本文整理汇总了C#中Peptide.monoisotopicMass方法的典型用法代码示例。如果您正苦于以下问题：C# Peptide.monoisotopicMass方法的具体用法？C# Peptide.monoisotopicMass怎么用？C# Peptide.monoisotopicMass使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Peptide的用法示例。
在下文中一共展示了Peptide.monoisotopicMass方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C#代码示例。
示例1: Update
//.........这里部分代码省略.........
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(),示例2: Update
//.........这里部分代码省略.........
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));
}
}
}
if (showLadders || showFragmentationSummary)
{
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);
}
// fill peptide info table
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;
// show/hide/update fragment table
if (!annotationPanels.showFragmentationTableCheckBox.Checked || ionSeries <= IonSeries.Auto)
{
annotationPanels.fragmentInfoGridView.Visible = false;
annotationPanels.fragmentInfoGridView.Rows.Clear();
return;
}
annotationPanels.fragmentInfoGridView.Visible = true;
annotationPanels.fragmentInfoGridView.SuspendLayout();
if (annotationPanels.fragmentInfoGridView.Columns.Count == 0)
{
#region Add columns for fragment types
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)示例3: Update
public override void Update( GraphItem item, pwiz.MSGraph.MSPointList points, GraphObjList annotations )
{
if( !Enabled )
return;
if( !( item is MassSpectrum ) )
return; // throw exception?
GraphObjList list = annotations;
Peptide peptide;
try
{
peptide = new Peptide( currentSequence,
pwiz.CLI.proteome.ModificationParsing.ModificationParsing_Auto,
pwiz.CLI.proteome.ModificationDelimiter.ModificationDelimiter_Brackets );
} catch( Exception )
{
return;
}
string unmodifiedSequence = peptide.sequence;
int sequenceLength = unmodifiedSequence.Length;
Fragmentation fragmentation = peptide.fragmentation( fragmentMassType == 0 ? true : false, true );
// Keeps track of number of fragments predicted and matched in each ion series
numFragmentsMatched.Clear();
numFragmentsPredicted.Clear();
for( int charge = min; charge <= max; ++charge )
{
for( int i = 1; i <= sequenceLength; ++i )
{
if( a ) addFragment( list, points, "a", i, charge, fragmentation.a( i, charge ) );
if( b ) addFragment( list, points, "b", i, charge, fragmentation.b( i, charge ) );
if( y ) addFragment( list, points, "y", i, charge, fragmentation.y( i, charge ) );
if( z ) addFragment( list, points, "z", i, charge, fragmentation.z( i, charge ) );
if( zRadical ) addFragment( list, points, "z*", i, charge, fragmentation.zRadical( i, charge ) );
if( i < sequenceLength )
{
if( c ) addFragment( list, points, "c", i, charge, fragmentation.c( i, charge ) );
if( x ) addFragment( list, points, "x", i, charge, fragmentation.x( i, charge ) );
}
}
}
if( showLadders )
{
string topSeries = a ? "a" : b ? "b" : c ? "c" : "";
string bottomSeries = x ? "x" : y ? "y" : z ? "z" : zRadical ? "z*" : "";
addIonSeries( list, points, peptide, fragmentation, topSeries, bottomSeries );
}
// fill peptide info table
annotationPanels.peptideInfoGridView.Rows.Clear();
var spectrum = ( item as MassSpectrum ).Element;
//if( spectrum.precursors.Count > 0 &&
// spectrum.precursors[0].selectedIons.Count > 0 &&
// spectrum.precursors[0].selectedIons[0].hasCVParam( pwiz.CLI.cv.CVID.MS_selected_ion_m_z ) &&
// spectrum.precursors[0].selectedIons[0].hasCVParam( pwiz.CLI.cv.CVID.MS_charge_state ) )
//{
// double selectedMz = (double) spectrum.precursors[0].selectedIons[0].cvParam( pwiz.CLI.cv.CVID.MS_selected_ion_m_z ).value;
// int chargeState = (int) spectrum.precursors[0].selectedIons[0].cvParam( pwiz.CLI.cv.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() );
if (spectrum.precursors.Count > 0 &&
spectrum.precursors[0].selectedIons.Count > 0 &&
spectrum.precursors[0].selectedIons[0].hasCVParam(pwiz.CLI.cv.CVID.MS_selected_ion_m_z))
{
double selectedMz = (double)spectrum.precursors[0].selectedIons[0].cvParam(pwiz.CLI.cv.CVID.MS_selected_ion_m_z).value;
// Add xcorr score
ZedGraph.IPointList peaks = (item as MassSpectrum).Points;
List<ScoringUtils.Peak> rawPeaks = new List<ScoringUtils.Peak>();
for (int i = 0; i < peaks.Count; ++i)
rawPeaks.Add(new ScoringUtils.Peak(peaks[i].X, peaks[i].Y));
// Remove the precursor and associated neutral loss peaks
ScoringUtils.erasePrecursorIons(selectedMz, ref rawPeaks); //selectedMz = precursorMz
if (spectrum.precursors[0].selectedIons[0].hasCVParam(pwiz.CLI.cv.CVID.MS_charge_state)) // known precursor charge state
{
int chargeState = (int)spectrum.precursors[0].selectedIons[0].cvParam(pwiz.CLI.cv.CVID.MS_charge_state).value;
double calculatedMass = (precursorMassType == 0 ? peptide.monoisotopicMass(chargeState) : peptide.molecularWeight(chargeState)) * chargeState;
double observedMass = selectedMz * chargeState;
// compute XCorr
double precursorMH = (selectedMz * chargeState) - ((chargeState - 1) * 1.007276);
double xcorr = ScoringUtils.computeXCorr(rawPeaks, peptide, precursorMH);
annotationPanels.peptideInfoGridView.Rows.Add("Observed precursor charge:", chargeState, "XCorr:", xcorr);
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 // unknown precursor charge state, assume +2 or +3
{
//.........这里部分代码省略.........