private void mnuCrosslink_Click(object sender, EventArgs e)
{
TreeNode node1 = tvMRM.SelectedNodes[0] as TreeNode;
TreeNode node2 = tvMRM.SelectedNodes[1] as TreeNode;
var mr = GetResult(node1);
SrmPairedPeptideItem item1 = node1.Tag as SrmPairedPeptideItem;
SrmPairedPeptideItem item2 = node2.Tag as SrmPairedPeptideItem;
SrmPairedPeptideItem light, heavy;
if (item1.LightPrecursorMZ < item2.LightPrecursorMZ)
{
light = item1;
heavy = item2;
}
else
{
light = item2;
heavy = item1;
}
if (light.AddErrorPairedPeptideItem(heavy, mr.Options.AllowedGaps, mr.Options.MzTolerance, mr.Options.RetentionTimeToleranceInSecond))
{
mr.Remove(heavy);
tvMRM.Nodes.Remove(node2);
AssignItem(light, node1);
SetCurrentResultModified();
}
}
private void mnuCrosslink_Click(object sender, EventArgs e)
{
TreeNode node1 = tvMRM.SelectedNodes[0] as TreeNode;
TreeNode node2 = tvMRM.SelectedNodes[1] as TreeNode;
SrmPairedPeptideItem item1 = node1.Tag as SrmPairedPeptideItem;
SrmPairedPeptideItem item2 = node2.Tag as SrmPairedPeptideItem;
SrmPairedPeptideItem item;
if (item1.LightPrecursorMZ < item2.LightPrecursorMZ)
{
item = item1;
item.SetHeavyPeptideItem(item2);
mrmPairs.Remove(item2);
}
else
{
item = item2;
item.SetHeavyPeptideItem(item1);
mrmPairs.Remove(item1);
}
tvMRM.Nodes.Remove(node2);
AssignItem(item, node1);
}
/// <summary>
/// 合并轻重标结果。如果自动识别未能把成对的肽段合并，就需要手工合并。
/// </summary>
/// <param name="heavy">重标肽段</param>
public void SetHeavyPeptideItem(SrmPairedPeptideItem heavy)
{
var sorted = (from h in heavy.ProductIonPairs
orderby h.Light.ProductIon
select h).ToList();
var sortedThis = (from h in this.ProductIonPairs
orderby h.Light.ProductIon
select h).ToList();
//首先去除完全一样的production
for (int i = sorted.Count - 1; i >= 0; i--)
{
var index = sortedThis.FindIndex(m => m.Light.ProductIon == sorted[i].Light.ProductIon);
if (index != -1)
{
sortedThis[index].SetHeavyIon(sorted[i]);
sorted.RemoveAt(i);
sortedThis.RemoveAt(index);
}
}
for (int i = 0; i < sorted.Count; i++)
{
sortedThis[i].SetHeavyIon(sorted[i]);
}
}
private void mnuSetScanEnabledOnly_Click(object sender, EventArgs e)
{
GraphPane graphScans = mnuSetScanEnabledOnly.Tag as GraphPane;
double min = graphScans.XAxis.Scale.Min;
double max = graphScans.XAxis.Scale.Max;
SrmPairedProductIon ion = graphScans.Tag as SrmPairedProductIon;
SrmPairedPeptideItem item = FindItemByProductIon(ion);
if (null == item)
{
return;
}
item.SetEnabledRetentionTimeRange(min, max);
CurrentResult.Update(item);
gvProductPair.Refresh();
DoUpdateProductIon();
tvMRM_AfterSelect(null, null);
SetCurrentResultModified();
}
private void tvMRM_AfterSelect(object sender, TreeViewEventArgs e)
{
if (displaying)
{
return;
}
DoUpdatePeptide();
var node = tvMRM.SelectedNode;
if (null == node || node.Level != 2)
{
return;
}
//设置当前product ion
SrmPairedProductIon item = node.Tag as SrmPairedProductIon;
SrmPairedPeptideItem pep = node.Parent.Tag as SrmPairedPeptideItem;
int rowIndex = pep.ProductIonPairs.IndexOf(item);
CurrencyManager cm = (CurrencyManager)this.BindingContext[pep.ProductIonPairs];
if (cm.Position != rowIndex)
{
cm.Position = rowIndex;
}
}
private static void Transfer(SrmPairedPeptideItem source, SrmPairedPeptideItem target, DataGridView gvSource, DataGridView gvTarget)
{
if (gvSource.SelectedRows.Count == 0)
{
return;
}
var rowIndecies = new List <int>();
for (int i = 0; i < gvSource.SelectedRows.Count; i++)
{
rowIndecies.Add(gvSource.SelectedRows[i].Index);
}
rowIndecies.Sort();
gvSource.DataSource = null;
gvTarget.DataSource = null;
try
{
for (int i = rowIndecies.Count - 1; i >= 0; i--)
{
target.ProductIonPairs.Add(source.ProductIonPairs[rowIndecies[i]]);
source.ProductIonPairs.RemoveAt(rowIndecies[i]);
}
}
finally
{
gvSource.DataSource = source.ProductIonPairs;
gvTarget.DataSource = target.ProductIonPairs;
}
}
private void tvMRM_AfterCheck(object sender, TreeViewEventArgs e)
{
if (displaying)
{
return;
}
var node = e.Node;
if (node.Level == 0)
{
return;
}
if (node.Level == 1)
{
SrmPairedPeptideItem pepItem = node.Tag as SrmPairedPeptideItem;
pepItem.Enabled = node.Checked;
return;
}
if (node.Level == 2)
{
SrmPairedProductIon item = node.Tag as SrmPairedProductIon;
item.Enabled = node.Checked;
SrmPairedPeptideItem pepItem = node.Parent.Tag as SrmPairedPeptideItem;
pepItem.CalculatePeptideRatio();
}
tvMRM_AfterSelect(null, null);
SetCurrentResultModified();
}
private XElement PeptideToItem(SrmPairedPeptideItem item)
{
if (null == item)
{
return(null);
}
return(new XElement("Item",
new XElement("Enabled", item.Enabled.ToString()),
new XElement("Ratio", MyConvert.Format("{0:0.0000}", item.Ratio)),
new XElement("SD", double.IsInfinity(item.SD) || double.IsNaN(item.SD) ? "-" : MyConvert.Format("{0:0.0000}", item.SD)),
new XElement("ObjectName", item.ObjectName),
new XElement("PrecursorFormula", item.PrecursorFormula),
new XElement("PrecursorCharge", item.PrecursorCharge),
from p in item.ProductIonPairs
select new XElement("ProductIonPair",
new XElement("Enabled", p.Enabled.ToString()),
new XElement("Ratio", MyConvert.Format("{0:0.0000}", p.Ratio)),
new XElement("Distance", MyConvert.Format("{0:0.0000}", p.Distance)),
new XElement("RegressionCorrelation", MyConvert.Format("{0:0.0000}", p.RegressionCorrelation)),
new XElement("LightArea", MyConvert.Format("{0:0.0}", p.LightArea)),
new XElement("HeavyArea", MyConvert.Format("{0:0.0}", p.HeavyArea)),
new XElement("Noise", MyConvert.Format("{0:0.00}", p.Noise)),
new XElement("LightSignalToNoise", MyConvert.Format("{0:0.00}", p.LightSignalToNoise)),
new XElement("HeavySignalToNoise", MyConvert.Format("{0:0.00}", p.HeavySignalToNoise)),
TransactionToElement(p.Light, "LightTransaction"),
TransactionToElement(p.Heavy, "HeavyTransaction"))));
}
public SrmFileItem(SrmPairedResult result, SrmPairedPeptideItem peptide, SrmPairedProductIon production)
{
this.PairedResult = result;
this.PairedPeptide = peptide;
this.PairedProductIon = production;
_precursorMz = new Pair <double, double>(peptide.LightPrecursorMZ, peptide.HeavyPrecursorMZ);
_productIonMz = new Pair <double, double>(production.LightProductIon, production.HeavyProductIon);
}
private CompoundItem FindComponent(SrmPairedPeptideItem pep)
{
var fileitem = (from f in allFiles.Compounds
where f.ObjectName.Equals(pep.ProductIonPairs[0].ObjectName) && f.PrecursurFormula.Equals(pep.ProductIonPairs[0].PrecursorFormula)
select f).FirstOrDefault();
return(fileitem);
}
public static SrmPairedResult ToPairedResult(this List <SrmTransition> transList)
{
SrmPairedResult result = new SrmPairedResult();
//所有母离子有相同名称、相同质荷比认为是来自相同precursor，合并为一个peptide。
var pepgroup = transList.GroupBy(m => m.PrecursorFormula + MyConvert.Format("{0:0.0000}", m.PrecursorMZ));
var peptides = new List <SrmPeptideItem>();
foreach (var g in pepgroup)
{
var pep = new SrmPeptideItem();
pep.PrecursorMZ = g.First().PrecursorMZ;
pep.ProductIons = new List <SrmTransition>(g);
peptides.Add(pep);
}
//具有相同母离子名称和电荷的transition认为是轻重标。
var lhgroup = peptides.GroupBy(m => m.ProductIons[0].PrecursorFormula + "_" + m.ProductIons[0].PrecursorCharge.ToString()).ToList();
// var lhgroup = peptides.GroupBy(m => m.ProductIons[0].PrecursorFormula + "_" + m.ProductIons[0].PrecursorCharge.ToString()).ToList();
foreach (var g in lhgroup)
{
if (g.Count() > 2)
{
throw new Exception(string.Format("There are {0} transition with same precursor formula and precursor charge: {1}, {2}", g.Count(), g.First().ProductIons[0].PrecursorFormula, g.First().ProductIons[0].PrecursorCharge));
}
else if (g.Count() > 1)
{
var items = g.ToList();
items.Sort((m1, m2) => m1.PrecursorMZ.CompareTo(m2.PrecursorMZ));
SrmPairedPeptideItem light = new SrmPairedPeptideItem(items[0]);
SrmPairedPeptideItem heavy = new SrmPairedPeptideItem(items[1]);
if (!string.IsNullOrEmpty(light.ProductIonPairs[0].Light.Ion))
{
light.SetHeavyPeptideItemByIon(heavy);
}
else
{
light.SetHeavyPeptideItem(heavy);
}
result.Add(light);
}
else
{
SrmPairedPeptideItem light = new SrmPairedPeptideItem(g.First());
result.Add(light);
}
}
return(result);
}
private static void AssignItem(SrmPairedPeptideItem mrm, TreeNode node)
{
node.Nodes.Clear();
node.Text = mrm.ToString();
node.Tag = mrm;
node.Checked = mrm.Enabled;
mrm.ProductIonPairs.ForEach(m =>
{
string ions = MyConvert.Format("{0:0.0000} : {1:0.0000}", m.Light.ProductIon, mrm.IsPaired ? m.Heavy.ProductIon : 0);
TreeNode subNode = node.Nodes.Add(ions);
subNode.Tag = m;
subNode.Checked = m.Enabled;
});
}
private void tcFiles_SelectedIndexChanged(object sender, EventArgs e)
{
if (tcFiles.TabCount > 0 && tcFiles.SelectedTab != null)
{
var fileName = tcFiles.SelectedTab.Text;
files.Compounds.ForEach(m => m.FileName = fileName);
gvCompounds.Refresh();
filePeptide = currentCompound.GetPeptideItem(fileName);
gvProductPair.DataSource = filePeptide.ProductIonPairs;
}
}
private static void WritePeptide(StreamWriter sw, SrmPairedPeptideItem pep, Color c)
{
String strHtmlColor = System.Drawing.ColorTranslator.ToHtml(c);
sw.WriteLine("<font color=\"{0}\">", strHtmlColor);
sw.WriteLine("{0} - {1} : {2:0.0000} - {3:0.0000}<br>", pep.ProductIonPairs[0].ObjectName, pep.ProductIonPairs[0].PrecursorFormula, pep.LightPrecursorMZ, pep.HeavyPrecursorMZ);
sw.WriteLine("</font>");
sw.WriteLine("<table border=\"1\">");
sw.WriteLine("<tr>");
sw.WriteLine("<th scope=\"col\">Enabled</th>");
sw.WriteLine("<th scope=\"col\">Light</th>");
sw.WriteLine("<th scope=\"col\">Heavy</th>");
sw.WriteLine("<th scope=\"col\">Ratio</th>");
sw.WriteLine("<th scope=\"col\">Correl</th>");
sw.WriteLine("<th scope=\"col\">ValidScan</th>");
sw.WriteLine("</tr>");
foreach (var ion in pep.ProductIonPairs)
{
sw.WriteLine("<tr>");
if (ion.Enabled)
{
sw.WriteLine("<td><input type=\"checkbox\" checked=\"checked\"></td>");
}
else
{
sw.WriteLine("<td><input type=\"checkbox\"></td>");
}
sw.WriteLine("<td>{0:0.0000}</td>", ion.LightProductIon);
sw.WriteLine("<td>{0:0.0000}</td>", ion.HeavyProductIon);
if (double.IsNaN(ion.Ratio) || double.IsInfinity(ion.Ratio))
{
sw.WriteLine("<td></td>");
sw.WriteLine("<td></td>");
}
else
{
sw.WriteLine("<td>{0:0.0000}</td>", ion.Ratio);
sw.WriteLine("<td>{0:0.0000}</td>", ion.RegressionCorrelation);
}
sw.WriteLine("<td>{0}</td>", ion.EnabledScanCount);
sw.WriteLine("</tr>");
}
sw.WriteLine("</table>");
}
/// <summary>
/// 根据Ion来合并轻重标结果。如果自动识别未能把成对的肽段合并，就需要手工合并。
/// </summary>
/// <param name="heavy">重标肽段</param>
public void SetHeavyPeptideItemByIon(SrmPairedPeptideItem heavy)
{
foreach (var light in this.ProductIonPairs)
{
var ion = light.Light.Ion;
foreach (var h in heavy.ProductIonPairs)
{
if (ion.Equals(h.Light.Ion))
{
light.SetHeavyIon(h);
heavy.ProductIonPairs.Remove(h);
break;
}
}
}
this.ProductIonPairs.RemoveAll(m => m.Heavy == null);
}
private void mnuSetScanEnabledOnlyToolStripMenuItem_Click(object sender, EventArgs e)
{
GraphPane graphScans = mnuSetScanEnabledOnlyToolStripMenuItem.Tag as GraphPane;
double min = graphScans.XAxis.Scale.Min;
double max = graphScans.XAxis.Scale.Max;
SrmPairedProductIon ion = graphScans.Tag as SrmPairedProductIon;
SrmPairedPeptideItem item = FindItemByProductIon(ion);
if (null == item)
{
return;
}
item.SetEnabledRetentionTimeRange(min, max);
mrmPairs.Update(item);
UpdateProductPairs();
DoUpdateProductIon();
tvMRM_AfterSelect(null, null);
}
private void gvFiles_SelectionChanged(object sender, EventArgs e)
{
if (gvFiles.SelectedRows.Count == 0)
{
return;
}
var fis = currentItems[gvFiles.SelectedRows[0].Index].Items;
currentCompound = new SrmPairedPeptideItem();
for (int i = 0; i < fis.Count; i++)
{
if (fis[i] == null)
{
currentCompound.ProductIonPairs.Add(null);
}
else
{
currentCompound.ProductIonPairs.Add(fis[i].PairedProductIon);
}
}
UpdateGraph();
}
private CompoundItem FindCompoundByPeptide(SrmPairedPeptideItem item)
{
return(files.Compounds.FirstOrDefault(m => m.HasPeptideItem(item)));
}
public UpdateMRMPairedPeptideItemEventArgs(SrmPairedPeptideItem item, SrmViewOption viewOption)
: base()
{
this.Item = item;
this.ViewOption = viewOption;
}
private bool IsPeptideInvalid(SrmPairedPeptideItem pep)
{
return(pep == null || pep.Ratio == -1 || (exportInvalidCompoundAsNA.Checked && !pep.Enabled));
}
private void WriteImage(string imageDir, string imageDirName, StreamWriter sw, SrmPairedPeptideItem pep)
{
var imageFile = MyConvert.Format("{0}\\{1}.png", imageDir, pep.PrecursorFormula);
zgcPeptide.GetImage().Save(imageFile, ImageFormat.Png);
sw.WriteLine("<img src=\"{0}/{1}.png\" width=\"800\" /><br>", imageDirName, pep.PrecursorFormula);
sw.WriteLine("<hr>");
}
public bool HasPeptideItem(SrmPairedPeptideItem item)
{
return(TransitionItems.Any(m => m.FileItems.Any(n => n.PairedPeptide == item)));
}
public bool PrecursorEquals(SrmPairedPeptideItem another, double mzTolerance)
{
return((Math.Abs(this.LightPrecursorMZ - another.LightPrecursorMZ) <= mzTolerance) &&
(Math.Abs(this.HeavyPrecursorMZ - another.HeavyPrecursorMZ) <= mzTolerance));
}
/// <summary>
/// 合并两个peptideitem。如果自动识别未能把来自同一个肽段的不同transaction合并，就需要手工合并。
/// </summary>
/// <param name="another">同一个肽段（对）的其他部分</param>
public void MergePeptideItem(SrmPairedPeptideItem another)
{
this.ProductIonPairs.AddRange(another.ProductIonPairs);
}
/// <summary>
/// 判断另外一个肽段是否是这个肽段的配对肽段，要求该肽段与本肽段的所有子离子质荷比完全相同，或者差值在给定允许集合内。
/// 允许两个肽段只有部分离子相等或者差值在给定集合内。
/// </summary>
/// <param name="another">另一个肽段</param>
/// <param name="allowedGaps">子离子质荷比之差的容许值集合</param>
/// <param name="mzTolerance">质荷比阈值</param>
/// <returns>配对是否成功</returns>
public bool AddErrorPairedPeptideItem(SrmPairedPeptideItem another, double[] allowedGaps, double mzTolerance, double rtTolerance)
{
if (another == null)
{
return(false);
}
if (!RetentionTimeEqualsTo(another, rtTolerance))
{
return(false);
}
List <double> thisions = (from p in this.ProductIonPairs
orderby p.Light.ProductIon
select p.Light.ProductIon).ToList();
List <double> anotherions = (from p in another.ProductIonPairs
select p.Light.ProductIon).ToList();
List <Pair <double, double> > pairs = new List <Pair <double, double> >();
for (int i = thisions.Count - 1; i >= 0; i--)
{
for (int j = anotherions.Count - 1; j >= 0; j--)
{
if (thisions[i] == anotherions[j])
{
pairs.Add(new Pair <double, double>(thisions[i], anotherions[j]));
thisions.RemoveAt(i);
anotherions.RemoveAt(j);
break;
}
}
}
for (int i = thisions.Count - 1; i >= 0; i--)
{
for (int j = anotherions.Count - 1; j >= 0; j--)
{
var gap = Math.Abs(thisions[i] - anotherions[j]);
if (InAllowedGap(gap, allowedGaps, mzTolerance))
{
pairs.Add(new Pair <double, double>(thisions[i], anotherions[j]));
thisions.RemoveAt(i);
anotherions.RemoveAt(j);
break;
}
}
}
if (pairs.Count == 0)
{
return(false);
}
if (thisions.Count > 0)
{
this.ProductIonPairs.RemoveAll(m => thisions.Contains(m.LightProductIon));
}
if (anotherions.Count > 0)
{
another.ProductIonPairs.RemoveAll(m => anotherions.Contains(m.LightProductIon));
}
SetHeavyPeptideItem(another);
return(true);
}
/// <summary>
/// 判断目标肽段与本肽段的保留时间是否一致
/// </summary>
/// <param name="another">目标肽段</param>
/// <param name="rtToleranceMilliseconds">保留时间阈值</param>
/// <returns></returns>
public bool RetentionTimeEqualsTo(SrmPairedPeptideItem another, double rtToleranceMilliseconds)
{
return(this.ProductIonPairs[0].Light.RetentionTimeEqualsTo(another.ProductIonPairs[0].Light, rtToleranceMilliseconds));
}
private SrmPairedPeptideItem ItemToPeptide(XElement item)
{
if (item == null)
{
return(null);
}
SrmPairedPeptideItem result = new SrmPairedPeptideItem();
result.Enabled = Convert.ToBoolean(item.Element("Enabled").Value);
result.ProductIonPairs = new List <SrmPairedProductIon>();
foreach (var p in item.Descendants("ProductIonPair"))
{
SrmPairedProductIon ion = new SrmPairedProductIon();
ion.Enabled = Convert.ToBoolean(p.Element("Enabled").Value);
ion.Ratio = MyConvert.ToDouble(p.Element("Ratio").Value);
ion.Distance = MyConvert.ToDouble(p.Element("Distance").Value);
ion.RegressionCorrelation = MyConvert.ToDouble(p.Element("RegressionCorrelation").Value);
var scanEle = p.Elements("Scan");
if (scanEle.Count() > 0)
{
var scans = (from a in scanEle
select new SrmPairedScan()
{
Light = SrmScanFileFormat.ElementToScan(a.Element("Light")),
Heavy = SrmScanFileFormat.ElementToScan(a.Element("Heavy"))
}).ToList();
if (scans.Count > 0)
{
if (scans[0].Light != null)
{
var light = new SrmTransition(scans[0].Light.PrecursorMz, scans[0].Light.ProductMz);
light.Intensities = (from s in scans
select s.Light).ToList();
ion.Light = light;
}
if (scans[0].Heavy != null)
{
var heavy = new SrmTransition(scans[0].Heavy.PrecursorMz, scans[0].Heavy.ProductMz);
heavy.Intensities = (from s in scans
select s.Heavy).ToList();
ion.Heavy = heavy;
}
}
}
else
{
ion.Light = ElementToTransaction(p.Element("LightTransaction"));
ion.Heavy = ElementToTransaction(p.Element("HeavyTransaction"));
}
if (p.Element("LightArea") != null)
{
ion.LightArea = MyConvert.ToDouble(p.Element("LightArea").Value);
ion.HeavyArea = MyConvert.ToDouble(p.Element("HeavyArea").Value);
}
result.ProductIonPairs.Add(ion);
}
if (item.Element("Ratio") != null)
{
result.Ratio = MyConvert.ToDouble(item.Element("Ratio").Value);
if (item.Element("SD").Value.Equals("-"))
{
result.SD = double.NaN;
}
else
{
result.SD = MyConvert.ToDouble(item.Element("SD").Value);
}
}
else
{
result.CalculatePeptideRatio();
}
var objname = string.Empty;
var pepname = string.Empty;
var pepcharge = 0;
if (item.Element("ObjectName") != null)
{
objname = item.Element("ObjectName").Value;
}
if (item.Element("PrecursorFormula") != null)
{
pepname = item.Element("PrecursorFormula").Value;
}
if (item.Element("PrecursorCharge") != null)
{
pepcharge = int.Parse(item.Element("PrecursorCharge").Value);
}
result.ProductIonPairs.ForEach(m =>
{
if (m.Light != null)
{
m.Light.ObjectName = objname;
m.Light.PrecursorFormula = pepname;
m.Light.PrecursorCharge = pepcharge;
}
if (m.Heavy != null)
{
m.Heavy.ObjectName = objname;
m.Heavy.PrecursorFormula = pepname;
m.Heavy.PrecursorCharge = pepcharge;
}
});
return(result);
}
