consequenceType.setCodon(String.valueOf(formattedReferenceCodon1Array) + "/" + String.valueOf(modifiedCodonArray).toUpperCase()); String modifiedCodon = String.valueOf(modifiedCodonArray);
protected boolean setInsertionAlleleAminoacidChange(String referenceCodon, char[] modifiedCodonArray, char[] formattedReferenceCodonArray, char[] formattedModifiedCodonArray, boolean useMitochondrialCode, boolean firstCodon) { // Set codon str, protein ref and protein alt ONLY for the first codon mofified by the insertion if (firstCodon) { firstCodon = false; // Only the exact codon where the deletion starts is set consequenceType.setCodon(String.valueOf(formattedReferenceCodonArray) + "/" + String.valueOf(formattedModifiedCodonArray)); // Assumes proteinVariantAnnotation attribute is already initialized consequenceType .getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, String.valueOf(modifiedCodonArray))); } return firstCodon; }
consequenceType.setCodon(String.valueOf(formattedReferenceCodon1Array) + "/" + String.valueOf(modifiedCodonArray).toUpperCase()); String modifiedCodon = String.valueOf(modifiedCodonArray);
protected boolean setInsertionAlleleAminoacidChange(String referenceCodon, char[] modifiedCodonArray, char[] formattedReferenceCodonArray, char[] formattedModifiedCodonArray, boolean useMitochondrialCode, boolean firstCodon) { // Set codon str, protein ref and protein alt ONLY for the first codon mofified by the insertion if (firstCodon) { firstCodon = false; // Only the exact codon where the deletion starts is set consequenceType.setCodon(String.valueOf(formattedReferenceCodonArray) + "/" + String.valueOf(formattedModifiedCodonArray)); // Assumes proteinVariantAnnotation attribute is already initialized consequenceType .getProteinVariantAnnotation() .setReference(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, referenceCodon)); consequenceType .getProteinVariantAnnotation() .setAlternate(VariantAnnotationUtils.getAminoacid(useMitochondrialCode, String.valueOf(modifiedCodonArray))); } return firstCodon; }
modifiedCodonArray = String.valueOf(modifiedCodonArray).toLowerCase().toCharArray(); modifiedCodonArray[variantPhaseShift] = Character.toUpperCase(modifiedCodonArray[variantPhaseShift]); consequenceType.setCodon(String.valueOf(referenceCodonArray) + "/" + String.valueOf(modifiedCodonArray));
modifiedCodonArray = String.valueOf(modifiedCodonArray).toLowerCase().toCharArray(); modifiedCodonArray[variantPhaseShift] = Character.toUpperCase(modifiedCodonArray[variantPhaseShift]); consequenceType.setCodon(String.valueOf(referenceCodonArray) + "/" + String.valueOf(modifiedCodonArray));
modifiedCodonArray = String.valueOf(modifiedCodonArray).toLowerCase().toCharArray(); modifiedCodonArray[variantPhaseShift] = Character.toUpperCase(modifiedCodonArray[variantPhaseShift]); consequenceType.setCodon(String.valueOf(referenceCodonArray) + "/" + String.valueOf(modifiedCodonArray));
modifiedCodonArray = String.valueOf(modifiedCodonArray).toLowerCase().toCharArray(); modifiedCodonArray[variantPhaseShift] = Character.toUpperCase(modifiedCodonArray[variantPhaseShift]); consequenceType.setCodon(String.valueOf(referenceCodonArray) + "/" + String.valueOf(modifiedCodonArray));
private void parseRemainingFields(ConsequenceType consequenceType, String[] lineFields) { consequenceType.setEnsemblGeneId(lineFields[3]); // fill Ensembl gene id consequenceType.setEnsemblTranscriptId(lineFields[4]); // fill Ensembl transcript id ProteinVariantAnnotation proteinVariantAnnotation = new ProteinVariantAnnotation(); if(!lineFields[7].equals("-")) { consequenceType.setCdnaPosition(parseStringInterval(lineFields[7])); // fill cdna position } if(!lineFields[8].equals("-")) { consequenceType.setCdsPosition(parseStringInterval(lineFields[8])); // fill cds position } if(!lineFields[9].equals("-")) { proteinVariantAnnotation.setPosition(parseStringInterval(lineFields[9])); // fill aa position } if(!lineFields[10].equals("-")) { String parts[] = lineFields[10].split("/"); if(parts.length == 2) { proteinVariantAnnotation.setReference(parts[0]); // fill aa change proteinVariantAnnotation.setAlternate(parts[1]); // fill aa change } } consequenceType.setProteinVariantAnnotation(proteinVariantAnnotation); consequenceType.setCodon(lineFields[11]); // fill codon change if(!lineFields[6].equals("") && !lineFields.equals("-")) { // VEP may leave this field empty consequenceType.setSequenceOntologyTerms( getSequenceOntologyTerms(Arrays.asList(lineFields[6].split(",")))); // fill so terms // consequenceType.setSoTermsFromSoNames(Arrays.asList(lineFields[6].split(","))); // fill so terms } }
consequenceType.setCodon(String.valueOf(formattedReferenceCodon1Array) + "/" + String.valueOf(modifiedCodonArray).toUpperCase()); String modifiedCodon = String.valueOf(modifiedCodonArray);
consequenceType.setCodon(String.valueOf(formattedReferenceCodon1Array) + "/" + String.valueOf(modifiedCodonArray).toUpperCase()); String modifiedCodon = String.valueOf(modifiedCodonArray);
if (fields.length > 5) { consequenceType.setCodon(fields[5]);