private void handleShowPrevExon(Tuple request) { SearchService searchService = ServiceLocator.instance().getSearchService(); ExonDTO exonDTO = searchService.findPrevExon(request.getInt("exon_id")); request.set("__action", "showExon"); request.set("exon_id", exonDTO.getId()); this.handleShowExon(request); }
@SuppressWarnings("unchecked") @Override protected void populateExpertSearchForm() { PhenoService phenoService = ServiceLocator.instance().getPhenoService(); SearchService searchService = ServiceLocator.instance().getSearchService(); Container expertSearchForm = this.getModel().getExpertSearchFormWrapper().getForm(); ((HiddenInput) expertSearchForm.get("__target")).setValue(this.getName()); ((HiddenInput) expertSearchForm.get("select")).setValue(this.getName()); if (this.getModel().getMutationSearchCriteriaVO().getVariation() != null) ((TextLineInput<String>) expertSearchForm.get("variation")) .setValue(this.getModel().getMutationSearchCriteriaVO().getVariation()); if (this.getModel().getMutationSearchCriteriaVO().getCdnaPosition() != null) ((IntInput) expertSearchForm.get("nuclno")) .setValue(this.getModel().getMutationSearchCriteriaVO().getCdnaPosition()); if (this.getModel().getMutationSearchCriteriaVO().getCodonNumber() != null) ((IntInput) expertSearchForm.get("aano")) .setValue(this.getModel().getMutationSearchCriteriaVO().getCodonNumber()); List<ValueLabel> exonIdOptions = new ArrayList<ValueLabel>(); exonIdOptions.add(new ValueLabel("", "Select")); for (ExonDTO exonSummaryVO : searchService.findAllExons()) exonIdOptions.add(new ValueLabel(exonSummaryVO.getId(), exonSummaryVO.getName())); ((SelectInput) expertSearchForm.get("exon_id")).setOptions(exonIdOptions); if (this.getModel().getMutationSearchCriteriaVO().getExonId() != null) ((SelectInput) expertSearchForm.get("exon_id")) .setValue(this.getModel().getMutationSearchCriteriaVO().getExonId()); else ((SelectInput) expertSearchForm.get("exon_id")).setValue("Select"); List<ValueLabel> typeOptions = new ArrayList<ValueLabel>(); typeOptions.add(0, new ValueLabel("", "Select")); for (String mutationType : phenoService.findObservedValues("Type of mutation")) typeOptions.add(new ValueLabel(mutationType, mutationType)); ((SelectInput) expertSearchForm.get("type")).setOptions(typeOptions); if (this.getModel().getMutationSearchCriteriaVO().getType() != null) ((SelectInput) expertSearchForm.get("type")) .setValue(this.getModel().getMutationSearchCriteriaVO().getType()); else ((SelectInput) expertSearchForm.get("type")).setValue("Select"); List<ValueLabel> phenotypeOptions = new ArrayList<ValueLabel>(); phenotypeOptions.add(new ValueLabel("", "Select")); for (String phenotypeName : phenoService.findObservedValues("Onset")) phenotypeOptions.add(new ValueLabel(phenotypeName, phenotypeName)); ((SelectInput) expertSearchForm.get("phenotype")).setOptions(phenotypeOptions); if (this.getModel().getMutationSearchCriteriaVO().getPhenotypeId() != null) ((SelectInput) expertSearchForm.get("phenotype")) .setValue(this.getModel().getMutationSearchCriteriaVO().getPhenotypeId()); else ((SelectInput) expertSearchForm.get("phenotype")).setValue("Select"); }
protected void populateExpertSearchForm() { PhenoService phenoService = ServiceLocator.instance().getPhenoService(); SearchService searchService = ServiceLocator.instance().getSearchService(); Container expertSearchForm = this.getModel().getExpertSearchFormWrapper().getForm(); expertSearchForm.get("__target").setValue(this.getName()); expertSearchForm.get("select").setValue(this.getName()); if (this.getModel().getMutationSearchCriteriaVO().getVariation() != null) ((TextLineInput) expertSearchForm.get("variation")) .setValue(this.getModel().getMutationSearchCriteriaVO().getVariation()); if (this.getModel().getMutationSearchCriteriaVO().getCdnaPosition() != null) ((IntInput) expertSearchForm.get("nuclno")) .setValue(this.getModel().getMutationSearchCriteriaVO().getCdnaPosition()); if (this.getModel().getMutationSearchCriteriaVO().getCodonNumber() != null) ((IntInput) expertSearchForm.get("aano")) .setValue(this.getModel().getMutationSearchCriteriaVO().getCodonNumber()); List<ValueLabel> exonIdOptions = new ArrayList<ValueLabel>(); exonIdOptions.add(new ValueLabel("", "Select")); for (ExonDTO exonSummaryVO : searchService.findAllExons()) exonIdOptions.add(new ValueLabel(exonSummaryVO.getId(), exonSummaryVO.getName())); ((SelectInput) expertSearchForm.get("exon_id")).setOptions(exonIdOptions); if (this.getModel().getMutationSearchCriteriaVO().getExonId() != null) ((SelectInput) expertSearchForm.get("exon_id")) .setValue(this.getModel().getMutationSearchCriteriaVO().getExonId()); else ((SelectInput) expertSearchForm.get("exon_id")).setValue("Select"); List<ValueLabel> typeOptions = new ArrayList<ValueLabel>(); typeOptions.add(0, new ValueLabel("", "Select")); for (String mutationType : phenoService.findObservedValues("Type of mutation")) typeOptions.add(new ValueLabel(mutationType, mutationType)); ((SelectInput) expertSearchForm.get("type")).setOptions(typeOptions); if (this.getModel().getMutationSearchCriteriaVO().getType() != null) ((SelectInput) expertSearchForm.get("type")) .setValue(this.getModel().getMutationSearchCriteriaVO().getType()); else ((SelectInput) expertSearchForm.get("type")).setValue("Select"); List<ValueLabel> consequenceOptions = new ArrayList<ValueLabel>(); consequenceOptions.add(0, new ValueLabel("", "Select")); for (String consequence : phenoService.findObservedValues("consequence")) consequenceOptions.add(new ValueLabel(consequence, consequence)); ((SelectInput) expertSearchForm.get("consequence")).setOptions(consequenceOptions); if (this.getModel().getMutationSearchCriteriaVO().getConsequence() != null) ((SelectInput) expertSearchForm.get("consequence")) .setValue(this.getModel().getMutationSearchCriteriaVO().getConsequence()); else ((SelectInput) expertSearchForm.get("consequence")).setValue("Select"); List<ValueLabel> domainOptions = new ArrayList<ValueLabel>(); domainOptions.add(new ValueLabel("", "Select")); for (ProteinDomainDTO domainVO : searchService.findAllProteinDomains()) domainOptions.add(new ValueLabel(domainVO.getDomainId(), domainVO.getDomainName())); ((SelectInput) expertSearchForm.get("domain_id")).setOptions(domainOptions); if (this.getModel().getMutationSearchCriteriaVO().getProteinDomainId() != null) ((SelectInput) expertSearchForm.get("domain_id")) .setValue(this.getModel().getMutationSearchCriteriaVO().getProteinDomainId()); else ((SelectInput) expertSearchForm.get("domain_id")).setValue("Select"); List<ValueLabel> phenotypeOptions = new ArrayList<ValueLabel>(); phenotypeOptions.add(new ValueLabel("", "Select")); for (String phenotypeName : phenoService.findObservedValues("Phenotype")) phenotypeOptions.add(new ValueLabel(phenotypeName, phenotypeName)); ((SelectInput) expertSearchForm.get("phenotype")).setOptions(phenotypeOptions); if (this.getModel().getMutationSearchCriteriaVO().getPhenotypeId() != null) ((SelectInput) expertSearchForm.get("phenotype")) .setValue(this.getModel().getMutationSearchCriteriaVO().getPhenotypeId()); else ((SelectInput) expertSearchForm.get("phenotype")).setValue("Select"); List<ValueLabel> inheritanceOptions = new ArrayList<ValueLabel>(); inheritanceOptions.add(0, new ValueLabel("", "Select")); for (String inheritance : phenoService.findObservedValues("Inheritance")) inheritanceOptions.add(new ValueLabel(inheritance, inheritance)); ((SelectInput) expertSearchForm.get("inheritance")).setOptions(inheritanceOptions); if (this.getModel().getMutationSearchCriteriaVO().getInheritance() != null) ((SelectInput) expertSearchForm.get("inheritance")) .setValue(this.getModel().getMutationSearchCriteriaVO().getInheritance()); else ((SelectInput) expertSearchForm.get("inheritance")).setValue("Select"); }
private void handleShowFirstExon(Tuple request) { SearchService searchService = ServiceLocator.instance().getSearchService(); ExonDTO exonDTO = searchService.findFirstExon(); request.set("exon_id", exonDTO.getId()); this.handleShowExon(request); }
/** * Get the gDNA position. * * @param position * @param exon * @return gDNA position * @throws RESyntaxException */ public static int getGDNAPosition(String position, ExonDTO exonDTO) { Pattern reExon = Pattern.compile("^(\\d+)$"); Pattern reIntron = Pattern.compile("^(\\d+)([+-])(\\d+)$"); Matcher mExon = reExon.matcher(position); Matcher mIntron = reIntron.matcher(position); if (mExon.matches()) { if ("R".equals(exonDTO.getOrientation())) { // exon.gDNA - (mutation.cDNA - exon.cDNA) return Math.abs( exonDTO.getGdnaStart() - (Integer.valueOf(mExon.group(1)) - exonDTO.getCdnaStart())); } else { // exon.gDNA + (mutation.cDNA - exon.cDNA) return Math.abs( exonDTO.getGdnaStart() + (Integer.valueOf(mExon.group(1)) - exonDTO.getCdnaStart())); } } else if (mIntron.matches()) { if (mIntron.group(2).equals("+")) { if ("R".equals(exonDTO.getOrientation())) { // intron.gdnaPos + 1 (back to exon) - difference ('+' means // downstream) return Math.abs(exonDTO.getGdnaStart() + 1 - Integer.valueOf(mIntron.group(3))); } else { // intron.gdnaPos - 1 (start at last position of exon) + // difference ('+' means upstream) return Math.abs(exonDTO.getGdnaStart() - 1 + Integer.valueOf(mIntron.group(3))); } } else { if ("R".equals(exonDTO.getOrientation())) { // intron.gdnaPos - intron.length + difference ('-' means // upstream) return Math.abs( exonDTO.getGdnaStart() - exonDTO.getLength() + Integer.valueOf(mIntron.group(3))); } else { // intron.gdnaPos - difference ('-' means downstream) return Math.abs(exonDTO.getGdnaStart() - Integer.valueOf(mIntron.group(3))); } } } else return 0; }