@Override public EntityType getEntityType() { EntityType entityType = entityTypeFactory.create(NAME); entityType.addAttribute(attributeFactory.create().setName(OMIM_GENE_SYMBOLS_COL_NAME), ROLE_ID); entityType.addAttribute(attributeFactory.create().setName(OMIM_PHENOTYPE_COL_NAME)); entityType.addAttribute(attributeFactory.create().setName(OMIM_MIM_NUMBER_COL_NAME)); entityType.addAttribute(attributeFactory.create().setName(OMIM_CYTO_LOCATION_COL_NAME)); entityType.addAttribute(attributeFactory.create().setName(OMIM_ENTRY_COL_NAME)); entityType.addAttribute(attributeFactory.create().setName(OMIM_TYPE_COL_NAME)); return entityType; }
private List<Attribute> createFitconOutputAttributes() { List<Attribute> attributes = newArrayList(); Attribute fitcon_score = attributeFactory.create() .setName(FITCON_SCORE) .setDataType(STRING) .setDescription( "fitness consequence score annotation of genetic variants using Fitcon scoring.") .setLabel(FITCON_SCORE_LABEL); attributes.add(fitcon_score); return attributes; }
public Attribute getHgvsPAttr() { return attributeFactory.create() .setName(HGVS_P) .setDataType(STRING) .setDescription( "If variant is coding, this field describes the variant using HGVS notation (Protein level). Since transcript ID is already mentioned in ‘feature ID’, it may be omitted here.(source:http://snpeff.sourceforge.net)"); }
public Attribute getCdsPositionAttr() { return attributeFactory.create() .setName(CDS_POSITION) .setDataType(STRING) .setDescription( "Position and number of coding bases (one based includes START and STOP codons)(source:http://snpeff.sourceforge.net)"); }
public Attribute getCdnaPositionAttr() { return attributeFactory.create() .setName(C_DNA_POSITION) .setDataType(STRING) .setDescription( "Position in cDNA and trancript’s cDNA length (one based)(source:http://snpeff.sourceforge.net)"); }
public Attribute getErrorsAttr() { return attributeFactory.create() .setName(ERRORS) .setDataType(STRING) .setDescription( "Add errors, warnings oErrors, Warnings or Information messages: Add errors, warnings or r informative message that can affect annotation accuracy. It can be added using either ‘codes’ (as shown in column 1, e.g. W1) or ‘message types’ (as shown in column 2, e.g. WARNING_REF_DOES_NOT_MATCH_GENOME). All these errors, warnings or information messages messages are optional.(source:http://snpeff.sourceforge.net)"); }
private Attribute createIdAttribute() { Attribute idAttribute = attributeFactory.create(); idAttribute.setName(ID_ATTR_NAME); idAttribute.setAuto(true); idAttribute.setIdAttribute(true); return idAttribute; }
public Attribute getAltAttr() { return attributeFactory.create() .setName(ALT) .setDataType(TEXT) .setDescription("The alternative allele on which this EFFECT applies"); } }
public Attribute getTypeAttr() { return attributeFactory.create() .setName(OMIM_ENTRY) .setDataType(TEXT) .setDescription("Number that represents the MIM database dataType for the phenotype") .setLabel("OMIM_Entry"); }
public Attribute getAnnotationAttr() { return attributeFactory.create() .setName(ANNOTATION) .setDataType(STRING) .setDescription( "Annotated using Sequence Ontology terms. Multiple effects can be concatenated using ‘&’ (source:http://snpeff.sourceforge.net)") .setAggregatable(true); }
public Attribute getGeneIdAttr() { return attributeFactory.create() .setName(GENE_ID) .setDataType(STRING) .setDescription("Gene ID") .setAggregatable(true); }
public Attribute getGeneNameAttr() { return attributeFactory.create() .setName(GENE_NAME) .setDataType(STRING) .setDescription( "Common gene name (HGNC). Optional: use closest gene when the variant is “intergenic”(source:http://snpeff.sourceforge.net)") .setAggregatable(true); }
public Attribute getPutativeImpactAttr() { return attributeFactory.create() .setName(PUTATIVE_IMPACT) .setDataType(STRING) .setDescription( "A simple estimation of putative impact / deleteriousness : {HIGH, MODERATE, LOW, MODIFIER}(source:http://snpeff.sourceforge.net)") .setAggregatable(true); }
public static Attribute getExacAcHomAttr(AttributeFactory attributeFactory) { return attributeFactory.create() .setName(EXAC_AC_HOM) .setDataType(STRING) .setDescription("The ExAC homozygous alternative genotype count") .setLabel(EXAC_AC_HOM_LABEL); }
public Attribute getPhenotypeAttr() { return attributeFactory.create() .setName(OMIM_DISORDER) .setDataType(TEXT) .setDescription("OMIM phenotype") .setLabel("OMIM_Disorders"); }
public EntityType getEntityType() { if (entityType == null) { entityType = entityTypeFactory.create(sheetName); for (String attrName : new CsvIterator(file, sheetName, null, separator).getColNamesMap().keySet()) { Attribute attr = attrMetaFactory.create().setName(attrName).setDataType(STRING); entityType.addAttribute(attr); } } return entityType; }
private EntityType createEffectsEntityType(ArrayList<Attribute> effectFieldAttributeList, String effectEntityName, List<Attribute> annotatorAttributes) { EntityType effectsEntityType = entityTypeFactory.create().setName(effectEntityName); effectsEntityType.addAttribute(attributeFactory.create().setName("identifier").setAuto(true).setVisible(false), EntityType.AttributeRole.ROLE_ID); effectsEntityType.addAttributes(effectFieldAttributeList); addAnnotatorAttributes(annotatorAttributes, effectsEntityType); effectsEntityType.addAttribute(attributeFactory.create().setName(VARIANT).setDataType(XREF)); return effectsEntityType; }
private void createResultEntityType(Entity effect, EntityType variantEMD) { if (vcfVariantEntityType == null || effectEntityType == null) { effectEntityType = effect.getEntityType(); vcfVariantEntityType = EntityType.newInstance(variantEMD); vcfVariantEntityType.addAttribute( attributeFactory.create().setName(EFFECT).setDataType(MREF).setRefEntity(effectEntityType)); } }
private void createResultEntityType(Entity effect, EntityType variantEMD) { if (vcfVariantEntityType == null || effectEntityType == null) { effectEntityType = effect.getEntityType(); vcfVariantEntityType = EntityType.newInstance(variantEMD); vcfVariantEntityType.addAttribute( attributeFactory.create().setName(EFFECT).setDataType(MREF).setRefEntity(effectEntityType)); } }
@Override public void init() { AnnotatorInfo info = getAnnotatorInfo(); QueryCreator queryCreator = new AttributeEqualsQueryCreator( attributeFactory.create().setName(GENE.getAttributeName())); ResultFilter resultFilter = new FirstResultFilter(); EntityAnnotator entityAnnotator = new CGDEntityAnnotator(CGD_RESOURCE, info, queryCreator, resultFilter, dataService, resources); annotator.init(entityAnnotator); }