From cf0257e13220b96823cab3c452f9e63b4d36392b Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Fri, 17 May 2019 20:37:15 +0200
Subject: [PATCH] use real msrun xml id
---
src/core/automaticfilterparameters.h | 10 ++++------
.../identification_sources/identificationdatasource.h | 5 +----
src/output/masschroqml.cpp | 5 ++++-
src/output/masschroqprm.h | 4 +---
4 files changed, 10 insertions(+), 14 deletions(-)
diff --git a/src/core/automaticfilterparameters.h b/src/core/automaticfilterparameters.h
index f9286bbfc..e26f0fa71 100644
--- a/src/core/automaticfilterparameters.h
+++ b/src/core/automaticfilterparameters.h
@@ -22,8 +22,7 @@
*implementation
******************************************************************************/
-#ifndef AUTOMATICFILTERPARAMETERS_H
-#define AUTOMATICFILTERPARAMETERS_H
+#pragma once
#include <pappsomspp/types.h>
class AutomaticFilterParameters
@@ -37,9 +36,10 @@ class AutomaticFilterParameters
void setFilterPeptideEvalue(pappso::pappso_double evalue);
void setFilterProteinEvalue(pappso::pappso_double evalue);
void setFilterMinimumPeptidePerMatch(unsigned int number);
-
+
/** @brief filter on peptide reproducibility accross MS runs
- * if a peptide is observed in less MS runs than this value, the peptide is not valid
+ * if a peptide is observed in less MS runs than this value, the peptide is
+ * not valid
*/
void setFilterPeptideObservedInLessSamplesThan(unsigned int number);
void setFilterCrossSamplePeptideNumber(bool cross);
@@ -61,5 +61,3 @@ class AutomaticFilterParameters
unsigned int m_filter_peptide_observed_in_less_samples_than = 1;
bool _filter_is_cross_sample_peptide_number = false;
};
-
-#endif // AUTOMATICFILTERPARAMETERS_H
diff --git a/src/core/identification_sources/identificationdatasource.h b/src/core/identification_sources/identificationdatasource.h
index 9e84003cc..5f2bff0de 100644
--- a/src/core/identification_sources/identificationdatasource.h
+++ b/src/core/identification_sources/identificationdatasource.h
@@ -21,8 +21,7 @@
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
-#ifndef IDENTIFICATIONDATASOURCE_H
-#define IDENTIFICATIONDATASOURCE_H
+#pragma once
#include <pappsomspp/massspectrum/massspectrum.h>
@@ -152,5 +151,3 @@ class IdentificationDataSource
PeptideEvidenceStore _peptide_evidence_store;
};
-
-#endif // IDENTIFICATIONDATASOURCE_H
diff --git a/src/output/masschroqml.cpp b/src/output/masschroqml.cpp
index fef927dd3..b0b711e9e 100644
--- a/src/output/masschroqml.cpp
+++ b/src/output/masschroqml.cpp
@@ -446,7 +446,10 @@ MassChroQml::writeAlignments()
_output_stream->writeStartElement("align");
_output_stream->writeAttribute("group_id", "fractiona1");
_output_stream->writeAttribute("method_id", "my_ms2");
- _output_stream->writeAttribute("reference_data_id", "msruna1");
+ std::vector<MsRunSp> msrun_list =
+ _sp_project.get()->getMsRunStore().getMsRunList();
+ _output_stream->writeAttribute("reference_data_id",
+ msrun_list.front().get()->getXmlId());
_output_stream->writeEndElement();
//</alignments>
_output_stream->writeEndElement();
diff --git a/src/output/masschroqprm.h b/src/output/masschroqprm.h
index f3081a5e6..0ad73cbb6 100644
--- a/src/output/masschroqprm.h
+++ b/src/output/masschroqprm.h
@@ -28,8 +28,7 @@
*implementation
******************************************************************************/
-#ifndef MASSCHROQPRM_H
-#define MASSCHROQPRM_H
+#pragma once
#include <QXmlStreamWriter>
#include <QFile>
@@ -56,4 +55,3 @@ class MassChroqPrm
IdentificationGroup *_p_identification_group;
};
-#endif // MASSCHROQPRM_H
--
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