMatch());
                    if (geneName != null) {
                        return geneName;
                    }
                }
                return "";
            case chromosome:
                if (!proteinMatch.isDecoy()) {
                    GeneFactory geneFactory = GeneFactory.getInstance();
                    String geneName = geneFactory.getGeneNameForUniProtProtein(proteinMatch.getMainMatch());
                    if (geneName != null) {
                        String chromosome = geneFactory.getChromosomeForGeneName(geneName);
                        if (chromosome != null) {
                            return chromosome;
                        }
                    }
                }

Examples of com.compomics.util.experiment.annotation.gene.GeneFactory

Related Classes of com.compomics.util.experiment.annotation.gene.GeneFactory