From 3dc2d5385aad6d49792e7ea9a80222902c0b9038 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 7 Apr 2017 16:23:37 +0200
Subject: [PATCH] WIP : writing MassChroqML should be OK
---
src/output/masschroqml.cpp | 75 ++++++++++++++++++++++++++++++++++++++
src/output/masschroqml.h | 3 ++
2 files changed, 78 insertions(+)
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index 9ad538a66..b60f05983 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -133,8 +133,83 @@ void MassChroQml::write(ProjectSp sp_project) {
writeIsotopeLabelList();
writeAlignments();
writeQuantificationMethods();
+ _output_stream->writeStartElement("quantification");
+ writeQuantificationResults();
+ writeQuantificationTraces();
+ writeQuantify();
+ _output_stream->writeEndElement();
+}
+
+
+
+void MassChroQml::writeQuantificationResults() {
+ //<quantification_results>
+ _output_stream->writeStartElement("quantification_results");
+ //<quantification_result output_file="result1"
+ // format="tsv" />
+ _output_stream->writeStartElement("quantification_result");
+ _output_stream->writeAttribute("output_file","result1");
+ _output_stream->writeAttribute("format","tsv");
+ _output_stream->writeEndElement();
+ //<quantification_result output_file="result2"
+ // format="ods" />
+ _output_stream->writeComment("<quantification_result output_file=\"result2\" format=\"ods\" />");
+ //<compar_result output_file="compar"
+ // format="ods" />
+
+ _output_stream->writeStartElement("compar_result");
+ _output_stream->writeAttribute("output_file","result1");
+ _output_stream->writeAttribute("format","ods");
+ _output_stream->writeEndElement();
+ //</quantification_results>
+ _output_stream->writeEndElement();
}
+void MassChroQml::writeQuantificationTraces() {
+ //<quantification_traces>
+
+ _output_stream->writeStartElement("quantification_traces");
+ //<peptide_traces peptide_ids="pep0 pep1" output_dir="pep_traces"
+ // format="tsv" />
+ _output_stream->writeComment("<peptide_traces peptide_ids=\"pep0 pep1\" output_dir=\"pep_traces\" format=\"tsv\" />");
+ /*
+ <all_xics_traces output_dir="all_xics_traces" format="tsv" />
+ <mz_traces mz_values="634.635 449.754 552.234" output_dir="mz_traces"
+ format="tsv" />
+ <mzrt_traces output_dir="mzrt_traces" format="tsv">
+ <mzrt_values>
+ <mzrt_value mz="732.317" rt="230.712" />
+ <mzrt_value mz="575.256" rt="254.788" />
+ </mzrt_values>
+ </mzrt_traces>*/
+ //</quantification_traces>
+
+ _output_stream->writeEndElement();
+}
+void MassChroQml::writeQuantify() {
+ //<quantify id="q1" withingroup="G1" quantification_method_id="my_qzivy">
+ _output_stream->writeStartElement("quantify");
+ _output_stream->writeAttribute("id","q1");
+ _output_stream->writeAttribute("withingroup","fractiona1");
+ _output_stream->writeAttribute("quantification_method_id","quant1");
+ //<peptides_in_peptide_list mode="real_or_mean" />
+ //</quantify>
+ //<quantify id="q2" withingroup="G2" quantification_method_id="my_moulon">
+ //<peptides_in_peptide_list mode="post_matching"
+ // isotope_label_refs="iso1 iso2" />
+
+ _output_stream->writeStartElement("peptides_in_peptide_list");
+ _output_stream->writeAttribute("mode","post_matching");
+ _output_stream->writeAttribute("ni_min_abundance","0.8");
+ _output_stream->writeEndElement();
+
+ _output_stream->writeComment("<mz_list>732.317 449.754 552.234 464.251 381.577 569.771 575.256</mz_list>");
+ _output_stream->writeComment("<mzrt_list>\n <mzrt mz=\"732.317\" rt=\"230.712\" />\n <mzrt mz=\"575.256\" rt=\"254.788\" />\n </mzrt_list>");
+
+ //</quantify>
+
+ _output_stream->writeEndElement();
+}
void MassChroQml::writeQuantificationMethods() {
//<quantification_methods>
diff --git a/src/output/masschroqml.h b/src/output/masschroqml.h
index 0e9757953..ff291ffc0 100644
--- a/src/output/masschroqml.h
+++ b/src/output/masschroqml.h
@@ -51,6 +51,9 @@ private:
void writeIsotopeLabelList();
void writeAlignments();
void writeQuantificationMethods();
+ void writeQuantificationResults();
+ void writeQuantificationTraces();
+ void writeQuantify();
private :
QFile * _output_file;
QXmlStreamWriter * _output_stream;
--
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