Source:
public ResponseEntity<List<Alteration>> variantsLookupGet( @ApiParam(value = "The entrez gene ID. entrezGeneId is prioritize than hugoSymbol if both parameters have been defined") @RequestParam(value = "entrezGeneId", required = false) Integer entrezGeneId , @ApiParam(value = "The gene symbol used in Human Genome Organisation.") @RequestParam(value = "hugoSymbol", required = false) String hugoSymbol , @ApiParam(value = "variant name.") @RequestParam(value = "variant", required = false) String variant , @ApiParam(value = "") @RequestParam(value = "variantType", required = false) String variantType , @ApiParam(value = "") @RequestParam(value = "consequence", required = false) String consequence , @ApiParam(value = "") @RequestParam(value = "proteinStart", required = false) Integer proteinStart , @ApiParam(value = "") @RequestParam(value = "proteinEnd", required = false) Integer proteinEnd ) { HttpStatus httpStatus = HttpStatus.OK; List<Alteration> alterationList = new ArrayList<>(); if (hugoSymbol != null || entrezGeneId != null) { Gene gene = GeneUtils.getGene(entrezGeneId, hugoSymbol); if (gene != null) { Set<Alteration> allAlterations = AlterationUtils.getAllAlterations(gene); if (variant == null && proteinStart == null && proteinEnd == null) { alterationList.addAll(allAlterations); } else { AlterationBo alterationBo = new ApplicationContextSingleton().getAlterationBo(); Alteration alteration = AlterationUtils.getAlteration(gene.getHugoSymbol(), variant, variantType, consequence, proteinStart, proteinEnd); alterationList.addAll(alterationBo.findRelevantAlterations(alteration, new ArrayList<Alteration>(AlterationUtils.getAllAlterations(gene)))); } } } else if (variant != null) { alterationList = AlterationUtils.lookupVariant(variant, false, AlterationUtils.getAllAlterations()); } return new ResponseEntity<>(alterationList, HttpStatus.OK); }

Target:
public ResponseEntity<List<Alteration>> variantsLookupGet( @ApiParam(value = "The entrez gene ID. entrezGeneId is prioritize than hugoSymbol if both parameters have been defined") @RequestParam(value = "entrezGeneId", required = false) Integer entrezGeneId , @ApiParam(value = "The gene symbol used in Human Genome Organisation.") @RequestParam(value = "hugoSymbol", required = false) String hugoSymbol , @ApiParam(value = "variant name.") @RequestParam(value = "variant", required = false) String variant , @ApiParam(value = "") @RequestParam(value = "variantType", required = false) String variantType , @ApiParam(value = "") @RequestParam(value = "consequence", required = false) String consequence , @ApiParam(value = "") @RequestParam(value = "proteinStart", required = false) Integer proteinStart , @ApiParam(value = "") @RequestParam(value = "proteinEnd", required = false) Integer proteinEnd ) { HttpStatus httpStatus = HttpStatus.OK; List<Alteration> alterationList = new ArrayList<>(); if (hugoSymbol != null || entrezGeneId != null) { Gene gene = GeneUtils.getGene(entrezGeneId, hugoSymbol); if (gene != null) { Set<Alteration> allAlterations = AlterationUtils.getAllAlterations(gene); if (variant == null && proteinStart == null && proteinEnd == null) { alterationList.addAll(allAlterations); } else { AlterationBo alterationBo = new ApplicationContextSingleton().getAlterationBo(); Alteration alteration = AlterationUtils.getAlteration(gene.getHugoSymbol(), variant, variantType, consequence, proteinStart, proteinEnd); alterationList.addAll(alterationBo.findRelevantAlterations(alteration, new ArrayList<Alteration>(allAlterations))); } } } else if (variant != null) { alterationList = AlterationUtils.lookupVariant(variant, false, AlterationUtils.getAllAlterations()); } return new ResponseEntity<>(alterationList, HttpStatus.OK); }