private void DoCompoundChanged(CompoundItem compound)
{
if (compoundInList != compound)
{
compoundInList = compound;
currentItems = GetFileItems(compound);;
gvFiles.Rows.Clear();
gvFiles.RowCount = currentItems.Count;
}
}
private void gvCompounds_SelectionChanged(object sender, EventArgs e)
{
if (gvCompounds.SelectedRows.Count == 0)
{
return;
}
currentCompound = visibleCompounds[gvCompounds.SelectedRows[0].Index];
DoCompoundChanged();
}
public void ExportCompound(string filename, bool removeDecoy, bool validOnly)
{
using (StreamWriter sw = new StreamWriter(filename))
{
sw.Write("ObjectName,CompoundFormula,LightMz,HeavyMz,Enabled");
var filenames = (from pr in allFiles.Items
orderby pr.PairedResult.PureFileName
select pr.PairedResult.PureFileName).Distinct().ToList();
filenames.ForEach(m => sw.Write(",{0}_Ratio,{0}_SD,{0}_ValidTransCount", m));
sw.WriteLine();
for (int i = 0; i < lvPeptides.Items.Count; i++)
{
if (validOnly && !lvPeptides.GetItemChecked(i))
{
continue;
}
CompoundItem item = lvPeptides.Items[i] as CompoundItem;
if (removeDecoy && item.IsDecoy)
{
continue;
}
sw.Write("{0},{1},{2:0.0000},{3:0.0000},{4}", item.ObjectName, item.PrecursurFormula, item.LightMz, item.HeavyMz, lvPeptides.GetItemChecked(i));
foreach (var file in filenames)
{
var pep = (from t in item.TransitionItems
from m in t.FileItems
where m.PairedResult.PureFileName.Equals(file)
select m.PairedPeptide).FirstOrDefault();
if (pep == null || pep.Ratio == -1)
{
sw.Write(",#N/A,0,0");
}
else
{
var transCount = pep.ProductIonPairs.Count(m => m.Enabled);
if (double.IsNaN(pep.SD) || double.IsInfinity(pep.SD))
{
sw.Write(",{0:0.0000},0,{1}", pep.Ratio, transCount);
}
else
{
sw.Write(",{0:0.0000},{1:0.0000},{2}", pep.Ratio, pep.SD, transCount);
}
}
}
sw.WriteLine();
}
}
}
public void BuildList()
{
_compounds = new List <CompoundItem>();
foreach (var m in Items)
{
CompoundItem citem = null;
foreach (var c in _compounds)
{
if (IsSameCompound(c, m))
{
citem = c;
break;
}
}
if (citem == null)
{
citem = new CompoundItem();
AssignSrmFileItemTo(m, citem);
_compounds.Add(citem);
}
TransitionItem titem = null;
foreach (var t in citem.TransitionItems)
{
if (t.TransitionEquals(m, this.MzTolerance))
{
titem = t;
break;
}
}
if (titem == null)
{
titem = new TransitionItem();
AssignSrmFileItemTo(m, titem);
citem.TransitionItems.Add(titem);
}
titem.FileItems.Add(m);
}
var fileNames = GetFileNames();
_compounds.ForEach(m => m.InitializeFileItems(fileNames));
_compounds.Sort((m1, m2) => m1.ToString().CompareTo(m2.ToString()));
_compounds.ForEach(m => m.TransitionItems.Sort((n1, n2) => n1.LightMz.CompareTo(n2.LightMz)));
}
private List <FileItems> GetFileItems(CompoundItem compound)
{
List <FileItems> tmpItems = new List <FileItems>();
foreach (var titem in compound.TransitionItems)
{
var item = new FileItems();
item.Precursor = GetString(titem);
item.Items = new List <SrmFileItem>();
for (int i = FirstProductIonColumn; i < gvFiles.Columns.Count; i++)
{
var fileitem = titem.FileItems.Find(m => m.PairedResult.PureFileName.Equals(gvFiles.Columns[i].Name));
item.Items.Add(fileitem);
}
tmpItems.Add(item);
}
return(tmpItems);
}
public void ExportTransition(string filename, bool removeDecoy, bool validOnly)
{
using (StreamWriter sw = new StreamWriter(filename))
{
sw.Write("ObjectName,CompoundFormula,LightPrecursorMz,LightProductIon,HeavyPrecursorMz,HeavyProductIon,Enabled");
var filenames = (from pr in allFiles.Items
orderby pr.PairedResult.PureFileName
select pr.PairedResult.PureFileName).Distinct().ToList();
filenames.ForEach(m => sw.Write(",{0}_Ratio,{0}_R2,{0}_LightArea,{0}_HeavyArea,{0}_ValidScanCount", m));
sw.WriteLine();
for (int i = 0; i < lvPeptides.Items.Count; i++)
{
if (validOnly && !lvPeptides.GetItemChecked(i))
{
continue;
}
CompoundItem item = lvPeptides.Items[i] as CompoundItem;
if (removeDecoy && item.IsDecoy)
{
continue;
}
var fileitems = GetFileItems(item);
foreach (var fitem in fileitems)
{
if (validOnly && !fitem.Enabled)
{
continue;
}
var product = (from f in fitem.Items
where f != null
select f).First().PairedProductIon;
sw.Write("{0},{1},{2:0.0000},{3:0.0000},{4:0.0000},{5:0.0000},{6}", item.ObjectName, item.PrecursurFormula, item.LightMz, product.LightProductIon, item.HeavyMz, product.HeavyProductIon, fitem.Enabled);
foreach (var file in filenames)
{
var pep = (from t in fitem.Items
where t.PairedResult.PureFileName.Equals(file)
select t.PairedProductIon).FirstOrDefault();
if (pep == null || pep.Ratio == -1)
{
sw.Write(",#N/A,0,#N/A,#N/A,0");
}
else
{
var scanCount = pep.EnabledScanCount;
if (double.IsNaN(pep.RegressionCorrelation) || double.IsInfinity(pep.RegressionCorrelation))
{
sw.Write(",{0:0.0000},0,{1:0.0},{2:0.0},{3}", pep.Ratio, pep.LightArea, pep.HeavyArea, scanCount);
}
else
{
sw.Write(",{0:0.0000},{1:0.0000},{2:0.0},{3:0.0},{4}", pep.Ratio, pep.RegressionCorrelation, pep.LightArea, pep.HeavyArea, scanCount);
}
}
}
sw.WriteLine();
}
}
}
}
public static bool AlwaysFalse(CompoundItem item)
{
return(false);
}
public static bool IsInvalid(CompoundItem item)
{
return(!item.Enabled);
}
public static bool IsDecoy(CompoundItem item)
{
return(item.IsDecoy);
}
