C# Peptide.modifications方法代码示例

        ///<summary>Adds user requested ion series on top of the chart.</summary>
        private void addIonSeries (GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
        {
            int ionSeriesChargeState = min;
            string sequence = peptide.sequence;
            ModificationMap modifications = peptide.modifications();

            // Select the color for the ion series.
            Color topSeriesColor;
            Color bottomSeriesColor;
            switch (topSeries)
            {
                default: topSeriesColor = Color.Gray; break;
                case "a": topSeriesColor = Color.YellowGreen; break;
                case "b": topSeriesColor = Color.BlueViolet; break;
                case "c": topSeriesColor = Color.Orange; break;
            }

            switch (bottomSeries)
            {
                default: bottomSeriesColor = Color.Gray; break;
                case "x": bottomSeriesColor = Color.Green; break;
                case "y": bottomSeriesColor = Color.Blue; break;
                case "z": bottomSeriesColor = Color.OrangeRed; break;
                case "z*": bottomSeriesColor = Color.Crimson; break;
            }
            // Ion series offsets. These offsets control where on the chart a particular ion series
            // get displayed
            double topSeriesOffset = 0.025;
            double bottomSeriesOffset = 0.1;
            if (topSeries.Length == 0)
                bottomSeriesOffset = topSeriesOffset;

            double topSeriesLeftPoint = 0.0;
            double bottomSeriesLeftPoint = 0.0;

            // Step through each fragmentation site
            for (int i = 1; i <= sequence.Length; ++i)
            {
                // Paint the top series first
                double rightPoint = 0.0;
                // Figure out the right mz for this fragmentaion site
                switch (topSeries)
                {
                    case "a": rightPoint = fragmentation.a(i, ionSeriesChargeState); break;
                    case "b": rightPoint = fragmentation.b(i, ionSeriesChargeState); break;
                    case "c": if (i < sequence.Length) rightPoint = fragmentation.c(i, ionSeriesChargeState); break;
                    default: continue;
                }

                // If the left mz and right mz are different
                if (rightPoint > 0 && topSeriesLeftPoint != rightPoint)
                {
                    LineObj line;
                    // Use a dashed line format if there are fragment ions supporting this
                    // amino acid
                    if (!aminoAcidHasFragmentEvidence(points, topSeriesLeftPoint, rightPoint))
                    {
                        // Draw the line from previous mz to site to this mz in trasparent color.
                        line = new LineObj(Color.FromArgb(115, topSeriesColor), topSeriesLeftPoint, topSeriesOffset, rightPoint, topSeriesOffset);
                        line.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
                    }
                    else
                    {
                        // Draw the line from previous mz to site to this mz in solid color.
                        line = new LineObj(topSeriesColor, topSeriesLeftPoint, topSeriesOffset, rightPoint, topSeriesOffset);
                    }
                    line.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
                    line.Line.Width = 2;
                    line.ZOrder = ZOrder.F_BehindGrid;
                    line.IsClippedToChartRect = true;
                    list.Add(line);
                    // Add a tick demarking the fragmentation site.
                    LineObj tick = new LineObj(topSeriesColor, rightPoint, (topSeriesOffset - 0.015), rightPoint, (topSeriesOffset + 0.015));
                    tick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
                    tick.Line.Width = 2;
                    tick.IsClippedToChartRect = true;
                    list.Add(tick);
                    // Add a text box in the middle of the left and right mz boundaries
                    StringBuilder label = new StringBuilder(sequence[i - 1].ToString());
                    // Figure out if any mods are there on this amino acid
                    double deltaMass = modifications[i - 1].monoisotopicDeltaMass();
                    // Round the mod mass and append it to the amino acid as a string
                    if (deltaMass > 0.0)
                    {
                        label.Append("+" + Math.Round(deltaMass));
                    }
                    else if (deltaMass < 0.0)
                    {
                        label.Append(Math.Round(deltaMass));
                    }
                    TextObj text = new TextObj(label.ToString(), (topSeriesLeftPoint + rightPoint) / 2.0,
                        topSeriesOffset, CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Center);
                    text.ZOrder = ZOrder.A_InFront;
                    text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
                    text.FontSpec.Border.IsVisible = false;
                    text.FontSpec.Fill.Color = Color.White;
                    text.IsClippedToChartRect = true;
                    list.Add(text);
                    topSeriesLeftPoint = rightPoint;
//.........这里部分代码省略.........

        public override void Update( GraphItem item, pwiz.MSGraph.MSPointList points, GraphObjList annotations )
        {
            double basePeakIntensity = 0;
            double cutoff = 0;
            foreach (var pointlist in points)
            {
                if (basePeakIntensity < pointlist.Y)
                    basePeakIntensity = pointlist.Y;
            }
            cutoff = basePeakIntensity * basePeakPercentage * 0.01;

            if( !Enabled )
                return;

            if( !( item is MassSpectrum ) )
                return; // throw exception?

            GraphObjList list = annotations;
            Peptide peptide;

            try
            {
                peptide = new Peptide( sequence,
                    pwiz.CLI.proteome.ModificationParsing.ModificationParsing_Auto,
                    pwiz.CLI.proteome.ModificationDelimiter.ModificationDelimiter_Brackets );
            } catch( Exception )
            {
                return;
            }

            //if (annotationPanels.peptideInfoGridView.InvokeRequired)
            //{
            //    annotationPanels.peptideInfoGridView.BeginInvoke(new MethodInvoker(() => Update(item, points, annotations)));
            //    //return;
            //}

            var spectrum = ( item as MassSpectrum ).Element;

            if (spectrum.precursors.Count > 0 && ionSeriesIsEnabled(IonSeries.Auto))
            {
                bool cid = (item as MassSpectrum).Element.precursors[0].activation.hasCVParam(CVID.MS_CID);
                bool etd = (item as MassSpectrum).Element.precursors[0].activation.hasCVParam(CVID.MS_ETD);
                ionSeries |= cid ? IonSeries.b | IonSeries.y : IonSeries.Off;
                ionSeries |= etd ? IonSeries.c | IonSeries.zRadical : IonSeries.Off;
            }

            string unmodifiedSequence = peptide.sequence;
            int sequenceLength = unmodifiedSequence.Length;
            Fragmentation fragmentation = peptide.fragmentation( fragmentMassType == 0 ? true : false, true );

            //test neutral
            ModificationMap modifications = peptide.modifications();
            ///
            #region adding labels for series a/b/c/x/y/z:::::::::naive fragmentation modeling

            if (!showBasophileModel)
            {
                for (int i = 1; i < sequenceLength; ++i)
                {
                    //test neutral loss
                    //note here the Cseq is slightly different than those in addFragmentSummary
                    string Nseq = peptide.sequence.Substring(0, i);
                    string Cseq = peptide.sequence.Substring(sequenceLength - i, i);
                    string NTempSeq = peptide.sequence.Substring(0, sequenceLength - i);
                    char[] Nseqchars = Nseq.ToCharArray();
                    char[] NTempSeqchars = NTempSeq.ToCharArray();
                    char[] seqchars = peptide.sequence.ToCharArray();
                    int Nphosmodi = 0;
                    int NTempPhosmodi = 0;
                    int Cphosmodi = 0;
                    int phosmodi = 0;
                    for (int k = 0; k < i; k++)
                    {
                        if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[k] == 'Y'))
                        {
                            Nphosmodi++;
                        }
                    }
                    for (int k = 0; k < sequenceLength - i; k++)
                    {
                        if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[k] == 'Y'))
                        {
                            NTempPhosmodi++;
                        }
                    }
                    for (int k = 0; k < sequenceLength; k++)
                    {
                        if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[k] == 'Y'))
                        {
                            phosmodi++;
                        }
                    }
                    Cphosmodi = phosmodi - NTempPhosmodi;

                    for (int charge = min; charge <= max; ++charge)
                    {
                        if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a", i, charge, fragmentation.a(i, charge));
                        if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b", i, charge, fragmentation.b(i, charge));
                        if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y", i, charge, fragmentation.y(i, charge));
                        if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z", i, charge, fragmentation.z(i, charge));
//.........这里部分代码省略.........

        ///<summary>Adds user requested ion series to the fragmentation summary.</summary>
        private void addFragmentationSummary (GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
        {
            int ionSeriesChargeState = min;
            string sequence = peptide.sequence;
            ModificationMap modifications = peptide.modifications();

            // Select the color for the ion series.
            Color topSeriesColor;
            Color bottomSeriesColor;
            switch (topSeries)
            {
                default: topSeriesColor = Color.Gray; break;
                case "a": topSeriesColor = Color.YellowGreen; break;
                case "b": topSeriesColor = Color.BlueViolet; break;
                case "c": topSeriesColor = Color.Orange; break;
            }

            switch (bottomSeries)
            {
                default: bottomSeriesColor = Color.Gray; break;
                case "x": bottomSeriesColor = Color.Green; break;
                case "y": bottomSeriesColor = Color.Blue; break;
                case "z": bottomSeriesColor = Color.OrangeRed; break;
                case "z*": bottomSeriesColor = Color.Crimson; break;
            }

            // Ion series offsets. These offsets control where on the chart a particular ion series get displayed
            double seriesTopLeftOffset = 0.2;

            // Set the constants for starting the label paint
            double topSeriesLeftPoint = 0.025;
            double residueWidth = 0.5 / ((double) sequence.Length);
            double topSeriesRightPoint = topSeriesLeftPoint + 0.5 - residueWidth;
            double tickStart = residueWidth / 2.0;

            // Process all the series except c and x
            for (int i = 1; i <= sequence.Length; ++i)
            {
                double topSeriesFragmentMZ = 0.0;
                double bottomSeriesFragmentMZ = 0.0;
                switch (topSeries)
                {
                    case "a": topSeriesFragmentMZ = fragmentation.a(i, ionSeriesChargeState); break;
                    case "b": topSeriesFragmentMZ = fragmentation.b(i, ionSeriesChargeState); break;
                    case "c": if (i < sequence.Length) topSeriesFragmentMZ = fragmentation.c(i, ionSeriesChargeState); break;
                    default: continue;
                }
                switch (bottomSeries)
                {
                    case "x": if (i < sequence.Length) bottomSeriesFragmentMZ = fragmentation.x(i, ionSeriesChargeState); break;
                    case "y": bottomSeriesFragmentMZ = fragmentation.y(i, ionSeriesChargeState); break;
                    case "z": bottomSeriesFragmentMZ = fragmentation.z(i, ionSeriesChargeState); break;
                    case "z*": bottomSeriesFragmentMZ = fragmentation.zRadical(i, ionSeriesChargeState); break;
                    default: continue;
                }

                // Check if the top and bottom fragments have evidence
                bool topSeriesHasMatch = false;
                bool bottomSeriesHasMatch = false;
                if (points != null)
                {
                    topSeriesHasMatch = topSeriesFragmentMZ > 0 && findPointWithTolerance(points, topSeriesFragmentMZ, tolerance) > -1;
                    bottomSeriesHasMatch = bottomSeriesFragmentMZ > 0 && findPointWithTolerance(points, bottomSeriesFragmentMZ, tolerance) > -1;
                }

                // Build the label for the amino acid
                // Add a text box in the middle of the left and right mz boundaries
                StringBuilder label = new StringBuilder(sequence[i - 1].ToString());

                // Figure out if any mods are there on this amino acid
                double deltaMass = modifications[i - 1].monoisotopicDeltaMass();

                // Round the mod mass and append it to the amino acid as a string
                if (deltaMass > 0.0)
                {
                    label.Append("+" + Math.Round(deltaMass));
                }
                else if (deltaMass < 0.0)
                {
                    label.Append(Math.Round(deltaMass));
                }

                TextObj text = new TextObj(label.ToString(), topSeriesLeftPoint, seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Center, AlignV.Center);
                text.ZOrder = ZOrder.A_InFront;
                text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
                text.FontSpec.Border.IsVisible = false;
                text.FontSpec.Fill.Color = Color.White;
                text.IsClippedToChartRect = false;
                list.Add(text);

                if (topSeriesHasMatch)
                {
                    // Paint the tick in the middle
                    LineObj tick = new LineObj(topSeriesColor, topSeriesLeftPoint + tickStart, (seriesTopLeftOffset - 0.05), topSeriesLeftPoint + tickStart, seriesTopLeftOffset);
                    tick.Location.CoordinateFrame = CoordType.ChartFraction;
                    tick.Line.Width = 2;
                    tick.IsClippedToChartRect = true;
                    list.Add(tick);
                    // Paint the hook
//.........这里部分代码省略.........

        ///<summary>Adds user requested ion series to the fragmentation summary.</summary>
        private void addFragmentationSummary(GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
        {
            ///cutoff definition for neutral loss
            double basePeakIntensity = 0;
            double cutoff = 0;
            foreach (var pointlist in points)
            {
                if (basePeakIntensity < pointlist.Y)
                    basePeakIntensity = pointlist.Y;
            }
            cutoff = basePeakIntensity * basePeakPercentage * 0.01;
            ///

            int ionSeriesChargeState = min;
            string sequence = peptide.sequence;
            int sequenceLength = peptide.sequence.Length;
            ModificationMap modifications = peptide.modifications();

            // Select the color for the ion series.
            Color topSeriesColor;
            Color bottomSeriesColor;
            switch (topSeries)
            {
                default: topSeriesColor = Color.Gray; break;
                case "a": topSeriesColor = Color.YellowGreen; break;
                case "b": topSeriesColor = Color.Red; break;
                case "c": topSeriesColor = Color.Orange; break;
            }

            switch (bottomSeries)
            {
                default: bottomSeriesColor = Color.Gray; break;
                case "x": bottomSeriesColor = Color.Green; break;
                case "y": bottomSeriesColor = Color.Blue; break;
                case "z": bottomSeriesColor = Color.OrangeRed; break;
                case "z*": bottomSeriesColor = Color.Crimson; break;
            }
            // Ion series offsets. These offsets control where on the chart a particular ion series
            // get displayed
            //change the seriesTopLeftOffset value to 0.1 to make the label higher in the image.
            //original is 0.031
            double seriesTopLeftOffset = 0.05;
            // Set the constants for starting the label paint
            double topSeriesLeftPoint = 0.025;
            //test and looks reasonalbe
            double residueWidth = 0.031;
            //double residueWidth = 0.25 / ((double)sequence.Length);

            // Process all the series except c and x

            //small block modified
            //here is a big bug: if go like orignal code, then the y ions is just the like the order of b ions, which are not right.
            //My modification is to seperate a/b/c and x/y/z ions, and then it will solve this problem.
            //it seems works well.

            ///
            #region Process a/b ions
            //first we are going to touch only a/b ions
            ///
            for (int i = 1; i <= sequence.Length; ++i)
            {
                double tickStart = residueWidth * 4 / 5.0;
                double topSeriesFragmentMZ = 0.0;

                //test neutral loss
                //this block is to give clear clue for phospate loss
                //exact number of phosphated amino acids are counted.
                string Nseq = peptide.sequence.Substring(0, i);
                char[] Nseqchars = Nseq.ToCharArray();
                int Nphosmodi = 0;
                for (int k = 0; k < i; k++)
                {
                    if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (Nseqchars[k] == 'S' || Nseqchars[k] == 'T' || Nseqchars[k] == 'Y'))
                    {
                        Nphosmodi++;
                    }
                }

                //correct the bug:
                //when multiple charges allowed for fragmentation, then there is no tick thing showing the existance of the fragment
                //what I did is: make top/bottomSeriesHasMatch true if there is fragment of any charges matched.
                //bug fixed
                bool topSeriesHasMatch = false;
                for (int z = min; z <= max; z++)
                {
                    switch (topSeries)
                    {
                        case "a": topSeriesFragmentMZ = fragmentation.a(i, z); break;
                        case "b": topSeriesFragmentMZ = fragmentation.b(i, z); break;
                        default: topSeriesFragmentMZ = 0.0; break;
                    }

                    // Check if the top and bottom fragments have evidence
                    if (points != null)
                    {
                        // Search index
                        int index = -1;
                        // Find the left mz value using a mass tolerance of 0.5 da.
                        index = points.FullLowerBound(topSeriesFragmentMZ - 0.5);
//.........这里部分代码省略.........