/// <summary>
/// This function exports a detailed protein modification report.
/// </summary>
public void exportProteinReport(Set <string> loci, StreamWriter writer)
{
if (loci.Count == 0)
{
return;
}
Map <string, Map <string, int> > table = new Map <string, Map <string, int> >();
Set <string> allSources = new Set <string>();
foreach (var locus in loci)
{
foreach (var peptide in proteins[locus].peptides)
{
foreach (var interp in proteins[locus].interpretations[peptide])
{
foreach (var variant in proteins[locus].variants[interp])
{
string key = locus + "," + interp;
foreach (var spectrum in proteins[locus].spectra[variant])
{
string sourceName = spectrum.id.source.group.name;
allSources.Add(sourceName);
++table[key][sourceName];
SourceGroupList parentGroups = new SourceGroupList();
foreach (var parent in spectrum.id.source.group.getAllParentGroupPaths())
{
allSources.Add(parent);
++table[key][parent];
}
}
}
}
}
}
writer.Write("Protein,peptide");
foreach (var source in allSources)
{
writer.Write("," + source);
}
writer.WriteLine();
foreach (var keys in table)
{
StringBuilder line = new StringBuilder();
line.Append(keys.Key);
foreach (var source in allSources)
{
line.Append("," + table[keys.Key][source]);
}
writer.WriteLine(line.ToString());
}
writer.Flush();
}
public void exportPeptideReport(Set <string> loci, StreamWriter writer)
{
if (loci.Count == 0)
{
return;
}
// Interpretation to variant map
Map <string, Set <VariantInfo> > uniqueVariants = new Map <string, Set <VariantInfo> >();
// Interpretation to protein ID map
Map <string, Set <ProteinInstanceInfo> > varToProteinMap = new Map <string, Set <ProteinInstanceInfo> >();
// Variant to spectrum map
Map <VariantInfo, Set <SpectrumInfo> > varToSpecMap = new Map <VariantInfo, Set <SpectrumInfo> >();
foreach (var locus in loci)
{
foreach (var peptide in proteins[locus].peptides)
{
foreach (var interp in proteins[locus].interpretations[peptide])
{
foreach (var variant in proteins[locus].variants[interp])
{
uniqueVariants[variant.ToInsPecTStyle()].Add(variant);
foreach (var spectrum in proteins[locus].spectra[variant])
{
varToSpecMap[variant].Add(spectrum);
}
foreach (var protein in variant.peptide.proteins.Values)
{
varToProteinMap[interp].Add(protein);
}
}
}
}
}
Map <string, Map <string, int> > table = new Map <string, Map <string, int> >();
Set <string> allSources = new Set <string>();
foreach (var interp in uniqueVariants.Keys)
{
foreach (var variant in uniqueVariants[interp])
{
foreach (var spectrum in varToSpecMap[variant])
{
string sourceName = spectrum.id.source.group.name;
allSources.Add(sourceName);
++table[interp][sourceName];
SourceGroupList parentGroups = new SourceGroupList();
foreach (var parent in spectrum.id.source.group.getAllParentGroupPaths())
{
allSources.Add(parent);
++table[interp][parent];
}
}
}
}
writer.Write("Peptide,Protein,Alternatives");
foreach (var source in allSources)
{
writer.Write("," + source);
}
writer.WriteLine();
foreach (var keys in table)
{
StringBuilder line = new StringBuilder();
line.Append(keys.Key);
Set <ProteinInstanceInfo> .Enumerator proIter = varToProteinMap[keys.Key].GetEnumerator();
proIter.MoveNext();
ProteinInstanceInfo first = proIter.Current;
line.Append("," + first.protein.locus);
StringBuilder alts = new StringBuilder();
while (proIter.MoveNext())
{
alts.Append(proIter.Current.protein.locus + ";");
}
line.Append("," + alts.ToString());
foreach (var source in allSources)
{
line.Append("," + table[keys.Key][source]);
}
writer.WriteLine(line.ToString());
}
writer.Flush();
}
public void exportPeptideReport(Set<string> loci, StreamWriter writer)
{
if(loci.Count == 0)
return;
// Interpretation to variant map
Map<string,Set<VariantInfo>> uniqueVariants = new Map<string,Set<VariantInfo>>();
// Interpretation to protein ID map
Map<string,Set<ProteinInstanceInfo>> varToProteinMap = new Map<string,Set<ProteinInstanceInfo>>();
// Variant to spectrum map
Map<VariantInfo, Set<SpectrumInfo>> varToSpecMap = new Map<VariantInfo,Set<SpectrumInfo>>();
foreach(var locus in loci)
foreach (var peptide in proteins[locus].peptides)
foreach (var interp in proteins[locus].interpretations[peptide])
foreach (var variant in proteins[locus].variants[interp])
{
uniqueVariants[variant.ToInsPecTStyle()].Add(variant);
foreach (var spectrum in proteins[locus].spectra[variant])
varToSpecMap[variant].Add(spectrum);
foreach (var protein in variant.peptide.proteins.Values)
varToProteinMap[interp].Add(protein);
}
Map<string, Map<string, int>> table = new Map<string, Map<string, int>>();
Set<string> allSources = new Set<string>();
foreach(var interp in uniqueVariants.Keys)
foreach(var variant in uniqueVariants[interp])
foreach(var spectrum in varToSpecMap[variant])
{
string sourceName = spectrum.id.source.group.name;
allSources.Add(sourceName);
++table[interp][sourceName];
SourceGroupList parentGroups = new SourceGroupList();
foreach (var parent in spectrum.id.source.group.getAllParentGroupPaths())
{
allSources.Add(parent);
++table[interp][parent];
}
}
writer.Write("Peptide,Protein,Alternatives");
foreach (var source in allSources)
writer.Write("," + source);
writer.WriteLine();
foreach ( var keys in table)
{
StringBuilder line = new StringBuilder();
line.Append(keys.Key);
Set<ProteinInstanceInfo>.Enumerator proIter = varToProteinMap[keys.Key].GetEnumerator();
proIter.MoveNext();
ProteinInstanceInfo first = proIter.Current;
line.Append(","+first.protein.locus);
StringBuilder alts = new StringBuilder();
while(proIter.MoveNext())
alts.Append(proIter.Current.protein.locus+";");
line.Append(","+alts.ToString());
foreach (var source in allSources)
{
line.Append("," + table[keys.Key][source]);
}
writer.WriteLine(line.ToString());
}
writer.Flush();
}
/// <summary>
/// This function exports a detailed protein modification report.
/// </summary>
public void exportProteinReport(Set<string> loci, StreamWriter writer)
{
if(loci.Count == 0)
return;
Map<string, Map<string, int>> table = new Map<string, Map<string, int>>();
Set<string> allSources = new Set<string>();
foreach (var locus in loci)
foreach (var peptide in proteins[locus].peptides)
foreach (var interp in proteins[locus].interpretations[peptide])
foreach (var variant in proteins[locus].variants[interp])
{
string key = locus + "," + interp;
foreach (var spectrum in proteins[locus].spectra[variant])
{
string sourceName = spectrum.id.source.group.name;
allSources.Add(sourceName);
++table[key][sourceName];
SourceGroupList parentGroups = new SourceGroupList();
foreach (var parent in spectrum.id.source.group.getAllParentGroupPaths())
{
allSources.Add(parent);
++table[key][parent];
}
}
}
writer.Write("Protein,peptide");
foreach(var source in allSources)
writer.Write(","+source);
writer.WriteLine();
foreach(var keys in table)
{
StringBuilder line = new StringBuilder();
line.Append(keys.Key);
foreach(var source in allSources)
{
line.Append("," + table[keys.Key][source]);
}
writer.WriteLine(line.ToString());
}
writer.Flush();
}