old apollo setLongestORF

gistfile1.txt

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;

        if (mrna.length() > 3) {
            for (String startCodon : translationTable.getStartCodons()) {
                int startIndex = mrna.indexOf(startCodon);
                while (startIndex >= 0) {
                    String mrnaSubstring = mrna.substring(startIndex);
                    String aa = SequenceUtil.translateSequence(mrnaSubstring, translationTable, true, readThroughStopCodon);
                    if (aa.length() > longestPeptide.length()) {
                        longestPeptide = aa;
                        bestStartIndex = startIndex;
                        bestStopIndex = startIndex + (aa.length() * 3);
                        if (!longestPeptide.substring(longestPeptide.length() - 1).equals(SequenceUtil.TranslationTable.STOP)) {
                            partialStop = true;
                            bestStopIndex += mrnaSubstring.length() % 3;
                        }
                    }
                    startIndex = mrna.indexOf(startCodon, startIndex + 1);
                }
            }
        }

        Date date = new Date();

        if (transcript.getType().equals("sequence:mRNA")) {

            boolean needCdsIndex = transcript.getCDS() == null;
            CDS cds = transcript.getCDS();
            if (cds == null) {
                cds = createCDS(transcript);
                transcript.setCDS(cds);
            }
            if (bestStartIndex >= 0) {
                int fmin = getSession().convertModifiedLocalCoordinateToSourceCoordinate(transcript, bestStartIndex);
                int fmax = getSession().convertModifiedLocalCoordinateToSourceCoordinate(transcript, bestStopIndex);
                if (cds.getStrand().equals(-1)) {
                    int tmp = fmin;
                    fmin = fmax + 1;
                    fmax = tmp + 1;
                }
                cds.setFmin(fmin);
                cds.setFminPartial(false);
                cds.setFmax(fmax);
                cds.setFmaxPartial(partialStop);
            } else {
                cds.setFmin(transcript.getFmin());
                cds.setFminPartial(true);
                String aa = SequenceUtil.translateSequence(mrna, translationTable, true, readThroughStopCodon);
                if (aa.substring(aa.length() - 1).equals(SequenceUtil.TranslationTable.STOP)) {
                    cds.setFmax(getSession().convertModifiedLocalCoordinateToSourceCoordinate(transcript, aa.length() * 3));
                    cds.setFmaxPartial(false);
                } else {
                    cds.setFmax(transcript.getFmax());
                    cds.setFmaxPartial(true);
                }
            }
            if (readThroughStopCodon) {
                String aa = SequenceUtil.translateSequence(getSession().getResiduesWithAlterationsAndFrameshifts(cds), translationTable, true, true);
                int firstStopIndex = aa.indexOf(SequenceUtil.TranslationTable.STOP);
                if (firstStopIndex < aa.length() - 1) {
                    StopCodonReadThrough stopCodonReadThrough = createStopCodonReadThrough(cds);
                    cds.setStopCodonReadThrough(stopCodonReadThrough);
                    int offset = transcript.getStrand() == -1 ? -2 : 0;
                    stopCodonReadThrough.setFmin(getSession().convertModifiedLocalCoordinateToSourceCoordinate(cds, firstStopIndex * 3) + offset);
                    stopCodonReadThrough.setFmax(getSession().convertModifiedLocalCoordinateToSourceCoordinate(cds, firstStopIndex * 3) + 3 + offset);
                }
            } else {
                cds.deleteStopCodonReadThrough();
            }
            setManuallySetTranslationStart(cds, false);
            setManuallySetTranslationEnd(cds, false);