コード例 #1
0
        private List <double> getPeakStatistics()
        {
            IList <object[]> queryRows;

            lock (session)
            {
                var randomIds = session.CreateQuery("SELECT psm.Id " + viewFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch))
                                .List <long>()
                                .Shuffle()
                                .Take(1000)
                                .OrderBy(o => o);
                string randomIdSet = String.Join(",", randomIds.Select(o => o.ToString()).ToArray());
                queryRows = session.CreateQuery("SELECT psm.Spectrum.Source.Name, psm.Spectrum, psm, DISTINCT_GROUP_CONCAT(pm.Offset || ':' || mod.MonoMassDelta), psm.Peptide.Sequence " +
                                                "FROM PeptideSpectrumMatch psm " +
                                                "LEFT JOIN psm.Modifications pm " +
                                                "LEFT JOIN pm.Modification mod " +
                                                "WHERE psm.Id IN (" + randomIdSet + ") " +
                                                "GROUP BY psm.Spectrum.id ")
                            .List <object[]>();
            }
            var spectrumRows = queryRows.Select(o => new SpectrumRow(o)).OrderBy(o => o.SourceName);

            precursorScatterPlot.Clear();
            chargeReducedScatterPlot.Clear();

            int spectraCount = 0;

            string spectrumListFilters = String.Empty;

            Invoke(new MethodInvoker(() =>
            {
                spectrumListFilters = spectrumFiltersTextBox.Text;
                zedGraphControl.MasterPane.AxisChange();
                zedGraphControl.Refresh();
            }));

            var points = new PointPairList();

            string currentSourceName = null;
            string currentSourcePath = null;

            msdata.MSData msd = null;

            lock (owner)
                foreach (var row in spectrumRows)
                {
                    if (row.SourceName != currentSourceName)
                    {
                        currentSourceName = row.SourceName;
                        currentSourcePath = IDPickerForm.LocateSpectrumSource(currentSourceName, session.Connection.GetDataSource());
                        msd = new pwiz.CLI.msdata.MSDataFile(currentSourcePath);

                        //var param = session.Query<AnalysisParameter>().Where(o => o.Name == "SpectrumListFilters").Min(o => o.Value);
                        //string spectrumListFilters = String.IsNullOrEmpty(param) ? String.Empty : param;
                        SpectrumListFactory.wrap(msd, spectrumListFilters.Split(";".ToCharArray(), StringSplitOptions.RemoveEmptyEntries));
                    }

                    string label = String.Format("{0}/{1}\n{2}", row.SourceName, msdata.id.abbreviate(row.Spectrum.NativeID), row.ModifiedSequence);

                    var spectrumList = msd.run.spectrumList;

                    ++spectraCount;

                    var pwizPeptide = new proteome.Peptide(row.ModifiedSequence, proteome.ModificationParsing.ModificationParsing_Auto,
                                                           proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
                    var fragmentation = pwizPeptide.fragmentation(true, true);

                    var    pwizSpectrum = spectrumList.spectrum(spectrumList.find(row.Spectrum.NativeID), true);
                    var    pointMap     = new seems.PointMap(new ZedGraph.PointPairList(pwizSpectrum.getMZArray().data, pwizSpectrum.getIntensityArray().data));
                    double tic          = pointMap.Values.Sum();

                    double precursorMz = row.Spectrum.PrecursorMZ;
                    double chargeReducedPrecursorMz = precursorMz * row.PeptideSpectrumMatch.Charge;

                    bool plotMatchedPeaks   = true;
                    bool removeMatchedPeaks = false;

                    double tolerance = 0.03;
                    seems.PointMap.Enumerator itr;
                    IonSeries[] ionSeries = Enum.GetValues(typeof(IonSeries)).Cast <IonSeries>().Where(o => o != IonSeries.Count).ToArray();

                    for (int z = 1; z <= 1; ++z)
                    {
                        for (int length = 1, end = pwizPeptide.sequence.Length; length <= end; ++length)
                        {
                            string NTermFragment = row.ModifiedSequence.Substring(0, length);
                            string CTermFragment = row.ModifiedSequence.Substring(row.ModifiedSequence.Length - length);

                            foreach (IonSeries series in ionSeries)
                            {
                                if ((series == IonSeries.c || series == IonSeries.cMinus1 || series == IonSeries.x) &&
                                    length == pwizPeptide.sequence.Length)
                                {
                                    continue;
                                }

                                itr = pointMap.FindNear(fragmentMass(fragmentation, series, length, z), tolerance);
                                if (itr != null && itr.IsValid)
                                {
                                    if (plotMatchedPeaks)
                                    {
                                        precursorScatterPlot.AddPoint(new PointPair(itr.Current.Key - precursorMz, itr.Current.Value / tic, (int)series, String.Format("{0} {1}\n{2} {3} {4} {5}", label, precursorMz, NTermFragment, itr.Current.Key, IonSeriesLabels[(int)series], length)));
                                        chargeReducedScatterPlot.AddPoint(new PointPair(itr.Current.Key - chargeReducedPrecursorMz, itr.Current.Value / tic, (int)series, String.Format("{0} {1}\n{2} {3} {4} {5}", label, chargeReducedPrecursorMz, NTermFragment, itr.Current.Key, IonSeriesLabels[(int)series], length)));
                                    }

                                    if (removeMatchedPeaks)
                                    {
                                        pointMap.Remove(itr);
                                    }
                                }
                            }
                        }
                    }

                    foreach (var pair in pointMap)
                    {
                        precursorScatterPlot.AddPoint(new PointPair(pair.Key - precursorMz, pair.Value / tic, 0, label));
                        chargeReducedScatterPlot.AddPoint(new PointPair(pair.Key - chargeReducedPrecursorMz, pair.Value / tic, 0, label));
                    }

                    if ((spectraCount % 100) == 0)
                    {
                        Invoke(new MethodInvoker(() =>
                        {
                            zedGraphControl.MasterPane.AxisChange();
                            zedGraphControl.Refresh();
                        }));
                    }
                }

            Invoke(new MethodInvoker(() =>
            {
                if (!lockZoomCheckBox.Checked)
                {
                    zedGraphControl.ZoomOutAll(zedGraphControl.GraphPane);
                }
                zedGraphControl.MasterPane.AxisChange();
                zedGraphControl.Refresh();
            }));
            return(new List <double>()); //percentTicBySpectrumByFragmentType[1];
        }
コード例 #2
0
        private void getFragmentationStatistics ()
        {
            IList<object[]> queryRows;
            lock (session)
            {
                var randomIds = session.CreateQuery("SELECT psm.Id " + viewFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch))
                                       .List<long>()
                                       .Shuffle()
                                       .Take(1000)
                                       .OrderBy(o => o);
                string randomIdSet = String.Join(",", randomIds.Select(o => o.ToString()).ToArray());
                queryRows = session.CreateQuery("SELECT psm.Spectrum.Source.Name, psm.Spectrum, psm, DISTINCT_GROUP_CONCAT(pm.Offset || ':' || mod.MonoMassDelta), psm.Peptide.Sequence " +
                                                "FROM PeptideSpectrumMatch psm " +
                                                "LEFT JOIN psm.Modifications pm " + 
                                                "LEFT JOIN pm.Modification mod " +
                                                "WHERE psm.Id IN (" + randomIdSet + ") " +
                                                "GROUP BY psm.Spectrum.id ")
                                   .List<object[]>();
            }
            var spectrumRows = queryRows.Select(o => new SpectrumRow(o)).OrderBy(o => o.SourceName);

            var percentTicBySpectrumByFragmentType = new List<PointPairList>();
            var percentPeakCountBySpectrumByFragmentType = new List<PointPairList>();
            var meanMzErrorBySpectrumByFragmentType = new List<PointPairList>();
            var percentTicListByFragmentType = new List<List<double>>();
            var percentPeakCountListByFragmentType = new List<List<double>>();
            var meanMzErrorListByFragmentType = new List<List<double>>();

            foreach(var graphControl in graphControls)
                graphControl.MasterPane.PaneList.ForEach(o => o.CurveList.ForEach(c => c.Clear()));

            for (int i = 0; i < (int) IonSeries.Count; ++i)
            {
                percentTicBySpectrumByFragmentType.Add(percentTicGraphControl.MasterPane.PaneList[i + 1].CurveList[3].Points as PointPairList);
                percentPeakCountBySpectrumByFragmentType.Add(percentPeakCountGraphControl.MasterPane.PaneList[i + 1].CurveList[3].Points as PointPairList);
                meanMzErrorBySpectrumByFragmentType.Add(meanMzErrorGraphControl.MasterPane.PaneList[i + 1].CurveList[3].Points as PointPairList);
                percentTicListByFragmentType.Add(new List<double>());
                percentPeakCountListByFragmentType.Add(new List<double>());
                meanMzErrorListByFragmentType.Add(new List<double>());
            }

            int spectraCount = 0;
            maxPercentTic = 10;
            maxPercentPeakCount = 10;
            maxMeanMzError = 0.1;
            var tolerance = fragmentTolerance;

            string spectrumListFilters = String.Empty;
            Invoke(new MethodInvoker(() =>
            {
                tolerance.value = Convert.ToDouble(fragmentToleranceTextBox.Text);
                tolerance.units = (MZTolerance.Units) fragmentToleranceUnitsComboBox.SelectedIndex;
                meanMzErrorGraphControl.GraphPane.YAxis.Title.Text = "Mean m/z error (" + tolerance.units.ToString() + ")";

                spectrumListFilters = spectrumFiltersTextBox.Text;
                setAutomaticScales();
            }));

            var points = new PointPairList();

            string currentSourceName = null;
            string currentSourcePath = null;
            msdata.MSData msd = null;

            lock (owner)
            foreach (var row in spectrumRows)
            {
                if (row.SourceName != currentSourceName)
                {
                    currentSourceName = row.SourceName;
                    currentSourcePath = IDPickerForm.LocateSpectrumSource(currentSourceName, session.Connection.GetDataSource());
                    if (String.IsNullOrEmpty(currentSourcePath))
                        throw new FileNotFoundException("source file not found");
                    msd = new pwiz.CLI.msdata.MSDataFile(currentSourcePath);

                    //var param = session.Query<AnalysisParameter>().Where(o => o.Name == "SpectrumListFilters").Min(o => o.Value);
                    //string spectrumListFilters = String.IsNullOrEmpty(param) ? String.Empty : param;
                    SpectrumListFactory.wrap(msd, spectrumListFilters.Split(";".ToCharArray(), StringSplitOptions.RemoveEmptyEntries));
                }

                string spectrumId = String.Format("{0}/{1}", row.SourceName, msdata.id.abbreviate(row.Spectrum.NativeID));

                var spectrumList = msd.run.spectrumList;

                ++spectraCount;

                var pwizPeptide = new proteome.Peptide(row.ModifiedSequence, proteome.ModificationParsing.ModificationParsing_Auto,
                                                       proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
                var fragmentation = pwizPeptide.fragmentation(true, true);

                var pwizSpectrum = spectrumList.spectrum(spectrumList.find(row.Spectrum.NativeID), true);
                var pointMap = new seems.PointMap(new ZedGraph.PointPairList(pwizSpectrum.getMZArray().data, pwizSpectrum.getIntensityArray().data));
                double tic = pointMap.Values.Sum();

                var percentTicByFragmentType = new List<double>(Enumerable.Repeat(0.0, (int) IonSeries.Count));
                var percentPeakCountByFragmentType = new List<double>(Enumerable.Repeat(0.0, (int) IonSeries.Count));
                var matchCountByFragmentType = new List<int>(Enumerable.Repeat(0, (int) IonSeries.Count));
                var meanMzErrorByFragmentType = new List<double>(Enumerable.Repeat(Double.NaN, (int) IonSeries.Count));

                seems.PointMap.Enumerator itr;
                double expected;
                IonSeries[] ionSeries = Enum.GetValues(typeof(IonSeries)).Cast<IonSeries>().Where(o => o != IonSeries.Count).ToArray();

                for (int z = 1; z <= 1; ++z)
                for (int length = 1, end = pwizPeptide.sequence.Length; length <= end; ++length)
                foreach (IonSeries series in ionSeries)
                {
                    if ((series == IonSeries.c || series == IonSeries.x) &&
                        length == pwizPeptide.sequence.Length)
                        continue;

                    expected = fragmentMass(fragmentation, series, length, z);
                    itr = pointMap.FindNear(expected, expected - (expected - tolerance));
                    if (itr != null && itr.IsValid)
                    {
                        percentTicByFragmentType[(int)series] += itr.Current.Value;
                        ++percentPeakCountByFragmentType[(int)series];
                        ++matchCountByFragmentType[(int)series];
                        if (Double.IsNaN(meanMzErrorByFragmentType[(int)series])) meanMzErrorByFragmentType[(int)series] = 0;
                        meanMzErrorByFragmentType[(int)series] += mzError(itr.Current.Key, expected);
                    }
                }

                var rng = new Random();

                for (int i = 0; i < percentTicBySpectrumByFragmentType.Count; ++i)
                {
                    // convert sum to mean
                    if (percentPeakCountByFragmentType[i] > 0)
                        meanMzErrorByFragmentType[i] /= matchCountByFragmentType[i];

                    // convert to percentages
                    percentTicByFragmentType[i] /= tic / 100;
                    percentPeakCountByFragmentType[i] /= pointMap.Count / 100.0;

                    maxPercentTic = Math.Max(maxPercentTic, percentTicByFragmentType[i]);
                    maxPercentPeakCount = Math.Max(maxPercentPeakCount, percentPeakCountByFragmentType[i]);

                    double jitter = (rng.NextDouble() - 0.5);
                    percentTicBySpectrumByFragmentType[i].Add(jitter, percentTicByFragmentType[i], String.Format("{0}: {1:G4}% ({2} matches)", spectrumId, percentTicByFragmentType[i], matchCountByFragmentType[i]));
                    percentPeakCountBySpectrumByFragmentType[i].Add(jitter, percentPeakCountByFragmentType[i], String.Format("{0}: {1:G4}% ({2} matches)", spectrumId, percentPeakCountByFragmentType[i], matchCountByFragmentType[i]));

                    percentTicListByFragmentType[i].Add(percentTicByFragmentType[i]);
                    percentPeakCountListByFragmentType[i].Add(percentPeakCountByFragmentType[i]);

                    if (!Double.IsNaN(meanMzErrorByFragmentType[i]))
                    {
                        maxMeanMzError = Math.Max(maxMeanMzError, Math.Abs(meanMzErrorByFragmentType[i]));
                        meanMzErrorBySpectrumByFragmentType[i].Add(jitter, meanMzErrorByFragmentType[i], String.Format("{0}: {1:G4}%", spectrumId, meanMzErrorByFragmentType[i]));
                        meanMzErrorListByFragmentType[i].Add(meanMzErrorByFragmentType[i]);
                    }
                }

                if ((spectraCount % 100) == 0)
                    setAutomaticScales();
            } // for each spectrum row

            Invoke(new MethodInvoker(() =>
            {
                for (int i = 0; i < percentTicBySpectrumByFragmentType.Count; ++i)
                {
                    if (percentTicListByFragmentType[i].Count < 5)
                        continue;
                    percentTicListByFragmentType[i].Sort();
                    percentPeakCountListByFragmentType[i].Sort();
                    addSixNumberSummary(percentTicGraphControl.MasterPane.PaneList[i + 1], percentTicListByFragmentType[i]);
                    addSixNumberSummary(percentPeakCountGraphControl.MasterPane.PaneList[i + 1], percentPeakCountListByFragmentType[i]);

                    if (meanMzErrorListByFragmentType[i].Count < 5)
                        continue;
                    meanMzErrorListByFragmentType[i].Sort();
                    addSixNumberSummary(meanMzErrorGraphControl.MasterPane.PaneList[i + 1], meanMzErrorListByFragmentType[i]);
                }
            }));
        }
コード例 #3
0
        private void getFragmentationStatistics()
        {
            IList <object[]> queryRows;

            lock (session)
            {
                var randomIds = session.CreateQuery("SELECT psm.Id " + viewFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch))
                                .List <long>()
                                .Shuffle()
                                .Take(1000)
                                .OrderBy(o => o);
                string randomIdSet = String.Join(",", randomIds.Select(o => o.ToString()).ToArray());
                queryRows = session.CreateQuery("SELECT psm.Spectrum.Source.Name, psm.Spectrum, psm, DISTINCT_GROUP_CONCAT(pm.Offset || ':' || mod.MonoMassDelta), psm.Peptide.Sequence " +
                                                "FROM PeptideSpectrumMatch psm " +
                                                "LEFT JOIN psm.Modifications pm " +
                                                "LEFT JOIN pm.Modification mod " +
                                                "WHERE psm.Id IN (" + randomIdSet + ") " +
                                                "GROUP BY psm.Spectrum.id ")
                            .List <object[]>();
            }
            var spectrumRows = queryRows.Select(o => new SpectrumRow(o)).OrderBy(o => o.SourceName);

            var percentTicBySpectrumByFragmentType       = new List <PointPairList>();
            var percentPeakCountBySpectrumByFragmentType = new List <PointPairList>();
            var meanMzErrorBySpectrumByFragmentType      = new List <PointPairList>();
            var percentTicListByFragmentType             = new List <List <double> >();
            var percentPeakCountListByFragmentType       = new List <List <double> >();
            var meanMzErrorListByFragmentType            = new List <List <double> >();

            foreach (var graphControl in graphControls)
            {
                graphControl.MasterPane.PaneList.ForEach(o => o.CurveList.ForEach(c => c.Clear()));
            }

            for (int i = 0; i < (int)IonSeries.Count; ++i)
            {
                percentTicBySpectrumByFragmentType.Add(percentTicGraphControl.MasterPane.PaneList[i + 1].CurveList[3].Points as PointPairList);
                percentPeakCountBySpectrumByFragmentType.Add(percentPeakCountGraphControl.MasterPane.PaneList[i + 1].CurveList[3].Points as PointPairList);
                meanMzErrorBySpectrumByFragmentType.Add(meanMzErrorGraphControl.MasterPane.PaneList[i + 1].CurveList[3].Points as PointPairList);
                percentTicListByFragmentType.Add(new List <double>());
                percentPeakCountListByFragmentType.Add(new List <double>());
                meanMzErrorListByFragmentType.Add(new List <double>());
            }

            int spectraCount = 0;

            maxPercentTic       = 10;
            maxPercentPeakCount = 10;
            maxMeanMzError      = 0.1;
            var tolerance = fragmentTolerance;

            string spectrumListFilters = String.Empty;

            Invoke(new MethodInvoker(() =>
            {
                tolerance.value = Convert.ToDouble(fragmentToleranceTextBox.Text);
                tolerance.units = (MZTolerance.Units)fragmentToleranceUnitsComboBox.SelectedIndex;
                meanMzErrorGraphControl.GraphPane.YAxis.Title.Text = "Mean m/z error (" + tolerance.units.ToString() + ")";

                spectrumListFilters = spectrumFiltersTextBox.Text;
                setAutomaticScales();
            }));

            var points = new PointPairList();

            string currentSourceName = null;
            string currentSourcePath = null;

            msdata.MSData msd = null;

            lock (owner)
                foreach (var row in spectrumRows)
                {
                    if (row.SourceName != currentSourceName)
                    {
                        currentSourceName = row.SourceName;
                        currentSourcePath = IDPickerForm.LocateSpectrumSource(currentSourceName, session.Connection.GetDataSource());
                        if (String.IsNullOrEmpty(currentSourcePath))
                        {
                            throw new FileNotFoundException("source file not found");
                        }
                        msd = new pwiz.CLI.msdata.MSDataFile(currentSourcePath);

                        //var param = session.Query<AnalysisParameter>().Where(o => o.Name == "SpectrumListFilters").Min(o => o.Value);
                        //string spectrumListFilters = String.IsNullOrEmpty(param) ? String.Empty : param;
                        SpectrumListFactory.wrap(msd, spectrumListFilters.Split(";".ToCharArray(), StringSplitOptions.RemoveEmptyEntries));
                    }

                    string spectrumId = String.Format("{0}/{1}", row.SourceName, msdata.id.abbreviate(row.Spectrum.NativeID));

                    var spectrumList = msd.run.spectrumList;

                    ++spectraCount;

                    var pwizPeptide = new proteome.Peptide(row.ModifiedSequence, proteome.ModificationParsing.ModificationParsing_Auto,
                                                           proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
                    var fragmentation = pwizPeptide.fragmentation(true, true);

                    var    pwizSpectrum = spectrumList.spectrum(spectrumList.find(row.Spectrum.NativeID), true);
                    var    pointMap     = new seems.PointMap(new ZedGraph.PointPairList(pwizSpectrum.getMZArray().data, pwizSpectrum.getIntensityArray().data));
                    double tic          = pointMap.Values.Sum();

                    var percentTicByFragmentType       = new List <double>(Enumerable.Repeat(0.0, (int)IonSeries.Count));
                    var percentPeakCountByFragmentType = new List <double>(Enumerable.Repeat(0.0, (int)IonSeries.Count));
                    var matchCountByFragmentType       = new List <int>(Enumerable.Repeat(0, (int)IonSeries.Count));
                    var meanMzErrorByFragmentType      = new List <double>(Enumerable.Repeat(Double.NaN, (int)IonSeries.Count));

                    seems.PointMap.Enumerator itr;
                    double      expected;
                    IonSeries[] ionSeries = Enum.GetValues(typeof(IonSeries)).Cast <IonSeries>().Where(o => o != IonSeries.Count).ToArray();

                    for (int z = 1; z <= 1; ++z)
                    {
                        for (int length = 1, end = pwizPeptide.sequence.Length; length <= end; ++length)
                        {
                            foreach (IonSeries series in ionSeries)
                            {
                                if ((series == IonSeries.c || series == IonSeries.x) &&
                                    length == pwizPeptide.sequence.Length)
                                {
                                    continue;
                                }

                                expected = fragmentMass(fragmentation, series, length, z);
                                itr      = pointMap.FindNear(expected, expected - (expected - tolerance));
                                if (itr != null && itr.IsValid)
                                {
                                    percentTicByFragmentType[(int)series] += itr.Current.Value;
                                    ++percentPeakCountByFragmentType[(int)series];
                                    ++matchCountByFragmentType[(int)series];
                                    if (Double.IsNaN(meanMzErrorByFragmentType[(int)series]))
                                    {
                                        meanMzErrorByFragmentType[(int)series] = 0;
                                    }
                                    meanMzErrorByFragmentType[(int)series] += mzError(itr.Current.Key, expected);
                                }
                            }
                        }
                    }

                    var rng = new Random();

                    for (int i = 0; i < percentTicBySpectrumByFragmentType.Count; ++i)
                    {
                        // convert sum to mean
                        if (percentPeakCountByFragmentType[i] > 0)
                        {
                            meanMzErrorByFragmentType[i] /= matchCountByFragmentType[i];
                        }

                        // convert to percentages
                        percentTicByFragmentType[i]       /= tic / 100;
                        percentPeakCountByFragmentType[i] /= pointMap.Count / 100.0;

                        maxPercentTic       = Math.Max(maxPercentTic, percentTicByFragmentType[i]);
                        maxPercentPeakCount = Math.Max(maxPercentPeakCount, percentPeakCountByFragmentType[i]);

                        double jitter = (rng.NextDouble() - 0.5);
                        percentTicBySpectrumByFragmentType[i].Add(jitter, percentTicByFragmentType[i], String.Format("{0}: {1:G4}% ({2} matches)", spectrumId, percentTicByFragmentType[i], matchCountByFragmentType[i]));
                        percentPeakCountBySpectrumByFragmentType[i].Add(jitter, percentPeakCountByFragmentType[i], String.Format("{0}: {1:G4}% ({2} matches)", spectrumId, percentPeakCountByFragmentType[i], matchCountByFragmentType[i]));

                        percentTicListByFragmentType[i].Add(percentTicByFragmentType[i]);
                        percentPeakCountListByFragmentType[i].Add(percentPeakCountByFragmentType[i]);

                        if (!Double.IsNaN(meanMzErrorByFragmentType[i]))
                        {
                            maxMeanMzError = Math.Max(maxMeanMzError, Math.Abs(meanMzErrorByFragmentType[i]));
                            meanMzErrorBySpectrumByFragmentType[i].Add(jitter, meanMzErrorByFragmentType[i], String.Format("{0}: {1:G4}%", spectrumId, meanMzErrorByFragmentType[i]));
                            meanMzErrorListByFragmentType[i].Add(meanMzErrorByFragmentType[i]);
                        }
                    }

                    if ((spectraCount % 100) == 0)
                    {
                        setAutomaticScales();
                    }
                }// for each spectrum row

            Invoke(new MethodInvoker(() =>
            {
                for (int i = 0; i < percentTicBySpectrumByFragmentType.Count; ++i)
                {
                    if (percentTicListByFragmentType[i].Count < 5)
                    {
                        continue;
                    }
                    percentTicListByFragmentType[i].Sort();
                    percentPeakCountListByFragmentType[i].Sort();
                    addSixNumberSummary(percentTicGraphControl.MasterPane.PaneList[i + 1], percentTicListByFragmentType[i]);
                    addSixNumberSummary(percentPeakCountGraphControl.MasterPane.PaneList[i + 1], percentPeakCountListByFragmentType[i]);

                    if (meanMzErrorListByFragmentType[i].Count < 5)
                    {
                        continue;
                    }
                    meanMzErrorListByFragmentType[i].Sort();
                    addSixNumberSummary(meanMzErrorGraphControl.MasterPane.PaneList[i + 1], meanMzErrorListByFragmentType[i]);
                }
            }));
        }
コード例 #4
0
        private List<double> getPeakStatistics ()
        {
            IList<object[]> queryRows;
            lock (session)
            {
                var randomIds = session.CreateQuery("SELECT psm.Id " + viewFilter.GetFilteredQueryString(DataFilter.FromPeptideSpectrumMatch))
                                       .List<long>()
                                       .Shuffle()
                                       .Take(1000)
                                       .OrderBy(o => o);
                string randomIdSet = String.Join(",", randomIds.Select(o => o.ToString()).ToArray());
                queryRows = session.CreateQuery("SELECT psm.Spectrum.Source.Name, psm.Spectrum, psm, DISTINCT_GROUP_CONCAT(pm.Offset || ':' || mod.MonoMassDelta), psm.Peptide.Sequence " +
                                                "FROM PeptideSpectrumMatch psm " +
                                                "LEFT JOIN psm.Modifications pm " +
                                                "LEFT JOIN pm.Modification mod " +
                                                "WHERE psm.Id IN (" + randomIdSet + ") " +
                                                "GROUP BY psm.Spectrum.id ")
                                   .List<object[]>();
            }
            var spectrumRows = queryRows.Select(o => new SpectrumRow(o)).OrderBy(o => o.SourceName);

            precursorScatterPlot.Clear();
            chargeReducedScatterPlot.Clear();

            int spectraCount = 0;

            string spectrumListFilters = String.Empty;
            Invoke(new MethodInvoker(() =>
            {
                spectrumListFilters = spectrumFiltersTextBox.Text;
                zedGraphControl.MasterPane.AxisChange();
                zedGraphControl.Refresh();
            }));

            var points = new PointPairList();

            string currentSourceName = null;
            string currentSourcePath = null;
            msdata.MSData msd = null;

            lock(owner)
            foreach (var row in spectrumRows)
            {
                if (row.SourceName != currentSourceName)
                {
                    currentSourceName = row.SourceName;
                    currentSourcePath = IDPickerForm.LocateSpectrumSource(currentSourceName, session.Connection.GetDataSource());
                    msd = new pwiz.CLI.msdata.MSDataFile(currentSourcePath);

                    //var param = session.Query<AnalysisParameter>().Where(o => o.Name == "SpectrumListFilters").Min(o => o.Value);
                    //string spectrumListFilters = String.IsNullOrEmpty(param) ? String.Empty : param;
                    SpectrumListFactory.wrap(msd, spectrumListFilters.Split(";".ToCharArray(), StringSplitOptions.RemoveEmptyEntries));
                }

                string label = String.Format("{0}/{1}\n{2}", row.SourceName, msdata.id.abbreviate(row.Spectrum.NativeID), row.ModifiedSequence);

                var spectrumList = msd.run.spectrumList;

                ++spectraCount;

                var pwizPeptide = new proteome.Peptide(row.ModifiedSequence, proteome.ModificationParsing.ModificationParsing_Auto,
                                                       proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
                var fragmentation = pwizPeptide.fragmentation(true, true);

                var pwizSpectrum = spectrumList.spectrum(spectrumList.find(row.Spectrum.NativeID), true);
                var pointMap = new seems.PointMap(new ZedGraph.PointPairList(pwizSpectrum.getMZArray().data, pwizSpectrum.getIntensityArray().data));
                double tic = pointMap.Values.Sum();

                double precursorMz = row.Spectrum.PrecursorMZ;
                double chargeReducedPrecursorMz = precursorMz * row.PeptideSpectrumMatch.Charge;

                bool plotMatchedPeaks = true;
                bool removeMatchedPeaks = false;

                double tolerance = 0.03;
                seems.PointMap.Enumerator itr;
                IonSeries[] ionSeries = Enum.GetValues(typeof(IonSeries)).Cast<IonSeries>().Where(o => o != IonSeries.Count).ToArray();

                for (int z = 1; z <= 1; ++z)
                for (int length = 1, end = pwizPeptide.sequence.Length; length <= end; ++length)
                {
                    string NTermFragment = row.ModifiedSequence.Substring(0, length);
                    string CTermFragment = row.ModifiedSequence.Substring(row.ModifiedSequence.Length - length);

                    foreach (IonSeries series in ionSeries)
                    {
                        if ((series == IonSeries.c || series == IonSeries.cMinus1 || series == IonSeries.x) &&
                            length == pwizPeptide.sequence.Length)
                            continue;

                        itr = pointMap.FindNear(fragmentMass(fragmentation, series, length, z), tolerance);
                        if (itr != null && itr.IsValid)
                        {
                            if (plotMatchedPeaks)
                            {
                                precursorScatterPlot.AddPoint(new PointPair(itr.Current.Key - precursorMz, itr.Current.Value / tic, (int)series, String.Format("{0} {1}\n{2} {3} {4} {5}", label, precursorMz, NTermFragment, itr.Current.Key, IonSeriesLabels[(int)series], length)));
                                chargeReducedScatterPlot.AddPoint(new PointPair(itr.Current.Key - chargeReducedPrecursorMz, itr.Current.Value / tic, (int)series, String.Format("{0} {1}\n{2} {3} {4} {5}", label, chargeReducedPrecursorMz, NTermFragment, itr.Current.Key, IonSeriesLabels[(int)series], length)));
                            }

                            if (removeMatchedPeaks)
                                pointMap.Remove(itr);
                        }
                    }
                }

                foreach (var pair in pointMap)
                {
                    precursorScatterPlot.AddPoint(new PointPair(pair.Key - precursorMz, pair.Value/tic, 0, label));
                    chargeReducedScatterPlot.AddPoint(new PointPair(pair.Key - chargeReducedPrecursorMz, pair.Value/tic, 0, label));
                }

                if ((spectraCount % 100) == 0)
                {
                    Invoke(new MethodInvoker(() =>
                    {
                        zedGraphControl.MasterPane.AxisChange();
                        zedGraphControl.Refresh();
                    }));
                }
            }

            Invoke(new MethodInvoker(() =>
            {
                if (!lockZoomCheckBox.Checked)
                {
                    zedGraphControl.ZoomOutAll(zedGraphControl.GraphPane);
                }
                zedGraphControl.MasterPane.AxisChange();
                zedGraphControl.Refresh();
            }));
            return new List<double>(); //percentTicBySpectrumByFragmentType[1];
        }