public SilacResultSplitter(string lightParamFile, string heavyParamFile)
{
SequestParamFile paramFile = new SequestParamFile();
SequestParam light = paramFile.ReadFromFile(@"F:\sqh\Project\wuyibo\Light.params");
SequestParam heavy = paramFile.ReadFromFile(@"F:\sqh\Project\wuyibo\Heavy.params");
this.lightCalc = light.GetPeptideMassCalculator();
this.heavyCalc = heavy.GetPeptideMassCalculator();
}
private void WriteModifications(SequestParam sp)
{
var aas = new Aminoacids();
foreach (SequestStaticModification ssm in sp.StaticModification.Keys)
{
double addMass = sp.StaticModification[ssm];
if (addMass != 0.0)
{
switch (ssm)
{
case SequestStaticModification.add_Cterm_peptide:
case SequestStaticModification.add_Cterm_protein:
case SequestStaticModification.add_Nterm_peptide:
case SequestStaticModification.add_Nterm_protein:
break;
default:
char aa = SequestParam.ModificationToAminoacid(ssm);
this.sw.WriteLine(
" <aminoacid_modification aminoacid=\"{0}\" massdiff=\"{1:0.0000}\" mass=\"{2:0.0000}\" variable=\"N\"/>",
aa, addMass, aas[aa].MonoMass + addMass);
break;
}
}
}
foreach (String aminoacids in sp.Diff_search_options.Keys)
{
double addMass = sp.Diff_search_options[aminoacids];
foreach (char aa in aminoacids)
{
this.sw.WriteLine(
" <aminoacid_modification aminoacid=\"{0}\" massdiff=\"{1:0.0000}\" mass=\"{2:0.0000}\" variable=\"Y\"/>",
aa, addMass, aas[aa].MonoMass + addMass);
}
}
}
public void WriteSequestParam(SequestParam sp)
{
if (!this.isMsmsRunSummaryOpened)
{
throw new Exception("Call OpenMsmsRunSummary before WriteSequestParam.");
}
if (this.sampleProtease == null)
{
this.sampleProtease = sp.Protease;
}
this.currentSequestParams = sp;
this.staticAminoacidModification = sp.GetStaticAminoacidModification();
//sample_enzyme
this.sw.WriteLine(" <sample_enzyme name=\"{0}\">",
this.sampleProtease.Name);
this.sw.WriteLine(" <specificity cut=\"{0}\" no_cut=\"{1}\" sense=\"{2}\"/>",
this.sampleProtease.CleaveageResidues,
this.sampleProtease.NotCleaveResidues,
this.sampleProtease.IsEndoProtease ? "C" : "N");
this.sw.WriteLine(" </sample_enzyme>");
//search_summary
this.sw.WriteLine(
" <search_summary base_name=\"{0}\" search_engine=\"SEQUEST\" precursor_mass_type=\"{1}\" fragment_mass_type=\"{2}\" out_data_type=\"{3}\" out_data=\"{4}\" search_id=\"{5}\">",
this.sourceFilename,
sp.Mass_type_parent_annotation,
sp.Mass_type_fragment_annotation,
this.rawDataType,
this.rawData,
this.searchId);
this.sw.WriteLine(" <search_database local_path=\"{0}\" type=\"{1}\"/>",
sp.First_database_name,
sp.Nucleotide_reading_frame == 0 ? "AA" : "NA");
this.sw.WriteLine(
" <enzymatic_search_constraint enzyme=\"{0}\" max_num_internal_cleavages=\"{1}\" min_number_termini=\"{2}\"/>",
sp.Protease.Name,
sp.Max_num_internal_cleavage_sites,
sp.Min_number_termini);
WriteModifications(sp);
//parameters
this.sw.WriteLine(" <parameter name=\"peptide_mass_tol\" value=\"{0:0.0000}\"/>", sp.Peptide_mass_tolerance);
this.sw.WriteLine(" <parameter name=\"ion_series\" value=\"{0}\"/>", sp.Ion_series);
this.sw.WriteLine(" <parameter name=\"fragment_ion_tol\" value=\"{0:0.0000}\"/>", sp.Fragment_ion_tolerance);
this.sw.WriteLine(" <parameter name=\"num_output_lines\" value=\"{0}\"/>", sp.Num_output_lines);
this.sw.WriteLine(" <parameter name=\"num_results\" value=\"{0}\"/>", sp.Num_results);
this.sw.WriteLine(" <parameter name=\"num_description_lines\" value=\"{0}\"/>", sp.Num_description_lines);
this.sw.WriteLine(" <parameter name=\"show_fragment_ions\" value=\"{0}\"/>", sp.Show_fragment_ions);
this.sw.WriteLine(" <parameter name=\"print_duplicate_references\" value=\"{0}\"/>",
sp.Print_duplicate_references);
this.sw.WriteLine(" <parameter name=\"max_num_differential_AA_per_mod\" value=\"{0}\"/>",
sp.Max_num_differential_AA_per_mod);
this.sw.WriteLine(" <parameter name=\"nucleotide_reading_frame\" value=\"{0}\"/>",
sp.Nucleotide_reading_frame);
this.sw.WriteLine(" <parameter name=\"normalize_Score\" value=\"{0}\"/>", sp.Normalize_Score);
this.sw.WriteLine(" <parameter name=\"remove_precursor_peak\" value=\"{0}\"/>", sp.Remove_precursor_peak);
this.sw.WriteLine(" <parameter name=\"ion_cutoff_percentage\" value=\"{0:0.0000}\"/>",
sp.Ion_cutoff_percentage);
this.sw.WriteLine(" <parameter name=\"max_num_internal_cleavage_sites\" value=\"{0}\"/>",
sp.Max_num_internal_cleavage_sites);
this.sw.WriteLine(" <parameter name=\"protein_mass_filter\" value=\"{0} {1}\"/>",
sp.Protein_mass_filter.First, sp.Protein_mass_filter.Second);
this.sw.WriteLine(" <parameter name=\"match_peak_count\" value=\"{0}\"/>", sp.Match_peak_count);
this.sw.WriteLine(" <parameter name=\"match_peak_allowed_error\" value=\"{0}\"/>",
sp.Match_peak_allowed_error);
this.sw.WriteLine(" <parameter name=\"match_peak_tolerance\" value=\"{0}\"/>", sp.Match_peak_tolerance);
this.sw.WriteLine(" <parameter name=\"partial_sequence\" value=\"{0}\"/>", sp.Partial_sequence);
this.sw.WriteLine(" <parameter name=\"sequence_header_filter\" value=\"{0}\"/>", sp.Sequence_header_filter);
//end of search_summary
this.sw.WriteLine(" </search_summary>");
}
