private int findPointWithTolerance(pwiz.MSGraph.MSPointList points, double mz, MZTolerance tolerance, bool scaled = false)
{
double lowestMatchMz = mz - tolerance;
double highestMatchMz = mz + tolerance;
var pointPairList = scaled ? points.ScaledList : points.FullList;
int index = scaled ? points.ScaledLowerBound(mz) : points.FullLowerBound(mz);
// if index is below the tolerance threshold, bump it to the next one or set to -1 if doing so would exceed the list size
if (index > -1 && pointPairList[index].X < lowestMatchMz)
index = index + 1 == pointPairList.Count ? -1 : index + 1;
if (index == -1 || pointPairList[index].X > highestMatchMz)
return -1;
return index;
}
///<summary>
/// Takes a left mz value and right mz value and returns true if both are found in the spectrum.
/// TODO: make mass tolerance user-configurable (currently hard-coded to 0.5 m/z)
///</summary>
private bool aminoAcidHasFragmentEvidence( pwiz.MSGraph.MSPointList points, double leftMZ, double rightMZ )
{
// Search index
int index = -1;
bool leftMZFound = false;
bool righMZFound = false;
if( points != null )
{
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound( leftMZ - 0.5 );
if (index != -1 && points.FullList[index].X <= (leftMZ + 0.5))
leftMZFound = true;
// Find the right mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(rightMZ - 0.5);
if (index != -1 && points.FullList[index].X <= (rightMZ + 0.5))
righMZFound = true;
}
// Return if both are found
return (leftMZFound & righMZFound);
}
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));
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*", i, charge, fragmentation.zRadical(i, charge));
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c", i, charge, fragmentation.c(i, charge));
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x", i, charge, fragmentation.x(i, charge));
}
//test neutral loss
#region water loss
if (waterLoss == true)
{
if (Nseq.Contains("S") || Nseq.Contains("T") || Nseq.Contains("E") || Nseq.Contains("D"))
{
if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a-water", i, charge, fragmentation.a(i, charge) - WATERMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b-water", i, charge, fragmentation.b(i, charge) - WATERMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c-water", i, charge, fragmentation.c(i, charge) - WATERMONOMASS / charge);
}
}
if (Cseq.Contains("S") || Cseq.Contains("T") || Cseq.Contains("E") || Cseq.Contains("D"))
{
if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y-water", i, charge, fragmentation.y(i, charge) - WATERMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z-water", i, charge, fragmentation.z(i, charge) - WATERMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*-water", i, charge, fragmentation.zRadical(i, charge) - WATERMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x-water", i, charge, fragmentation.x(i, charge) - WATERMONOMASS / charge);
}
}
}
#endregion
//test neutral loss
#region ammonium loss
if (ammoniumLoss == true)
{
if (Nseq.Contains("R") || Nseq.Contains("K") || Nseq.Contains("Q") || Nseq.Contains("N"))
{
if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a-ammonium", i, charge, fragmentation.a(i, charge) - AMMONIUMMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b-ammonium", i, charge, fragmentation.b(i, charge) - AMMONIUMMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c-ammonium", i, charge, fragmentation.c(i, charge) - AMMONIUMMONOMASS / charge);
}
}
if (Cseq.Contains("R") || Cseq.Contains("K") || Cseq.Contains("Q") || Cseq.Contains("N"))
{
if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y-ammonium", i, charge, fragmentation.y(i, charge) - AMMONIUMMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z-ammonium", i, charge, fragmentation.z(i, charge) - AMMONIUMMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*-ammonium", i, charge, fragmentation.zRadical(i, charge) - AMMONIUMMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x-ammonium", i, charge, fragmentation.x(i, charge) - AMMONIUMMONOMASS / charge);
}
}
}
#endregion
//test neutral loss
#region phosphate loss
if (phosphateLoss == true)
{
int minNPhosphate = Math.Min(Nphosmodi, numPhosphate);
if (minNPhosphate > 0)
{
if (ionSeriesIsEnabled(IonSeries.a))
{
for (int k = 1; k <= minNPhosphate; k++)
{
addFragment(list, points, "a-" + k + "phos", i, charge, fragmentation.a(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
if (ionSeriesIsEnabled(IonSeries.b))
{
for (int k = 1; k <= minNPhosphate; k++)
{
addFragment(list, points, "b-" + k + "phos", i, charge, fragmentation.b(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c))
{
for (int k = 1; k <= minNPhosphate; k++)
{
addFragment(list, points, "c-" + k + "phos", i, charge, fragmentation.c(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
}
}
int minCPhosphate = Math.Min(Cphosmodi, numPhosphate);
if (minCPhosphate > 0)
{
if (ionSeriesIsEnabled(IonSeries.y))
{
for (int k = 1; k <= minCPhosphate; k++)
{
addFragment(list, points, "y-" + k + "phos", i, charge, fragmentation.y(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
if (ionSeriesIsEnabled(IonSeries.z))
{
for (int k = 1; k <= minCPhosphate; k++)
addFragment(list, points, "z-" + k + "phos", i, charge, fragmentation.z(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
{
for (int k = 1; k <= minCPhosphate; k++)
addFragment(list, points, "z*-" + k + "phos", i, charge, fragmentation.zRadical(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.x))
{
for (int k = 1; k <= minCPhosphate; k++)
addFragment(list, points, "x-" + k + "phos", i, charge, fragmentation.x(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
}
}
#endregion
}
}
}
//for basophile fragmentation modeling
else if (showBasophileModel)
{
//clear the panel
//annotationPanels.bCheckBox.Checked = false;
//annotationPanels.yCheckBox.Checked = false;
String peptideSeq = peptide.sequence;
int seqLength = peptideSeq.Length;
char[] seq = peptideSeq.ToCharArray();
int totalR = 0, totalK = 0, totalH = 0;
for (int i = 0; i < seqLength; ++i)
{
if (seq[i] == 'R')
++totalR;
else if (seq[i] == 'K')
++totalK;
else if (seq[i] == 'H')
++totalH;
}
for (int c = 1; c < seqLength; c++)
{
int totalNR = 0, totalNK = 0, totalNH = 0, totalNL = 0;
int totalCR = 0, totalCK = 0, totalCH = 0, totalCL = 0;
for (int i = 0; i < c; ++i)
{
if (seq[i] == 'R') { ++totalNR; }
else if (seq[i] == 'K') { ++totalNK; }
else if (seq[i] == 'H') { ++totalNH; }
}
totalNL = c;
totalCR = totalR - totalNR;
totalCK = totalK - totalNK;
totalCH = totalH - totalNH;
totalCL = seqLength - totalNL;
double y1_logit = 0.1098112 * totalNR + 0.2085831 * totalNK + 0.1512109 * totalNH + 0.0460839 * totalNL
- 0.3872417 * totalCR - 0.3684911 * totalCK - 0.1634741 * totalCH - 0.1693931 * totalCL + 1.2632997;
double y2_logit = -0.6345364 * totalNR - 0.3365917 * totalNK - 0.4577882 * totalNH - 0.1492703 * totalNL
+ 0.7738133 * totalCR + 0.6036758 * totalCK + 0.5942542 * totalCH + 0.0701467 * totalCL + 0.0806280;
double b1_logit = 0.0801432 * totalNR - 0.1088081 * totalNK - 0.1338220 * totalNH - 0.1413059 * totalNL
- 0.3157957 * totalCR - 0.2708274 * totalCK - 0.3703136 * totalCH + 0.0157418 * totalCL + 1.2124699;
double b2_logit = 0.8606449 * totalNR + 0.2763119 * totalNK + 0.4969152 * totalNH + 0.0685712 * totalNL
- 1.3346995 * totalCR - 1.0977316 * totalCK - 1.0973677 * totalCH - 0.2028884 * totalCL + 1.9355980;
if (ionSeriesIsEnabled(IonSeries.b))
{
if (b1_logit > -0.5) addFragment(list, points, "b", c, 1, fragmentation.b(c, 1));
if (b2_logit > 0) addFragment(list, points, "b", c, 2, fragmentation.b(c, 2));
}
if (ionSeriesIsEnabled(IonSeries.y))
{
if (y1_logit > -0.5) addFragment(list, points, "y", seqLength - c, 1, fragmentation.y(seqLength - c, 1));
if (y2_logit > -0.5) addFragment(list, points, "y", seqLength - c, 2, fragmentation.y(seqLength - c, 2));
}
//if (b1_logit > -0.5)
// if (ionSeriesIsEnabled(IonSeries.b))
// addFragment(list, points, "b", c, 1, fragmentation.b(c, 1));
//if (b2_logit > 0)
// if (ionSeriesIsEnabled(IonSeries.b))
// addFragment(list, points, "b", c, 2, fragmentation.b(c, 2));
//if (y1_logit > -0.5)
// if (ionSeriesIsEnabled(IonSeries.y))
// addFragment(list, points, "y", seqLength - c, 1, fragmentation.y(seqLength - c, 1));
//if (y2_logit > -0.5)
// if (ionSeriesIsEnabled(IonSeries.y))
// addFragment(list, points, "y", seqLength - c, 2, fragmentation.y(seqLength - c, 2));
}
}
#endregion
if ( showLadders || showFragmentationSummary)
{
//test neutral loss
//string topSeries = ionSeriesIsEnabled(IonSeries.a) ? "a" : ionSeriesIsEnabled(IonSeries.b) ? "b" : ionSeriesIsEnabled(IonSeries.c) ? "c" : "";
//string bottomSeries = ionSeriesIsEnabled(IonSeries.x) ? "x" : ionSeriesIsEnabled(IonSeries.y) ? "y" : ionSeriesIsEnabled(IonSeries.z) ? "z" : ionSeriesIsEnabled(IonSeries.zRadical) ? "z*" : "";
//if (showLadders)
// addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
//if (showFragmentationSummary)
// addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
string topSeries = "";
string bottomSeries = "";
if (ionSeriesIsEnabled(IonSeries.a))
{
topSeries = "a";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.b))
{
topSeries = "b";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.c))
{
topSeries = "c";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.x))
{
bottomSeries = "x";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.y))
{
bottomSeries = "y";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.z))
{
bottomSeries = "z";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
{
bottomSeries = "z*";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
}
annotationPanels.peptideInfoGridView.Rows.Clear();
if( spectrum.precursors.Count > 0 &&
spectrum.precursors[0].selectedIons.Count > 0 &&
spectrum.precursors[0].selectedIons[0].hasCVParam( CVID.MS_selected_ion_m_z ) &&
spectrum.precursors[0].selectedIons[0].hasCVParam( CVID.MS_charge_state ) )
{
double selectedMz = (double) spectrum.precursors[0].selectedIons[0].cvParam( CVID.MS_selected_ion_m_z ).value;
int chargeState = (int) spectrum.precursors[0].selectedIons[0].cvParam( CVID.MS_charge_state ).value;
double calculatedMass = ( precursorMassType == 0 ? peptide.monoisotopicMass( chargeState ) : peptide.molecularWeight( chargeState ) ) * chargeState;
double observedMass = selectedMz * chargeState;
annotationPanels.peptideInfoGridView.Rows.Add( "Calculated mass:", calculatedMass, "Mass error (daltons):", observedMass - calculatedMass );
annotationPanels.peptideInfoGridView.Rows.Add( "Observed mass:", observedMass, "Mass error (ppm):", ( ( observedMass - calculatedMass ) / calculatedMass ) * 1e6 );
} else
annotationPanels.peptideInfoGridView.Rows.Add( "Calculated neutral mass:", precursorMassType == 0 ? peptide.monoisotopicMass() : peptide.molecularWeight() );
annotationPanels.peptideInfoGridView.Columns[1].DefaultCellStyle.Format = "F4";
foreach( DataGridViewRow row in annotationPanels.peptideInfoGridView.Rows )
row.Height = row.InheritedStyle.Font.Height + 2;
// TODO: fragmentInfoGridView is slow: make it faster, optional, or both!
annotationPanels.fragmentInfoGridView.SuspendLayout();
if( ionSeries > IonSeries.Auto )
{
if( annotationPanels.fragmentInfoGridView.Columns.Count == 0 )
{
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"a" + charge.ToString(),
"a" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"b" + charge.ToString(),
"b" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"c" + charge.ToString(),
"c" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
annotationPanels.fragmentInfoGridView.Columns.Add("N", "#");
annotationPanels.fragmentInfoGridView.Columns.Add("Sequence", "seq");
annotationPanels.fragmentInfoGridView.Columns.Add("C", "#");
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"x" + charge.ToString(),
"x" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"y" + charge.ToString(),
"y" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z" + charge.ToString(),
"z" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z*" + charge.ToString(),
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
foreach( DataGridViewColumn column in annotationPanels.fragmentInfoGridView.Columns )
{
column.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleCenter;
if( column.Name != "N" && column.Name != "C" && column.Name != "Sequence" )
column.DefaultCellStyle.Format = "F3";
}
}
while( annotationPanels.fragmentInfoGridView.Rows.Count > sequenceLength )
annotationPanels.fragmentInfoGridView.Rows.RemoveAt( annotationPanels.fragmentInfoGridView.Rows.Count - 1 );
if( sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count > 0 )
annotationPanels.fragmentInfoGridView.Rows.Add( sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count );
for( int i = 1; i <= sequenceLength; ++i )
{
int cTerminalLength = sequenceLength - i + 1;
var row = annotationPanels.fragmentInfoGridView.Rows[i - 1];
var values = new List<object>(10);
//var row = annotationPanels.fragmentInfoGridView.Rows.Add()];
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.a(i, charge));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.b(i, charge));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
if (i < sequenceLength)
values.Add(fragmentation.c(i, charge));
else
values.Add("");
values.Add(i);
values.Add(unmodifiedSequence[i - 1]);
values.Add(cTerminalLength);
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
if (i > 1)
values.Add(fragmentation.x(cTerminalLength, charge));
else
values.Add("");
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.y(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.z(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.zRadical(cTerminalLength, charge));
row.SetValues(values.ToArray());
}
//add my code in between
//the purpose is to switch the fragmentInfoGridView table into a html
//to solve the bug that the table can be copied, but the bold font information can not be copied
//basically, a stringbuilder object is created and going to copy values, formats from gridview, and then output
//currently the html output is only stored in local, and I am trying to adapt it into a applet-like viewer.
//first a stringbuilder is created
StringBuilder sb_original = new StringBuilder();
//Setting HTML and table tags
sb_original.Append("<html>");
sb_original.Append("<head>");
sb_original.Append("<title>fragmentGridView2HTML</title>");
sb_original.Append("</head>");
sb_original.Append("<body>");
sb_original.Append("<br>");
sb_original.AppendLine("<" + "table border='2' cellpadding='1' cellspacing='1'>");
sb_original.AppendLine("<tr>");
//setting table headers
//make them bold
for (int i = 0; i < annotationPanels.fragmentInfoGridView.Columns.Count; i++)
{
sb_original.AppendLine("<th>" + annotationPanels.fragmentInfoGridView.Columns[i].HeaderText + "</th>");
}
sb_original.AppendLine("</tr>");
//starting copying cells to html
foreach( DataGridViewRow row in annotationPanels.fragmentInfoGridView.Rows )
{
sb_original.AppendLine("<tr>");
row.Height = row.InheritedStyle.Font.Height + 2;
foreach( DataGridViewCell cell in row.Cells )
{
if (!(cell.Value is double))
{
//note: added two line here
sb_original.AppendLine("<td>" + cell.FormattedValue + "</td>");
continue;
}
double mz = (double) cell.Value;
int index = -1;
if( points != null )
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5))
{
//note: added two line here
//first is to pass value to sb;
//second is to change the cell fontstyle back to regular, if previouly bold
sb_original.AppendLine("<td>" + cell.FormattedValue + "</td>");
cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Regular);
continue;
}
cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Bold);
//note: added one line here
sb_original.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
}
}
sb_original.AppendLine("</tr>");
sb_original.AppendLine("</body>");
sb_original.AppendLine("</head>");
sb_original.AppendLine("</html>");
//for storation of stringbuilder into local file
//test only
string file_original = "C:\\Temp\\originalTable.html";
Directory.CreateDirectory(Path.GetDirectoryName(file_original));
TextWriter tw_original = new StreamWriter(file_original);
tw_original.WriteLine(sb_original.ToString());
tw_original.Flush();
tw_original.Close();
/////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////
//test neutral loss
#region Neutral Loss
StringBuilder sb_neutral = new StringBuilder();
if (waterLoss == false && ammoniumLoss == false && phosphateLoss == false)
{
sb_neutral = sb_original;
}
else //if any of the neutral loss is clicked
{
#region if any of the neutral loss is clicked
DataGridView neutralLossDataGridView = new DataGridView();
///
#region add first columns part
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString(),
"a" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "waterLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "ammoniumLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "phosphateLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "phosphateLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-"+k+"PHO" : "-"+k+"PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString(),
"b" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "waterLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "ammoniumLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "phosphateLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "phosphateLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString(),
"c" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "waterLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "ammoniumLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "phosphateLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "phosphateLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
#endregion
neutralLossDataGridView.Columns.Add("N", "#");
neutralLossDataGridView.Columns.Add("Sequence", "seq");
neutralLossDataGridView.Columns.Add("C", "#");
///
#region add second columns part
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString(),
"x" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "waterLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "ammoniumLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "phosphateLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "phosphateLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString(),
"y" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "waterLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "ammoniumLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "phosphateLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "phosphateLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString(),
"z" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "waterLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "ammoniumLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "phosphateLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "phosphateLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString(),
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "waterLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "ammoniumLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "phosphateLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "phosphateLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
#endregion
while (neutralLossDataGridView.Rows.Count > sequenceLength)
neutralLossDataGridView.Rows.RemoveAt(neutralLossDataGridView.Rows.Count - 1);
if (sequenceLength - neutralLossDataGridView.Rows.Count > 0)
neutralLossDataGridView.Rows.Add(sequenceLength - neutralLossDataGridView.Rows.Count);
char[] aminoAcids = peptide.sequence.ToCharArray();
for (int i = 1; i <= sequenceLength; ++i)
{
int Nphosmodi = 0;
int Cphosmodi = 0;
int cTerminalLength = sequenceLength - i + 1;
var row = neutralLossDataGridView.Rows[i - 1];
var values = new List<object>();
//define the amino acides that are capable of losing water
//AA = S,T,E,D
bool nSTED = false;
bool cSTED = false;
bool nRKQN = false;
bool cRKQN = false;
for (int index = 0; index < i; index++)
{
if (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'E' || aminoAcids[index] == 'D')
nSTED = true;
if (aminoAcids[index] == 'R' || aminoAcids[index] == 'K' || aminoAcids[index] == 'Q' || aminoAcids[index] == 'N')
nRKQN = true;
if (Math.Round(modifications[index].monoisotopicDeltaMass()) == 80 && (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'Y'))
Nphosmodi++;
}
//here is more tricky. since the display is
//b1 ----- y(seq-1+1)
//b2 ----- y(seq-2+1)
for (int index = sequenceLength - 1; index >= i - 1; index--)
{
if (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'E' || aminoAcids[index] == 'D')
cSTED = true;
if (aminoAcids[index] == 'R' || aminoAcids[index] == 'K' || aminoAcids[index] == 'Q' || aminoAcids[index] == 'N')
cRKQN = true;
if (Math.Round(modifications[index].monoisotopicDeltaMass()) == 80 && (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'Y'))
Cphosmodi++;
}
int minNPhosphate = Math.Min(numPhosphate, Nphosmodi);
int minCPhosphate = Math.Min(numPhosphate, Cphosmodi);
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.a(i, charge), 3));
if (waterLoss == true)
{
if (nSTED) values.Add(Math.Round(fragmentation.a(i, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (nRKQN) values.Add(Math.Round(fragmentation.a(i, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minNPhosphate)
{
values.Add(Math.Round(fragmentation.a(i, charge) - k*PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.b(i, charge), 3));
if (waterLoss == true)
{
if (nSTED) values.Add(Math.Round(fragmentation.b(i, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (nRKQN) values.Add(Math.Round(fragmentation.b(i, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minNPhosphate)
{
values.Add(Math.Round(fragmentation.b(i, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
{
if (i < sequenceLength)
values.Add(Math.Round(fragmentation.c(i, charge), 3));
else
values.Add("-");
if (waterLoss == true)
{
if (nSTED && i < sequenceLength)
values.Add(Math.Round(fragmentation.c(i, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (nRKQN && i < sequenceLength)
values.Add(Math.Round(fragmentation.c(i, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
if (i < sequenceLength)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minNPhosphate)
{
values.Add(Math.Round(fragmentation.c(i, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
else values.Add("-");
}
}
values.Add(i);
values.Add(unmodifiedSequence[i - 1]);
values.Add(cTerminalLength);
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
{
if (i > 1)
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge), 3));
else
values.Add("-");
if (waterLoss == true)
{
if (cSTED && i > 1)
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN && i > 1)
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
if (i > 1)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
else values.Add("-");
}
}
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge), 3));
if (waterLoss == true)
{
if (cSTED) values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN) values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge), 3));
if (waterLoss == true)
{
if (cSTED) values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN) values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge), 3));
if (waterLoss == true)
{
if (cSTED) values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN) values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
row.SetValues(values.ToArray());
}//end for
//add sb_neutral loss table
#region add sb_neutral loss table
sb_neutral.Append("<html>");
sb_neutral.Append("<head>");
sb_neutral.Append("<title>neutralLossFragmentGridView2HTML</title>");
sb_neutral.Append("</head>");
sb_neutral.Append("<body>");
sb_neutral.Append("<br>");
sb_neutral.AppendLine("<" + "table border='2' cellpadding='1' cellspacing='1'>");
sb_neutral.AppendLine("<tr>");
for (int i = 0; i < neutralLossDataGridView.Columns.Count; i++)
{
sb_neutral.AppendLine("<th>" + neutralLossDataGridView.Columns[i].HeaderText + "</th>");
}
foreach (DataGridViewRow row in neutralLossDataGridView.Rows)
{
sb_neutral.AppendLine("<tr>");
#region basepeakthresholding is false
if (basePeakThresholding == false)
{
foreach (DataGridViewCell cell in row.Cells)
{
if (!(cell.Value is double))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
continue;
}
double mz = (double)cell.Value;
int index = -1;
if (points != null)
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
//cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Regular);
continue;
}
//cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Bold);
sb_neutral.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
}
}
#endregion
else//basepeakthresholding is true
{
int columnIndex = 0;
foreach (DataGridViewCell cell in row.Cells)
{
if (neutralLossDataGridView.Columns[columnIndex].HeaderText.Contains("H2O") || neutralLossDataGridView.Columns[columnIndex].HeaderText.Contains("NH3") || neutralLossDataGridView.Columns[columnIndex].HeaderText.Contains("PHO"))
{
if (!(cell.Value is double))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
double mz = (double)cell.Value;
int index = -1;
if (points != null)
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5) || points.FullList[index].Y < cutoff)
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
sb_neutral.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
columnIndex++;
}
else
{
if (!(cell.Value is double))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
double mz = (double)cell.Value;
int index = -1;
if (points != null)
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
sb_neutral.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
columnIndex++;
}
}
}
}
sb_neutral.AppendLine("</tr>");
sb_neutral.AppendLine("</body>");
sb_neutral.AppendLine("</head>");
sb_neutral.AppendLine("</html>");
#endregion
#endregion
} //end of else
string file_neutral = "C:\\Temp\\neutralLossTable.html";
Directory.CreateDirectory(Path.GetDirectoryName(file_neutral));
TextWriter tw_neutral = new StreamWriter(file_neutral);
tw_neutral.WriteLine(sb_neutral.ToString());
tw_neutral.Flush();
tw_neutral.Close();
#endregion
}
else
annotationPanels.fragmentInfoGridView.Rows.Clear();
annotationPanels.fragmentInfoGridView.ResumeLayout();
}
///<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);
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
//test neutral loss
#region water loss a/b top series
if (waterLoss == true)
{
if (Nseq.Contains("S") || Nseq.Contains("T") || Nseq.Contains("E") || Nseq.Contains("D"))
{
// 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 - WATERMONOMASS/z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y >= cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
#endregion
//test neutral loss
#region ammonium loss a/b top series
if (ammoniumLoss == true)
{
if (Nseq.Contains("R") || Nseq.Contains("K") || Nseq.Contains("Q") || Nseq.Contains("N"))
{
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 - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
#endregion
//test neutral loss
#region phosphate loss a/b top series
if (phosphateLoss == true)
{
//need to judge qualified number of AAs;
int minPhosphate = Math.Min(Nphosmodi, numPhosphate);
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
//first need to judge if there are as many as phos AAs
//then if AA <= phos, then deal with AA;
//if AA > phos, then deal with phos.
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 - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
}
#endregion
}
// 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();
string deltaMassString = deltaMass.ToString();
TextObj text = new TextObj(label.ToString(), topSeriesLeftPoint,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
text.ZOrder = ZOrder.E_BehindCurves;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
text.IsClippedToChartRect = true;
list.Add(text);
SizeF size = text.LayoutArea;
float width = size.Width;
if (deltaMass > 0.0)
{
deltaMassString = "+" + Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.011,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.A_InFront;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false ;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
else if (deltaMass < 0.0)
{
deltaMassString = Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.01,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.B_BehindLegend;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false ;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
if (topSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(topSeriesColor, topSeriesLeftPoint + tickStart, (seriesTopLeftOffset - 0.03), topSeriesLeftPoint + tickStart, seriesTopLeftOffset);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(topSeriesColor, topSeriesLeftPoint, (seriesTopLeftOffset - 0.05), topSeriesLeftPoint + tickStart, seriesTopLeftOffset - 0.03);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
}
// Reset the series starting point
topSeriesLeftPoint = 0.025;
#endregion
///
#region Process y/z ions
//then for y/z ions:
//note: since the fragmentsummary starts the ticking/lining from left to right,
//so we need to adjust the starting point of bottoms series from the highest to lowest.
///
for (int i = sequence.Length; i >= 1; --i)
{
double tickStart = residueWidth / 5.0;
double bottomSeriesFragmentMZ = 0.0;
bool bottomSeriesHasMatch = false;
//test neutral
string Cseq = peptide.sequence.Substring(sequenceLength - i, i);
char[] seqchars = peptide.sequence.ToCharArray();
int Cphosmodi = 0;
for (int k = sequenceLength - i; k < sequenceLength; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[k] == 'Y'))
{
Cphosmodi++;
}
}
for (int z = min; z <= max; z++)
{
switch (bottomSeries)
{
case "y": bottomSeriesFragmentMZ = fragmentation.y(i, z); break;
case "z": bottomSeriesFragmentMZ = fragmentation.z(i, z); break;
case "z*": bottomSeriesFragmentMZ = fragmentation.zRadical(i, z); break;
default: bottomSeriesFragmentMZ = 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(bottomSeriesFragmentMZ - 0.5);
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
//test neutral loss
#region water loss y/z bottom series
if (waterLoss == true)
{
if (Cseq.Contains("S") || Cseq.Contains("T") || Cseq.Contains("E") || Cseq.Contains("D"))
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - WATERMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
}
#endregion
//test neutral loss
#region ammonium loss y/z bottom series
if (ammoniumLoss == true)
{
if (Cseq.Contains("R") || Cseq.Contains("K") || Cseq.Contains("Q") || Cseq.Contains("N"))
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
#endregion
//test neutral loss
#region phosphate loss y/z bottom series
if (phosphateLoss == true)
{
int minPhosphate = Math.Min(Cphosmodi, numPhosphate);
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
}
}
#endregion
}
if (bottomSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(bottomSeriesColor, topSeriesLeftPoint - tickStart, seriesTopLeftOffset, topSeriesLeftPoint - tickStart, seriesTopLeftOffset + 0.03);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(bottomSeriesColor, topSeriesLeftPoint - tickStart, seriesTopLeftOffset + 0.03, topSeriesLeftPoint + 2.0 * tickStart, seriesTopLeftOffset + 0.05);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
}
// Reset the series starting point
topSeriesLeftPoint = 0.025;
#endregion
///
#region Process x/c series
///
//the reason that I didn't split c/x as ab/yz, is that c/x doesn't have to deal with the termini. so good to go.
//disable the function of neutral losses
for (int i = 1; i < sequence.Length; ++i)
{
double tickStart = residueWidth *4 / 5.0;
double topSeriesFragmentMZ = 0.0;
double bottomSeriesFragmentMZ = 0.0;
// Check if the top and bottom fragments have evidence
bool topSeriesHasMatch = false;
bool bottomSeriesHasMatch = false;
///
//test neutral loss
//test neutral
//adjust the "i" accordingly, must let the C ions be left=>right.
//if it goes from left to right, then N series is i;
//C series is more tricky. Get a NTempSeq from 0 to sequenceLength-i; then get C from total.
///
string Nseq = peptide.sequence.Substring(0, i);
string NTempSeq = peptide.sequence.Substring(0, sequenceLength - i);
string Cseq = peptide.sequence.Substring(i, sequenceLength-i);
char[] Nseqchars = Nseq.ToCharArray();
char[] seqchars = peptide.sequence.ToCharArray();
char[] NTempSeqChars = NTempSeq.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 && (Nseqchars[k] == 'S' || Nseqchars[k] == 'T' || Nseqchars[k] == 'Y'))
{
Nphosmodi++;
}
}
for (int k = 0; k < sequenceLength - i; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (NTempSeqChars[k] == 'S' || NTempSeqChars[k] == 'T' || NTempSeqChars[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 z = min; z <= max; z++)
{
switch (topSeries)
{
case "c": topSeriesFragmentMZ = fragmentation.c(i, z); break;
default: topSeriesFragmentMZ = 0.0; break;
}
switch (bottomSeries)
{
case "x": bottomSeriesFragmentMZ = fragmentation.x(sequence.Length - i, z); break;
default: bottomSeriesFragmentMZ = 0.0; break;
}
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);
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ + 0.5))
topSeriesHasMatch = true;
// Reset the search index
index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - 0.5);
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ + 0.5))
bottomSeriesHasMatch = true;
}
//disable neutral losses for c/x series
//test neutral loss
#region water loss c/x
if (waterLoss == true)
{
if (Nseq.Contains("S") || Nseq.Contains("T") || Nseq.Contains("E") || Nseq.Contains("D"))
{
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 - WATERMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
topSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
topSeriesHasMatch = true;
}
}
}
if (Cseq.Contains("S") || Cseq.Contains("T") || Cseq.Contains("E") || Cseq.Contains("D"))
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - WATERMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
bottomSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
bottomSeriesHasMatch = true;
}
}
}
}
#endregion
////test neutral loss
#region ammonium loss c/x
if (ammoniumLoss == true)
{
if (points != null)
{
if (Nseq.Contains("R") || Nseq.Contains("K") || Nseq.Contains("Q") || Nseq.Contains("N"))
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
topSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
topSeriesHasMatch = true;
}
}
if (Cseq.Contains("R") || Cseq.Contains("K") || Cseq.Contains("Q") || Cseq.Contains("N"))
{
// Reset the search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
bottomSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
bottomSeriesHasMatch = true;
}
}
}
}
#endregion
////test neutral loss
#region phosphate loss c/x
if (phosphateLoss == true)
{
int minPhosphate = Math.Min(Nphosmodi, numPhosphate);
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
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 - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
minPhosphate = Math.Min(Cphosmodi, numPhosphate);
{
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
}
}
}
#endregion
}
// 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();
string deltaMassString = deltaMass.ToString();
// 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.Left, AlignV.Center);
text.ZOrder = ZOrder.B_BehindLegend;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
text.IsClippedToChartRect = true;
list.Add(text);
SizeF size = text.LayoutArea;
float width = size.Width;
if (deltaMass > 0.0)
{
deltaMassString = "+" + Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.01,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.B_BehindLegend;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
else if (deltaMass < 0.0)
{
deltaMassString = Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.01,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.B_BehindLegend;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
if (topSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(topSeriesColor, topSeriesLeftPoint + tickStart, (seriesTopLeftOffset - 0.03), topSeriesLeftPoint + tickStart, seriesTopLeftOffset);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(topSeriesColor, topSeriesLeftPoint, (seriesTopLeftOffset - 0.05), topSeriesLeftPoint + tickStart, seriesTopLeftOffset - 0.03);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
if (bottomSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(bottomSeriesColor, topSeriesLeftPoint + tickStart, seriesTopLeftOffset, topSeriesLeftPoint + tickStart, seriesTopLeftOffset + 0.03);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(bottomSeriesColor, topSeriesLeftPoint + tickStart, seriesTopLeftOffset + 0.03, topSeriesLeftPoint + 2.0 * tickStart, seriesTopLeftOffset + 0.05);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
}
#endregion
}