nathandunn

if (the_mRNA.length() > 3) {
      // Find the first start codon
      int start_index = the_mRNA.indexOf(standard_start_codon);
      while (start_index >= 0) {
        String aa = getTrimmedAA(get_ORF(the_mRNA, start_index, -1), 
                                 start_index);
        if (aa.length() > longest_peptide.length()) {
          longest_peptide = aa;
          best_start_index = start_index;
        }

nathandunn

public void setLongestORF(Transcript transcript, SequenceUtil.TranslationTable translationTable, boolean allowPartialExtension, boolean readThroughStopCodon) {
        String mrna = getSession().getResiduesWithAlterationsAndFrameshifts(transcript);
        if (mrna == null || mrna.equals("null")) {
            return;
        }
        String longestPeptide = "";
        int bestStartIndex = -1;
        int bestStopIndex = -1;
        boolean partialStop = false;