Examples of proteinToAminoAcidSequence()

Examples of au.org.intersect.samifier.domain.CodonTranslationTable.proteinToAminoAcidSequence()

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                    if (direction != 1) {
                        StringBuilder invertedReversedSequence = new StringBuilder(
                                StringUtils.replaceChars(nucleotideString,
                                        "ACGT", "TGCA")).reverse();
                        predictedAminoAcidSequence = translationTable
                                .proteinToAminoAcidSequence(invertedReversedSequence
                                        .toString());
                    } else {
                        predictedAminoAcidSequence = translationTable
                                .proteinToAminoAcidSequence(nucleotideString);
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Examples of au.org.intersect.samifier.domain.CodonTranslationTable.proteinToAminoAcidSequence()

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                                        "ACGT", "TGCA")).reverse();
                        predictedAminoAcidSequence = translationTable
                                .proteinToAminoAcidSequence(invertedReversedSequence
                                        .toString());
                    } else {
                        predictedAminoAcidSequence = translationTable
                                .proteinToAminoAcidSequence(nucleotideString);
                    }

                    if (!predictedAminoAcidSequence.equals(mascotPeptideString)) {
                        String samEntryStrng = new SAMEntry(resultName,
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Examples of au.org.intersect.samifier.domain.CodonTranslationTable.proteinToAminoAcidSequence()

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            }
            int modulo = protein.length() % GenomeConstant.BASES_PER_CODON;
            if (modulo != 0) {
                protein = protein.substring(0, protein.length() - modulo);
            }
            System.out.println(table.proteinToAminoAcidSequence(protein));
        } catch (Exception e) {
            System.err.println(e);
            System.exit(1);
        }
    }
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