From e51036c5cb12defb893e4a5932731564f9239ad1 Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Wed, 3 Oct 2018 22:31:39 +0200
Subject: [PATCH] some missing information to parse in a near futur
---
src/input/identificationpwizreader.cpp | 29 ++++++++++++++++++++++++--
1 file changed, 27 insertions(+), 2 deletions(-)
diff --git a/src/input/identificationpwizreader.cpp b/src/input/identificationpwizreader.cpp
index 8dc3d464..0f5ed82e 100644
--- a/src/input/identificationpwizreader.cpp
+++ b/src/input/identificationpwizreader.cpp
@@ -270,6 +270,31 @@ IdentificationPwizReader::read(
std::map<QString, ProteinMatch *> map_id2protein;
std::map<QString, PeptideXtpSp> map_id2peptide;
+ /* MISSING
+ *
+ <Inputs>
+ <SearchDatabase numDatabaseSequences="136828"
+ location="/home/thierry/test/MS-GF+/Genome_Z_mays_v5a_conta.fasta"
+ id="SearchDB_1"> <FileFormat> <cvParam cvRef="PSI-MS" accession="MS:1001348"
+ name="FASTA format"/>
+ </FileFormat>
+ <DatabaseName>
+ <userParam name="Genome_Z_mays_v5a_conta.fasta"/>
+ </DatabaseName>
+ </SearchDatabase>
+ <SpectraData
+ location="/home/thierry/test/MS-GF+/20170308_test_dig_Liquide_01.mzXML"
+ id="SID_1" name="20170308_test_dig_Liquide_01.mzXML"> <FileFormat> <cvParam
+ cvRef="PSI-MS" accession="MS:1000566" name="ISB mzXML file"/>
+ </FileFormat>
+ <SpectrumIDFormat>
+ <cvParam cvRef="PSI-MS" accession="MS:1000776" name="scan number only
+ nativeID format"/>
+ </SpectrumIDFormat>
+ </SpectraData>
+ </Inputs>
+ *
+ */
for(pwiz::identdata::DBSequencePtr seq_ptr :
_pwiz_ident_data_file->sequenceCollection.dbSequences)
{
@@ -479,8 +504,8 @@ IdentificationPwizReader::read(
// throw pappso::PappsoException(QObject::tr("Scan number not
// found"));
//<cvParam cvRef="PSI-MS" accession="MS:1000016" name="scan
- //start time" value="4075.63" unitAccession="UO:0000010"
- //unitName="second" unitCvRef="UO"/>
+ // start time" value="4075.63" unitAccession="UO:0000010"
+ // unitName="second" unitCvRef="UO"/>
rt = getQVariantDoubleParam(spectrum_ptr.get(),
pwiz::cv::MS_scan_start_time);
}
--
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