Package eu.isas.peptideshaker.gui.protein_sequence

Examples of eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation


                        if (ptmColor == null) {
                            ptmColor = Color.lightGray;
                        }

                        ArrayList<ResidueAnnotation> annotations = new ArrayList<ResidueAnnotation>(1);
                        annotations.add(new ResidueAnnotation(ptmName, null, false));
                        proteinTooltips.put(sparkLineDataSeriesPtm.size(), annotations);

                        data = new ArrayList<Double>(1);
                        data.add(new Double(1));
                        sparklineDataseriesPtm = new JSparklinesDataSeries(data, ptmColor, null);
View Full Code Here


                    annotation += ", " + Util.roundDouble(100 * lastP, 1) + "% chance of coverage";
                } else if (lastP > 0.01) {
                    annotation += ", possible to cover";
                }
                ArrayList<ResidueAnnotation> annotations = new ArrayList<ResidueAnnotation>(1);
                annotations.add(new ResidueAnnotation(annotation, null, false));
                for (int j = lastIndex; j < i; j++) {
                    residueAnnotation.put(j, new ArrayList<ResidueAnnotation>(annotations));
                }
                lastP = p;
                lastIndex = i;
            }
        }
        int i = coverage.length;
        String annotation = (lastIndex + 1) + "-" + (i);
        if (metrics.getPeptideLengthDistribution() != null) {
            annotation += ", " + Util.roundDouble(100 * lastP, 1) + "% chance of coverage";
        } else if (lastP > 0.01) {
            annotation += ", possible to cover";
        }
        ArrayList<ResidueAnnotation> annotations = new ArrayList<ResidueAnnotation>(1);
        annotations.add(new ResidueAnnotation(annotation, null, false));
        for (int j = lastIndex; j < i; j++) {
            residueAnnotation.put(j, new ArrayList<ResidueAnnotation>(annotations));
        }

        // batch load the required data
        identification.loadPeptideMatches(proteinMatch.getPeptideMatchesKeys(), null);

        for (String peptideKey : proteinMatch.getPeptideMatchesKeys()) {
            PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
            String peptideSequence = peptideMatch.getTheoreticPeptide().getSequence();
            boolean enzymaticPeptide = true;
            if (!allPeptides) {
                enzymaticPeptide = currentProtein.isEnzymaticPeptide(peptideSequence, searchParameters.getEnzyme(),
                        sequenceMatchingPreferences);
            }
            if (allPeptides || (enzymatic && enzymaticPeptide) || (!enzymatic && !enzymatic)) {
                String modifiedSequence = getTaggedPeptideSequence(peptideMatch, true, false, true);
                AminoAcidPattern aminoAcidPattern = new AminoAcidPattern(peptideSequence);
                ArrayList<Integer> startIndexes = aminoAcidPattern.getIndexes(sequence, sequenceMatchingPreferences);
                for (int index : startIndexes) {
                    int peptideTempStart = index;
                    int peptideTempEnd = peptideTempStart + peptideSequence.length();
                    ResidueAnnotation newAnnotation = new ResidueAnnotation(peptideTempStart + " - " + modifiedSequence + " - " + peptideTempEnd, peptideKey, true);
                    for (int j = peptideTempStart - 1; j < peptideTempEnd - 1; j++) {
                        annotations = residueAnnotation.get(j);
                        if (annotations == null) {
                            annotations = new ArrayList<ResidueAnnotation>();
                            residueAnnotation.put(j, annotations);
View Full Code Here

TOP

Related Classes of eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation

Copyright © 2018 www.massapicom. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.