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;
}