From 7f2d3bad9e2ae079983f52ce4fb165a27c77e28b Mon Sep 17 00:00:00 2001
From: Thomas Renne <thomas.renne@u-psud.fr>
Date: Tue, 21 Apr 2020 10:43:07 +0200
Subject: [PATCH] Add TDF MsRunStatistics to MsIdentification view
---
src/core/msrun.cpp | 37 +++++++++++++++++++
src/core/msrun.h | 1 +
.../msidlistworkerstatus.cpp | 17 +++++++++
.../msidlistworkerstatus.h | 7 ++--
.../msidentificationtablemodel.cpp | 10 -----
.../msidentificationtablemodel.h | 3 +-
src/input/pepxmlsaxhandler.cpp | 2 +-
src/utils/types.h | 3 +-
8 files changed, 63 insertions(+), 17 deletions(-)
diff --git a/src/core/msrun.cpp b/src/core/msrun.cpp
index e7ceae2b..f523a05b 100644
--- a/src/core/msrun.cpp
+++ b/src/core/msrun.cpp
@@ -335,6 +335,43 @@ MsRun::checkMsRunStatistics(MsRunStatisticsHandler *currentHandler)
}
}
+void
+MsRun::checkMsRunStatisticsForTdf(MsRunStatisticsHandler *currentHandler)
+{
+ QVariant msrun_var = getMsRunStatistics(MsRunStatistics::total_spectra);
+ if(msrun_var.isNull())
+ {
+ try
+ {
+ QString directory =
+ QFileInfo(getFileName()).absoluteDir().absolutePath();
+ pappso::TimsData *tims_data = new pappso::TimsData(directory);
+ if(currentHandler->shouldStop())
+ { // statistics handler was stopped : don't use collected statistics
+ // because it is only partial
+ }
+ else
+ {
+ setMsRunStatistics(MsRunStatistics::total_spectra, "NA");
+ setMsRunStatistics(
+ MsRunStatistics::total_spectra_ms1,
+ (unsigned int)tims_data->getTotalNumberOfPrecursors());
+ setMsRunStatistics(
+ MsRunStatistics::total_spectra_ms2,
+ (unsigned int)tims_data->getTotalNumberOfScans());
+ setMsRunStatistics(MsRunStatistics::total_spectra_ms3, 0);
+ setMsRunStatistics(MsRunStatistics::tic_spectra_ms1, "NA");
+ setMsRunStatistics(MsRunStatistics::tic_spectra_ms2, "NA");
+ setMsRunStatistics(MsRunStatistics::tic_spectra_ms3, "NA");
+ }
+ }
+ catch(pappso::ExceptionNotFound &error)
+ {
+ // no file found, no statistics
+ }
+ }
+}
+
pappso::MsRunXicExtractorInterfaceSp
MsRun::getMsRunXicExtractorInterfaceSp()
{
diff --git a/src/core/msrun.h b/src/core/msrun.h
index e6436651..031c1e28 100644
--- a/src/core/msrun.h
+++ b/src/core/msrun.h
@@ -83,6 +83,7 @@ class MsRun : public pappso::MsRunId
void checkMsRunStatistics();
void checkMsRunStatistics(MsRunStatisticsHandler *currentHandler);
+ void checkMsRunStatisticsForTdf(MsRunStatisticsHandler *currentHandler);
pappso::MsRunXicExtractorInterfaceSp getMsRunXicExtractorInterfaceSp();
diff --git a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp
index dc17389a..3c865363 100644
--- a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp
+++ b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.cpp
@@ -180,6 +180,23 @@ MsIdListWorkerStatus::doComputeMsNumberForTDF(
{
try
{
+ if(mpa_currentHandler == nullptr)
+ {
+ mpa_currentHandler =
+ new MsIdentificationTableMsRunStatisticsHandler;
+ identificationDataSource->getMsRunSp()
+ ->checkMsRunStatisticsForTdf(mpa_currentHandler);
+ if(!mpa_currentHandler->shouldStop())
+ {
+ // if statistics computing is interrupted : don't take
+ // into account results because it is partial
+ m_identificationReady.push_back(
+ identificationDataSource.get());
+ }
+
+ delete mpa_currentHandler;
+ mpa_currentHandler = nullptr;
+ }
}
catch(pappso::PappsoException &error)
{
diff --git a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h
index 2eb70ea9..ba61ff05 100644
--- a/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h
+++ b/src/gui/lists/ms_identification_run_list_view/ms_identification_worker/msidlistworkerstatus.h
@@ -63,7 +63,6 @@ enum class WorkerStatus : std::int8_t
Ready = 3,
NotReady = 4,
Error = 5,
- NotAvailable = 6,
};
class MsIdentificationListWindow;
class MsIdListWorkerStatus
@@ -78,8 +77,10 @@ class MsIdListWorkerStatus
*/
WorkerStatus getStatus(IdentificationDataSourceSp identificationDataSource);
void doComputeMsNumber(IdentificationDataSourceSp identificationDataSource);
- void doComputeMsNumberForTDF(IdentificationDataSourceSp identificationDataSource);
- void doComputeMsNumberForMzXML(IdentificationDataSourceSp identificationDataSource);
+ void
+ doComputeMsNumberForTDF(IdentificationDataSourceSp identificationDataSource);
+ void doComputeMsNumberForMzXML(
+ IdentificationDataSourceSp identificationDataSource);
void changeWaitingQueue(int row);
diff --git a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp
index 9280959d..7b2d73f9 100644
--- a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp
+++ b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.cpp
@@ -400,18 +400,8 @@ MsIdentificationTableModel::data(const QModelIndex &index, int role) const
}
if(col == (std::int8_t)msIdentificationListColumn::nb_tic_1)
{
- // if(QFileInfo(m_identificationDataSourceSpList.at(row)
- // ->getMsRunSp()
- // ->getFileName())
- // .completeSuffix() == "tdf")
- // {
- // return QVariant("NA");
- // }
- // else
- // {
return getMsRunStatisticsNumber(row,
MsRunStatistics::tic_spectra_ms1);
- // }
}
if(col == (std::int8_t)msIdentificationListColumn::nb_tic_2)
{
diff --git a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h
index c43fb920..c843159f 100644
--- a/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h
+++ b/src/gui/lists/ms_identification_run_list_view/msidentificationtablemodel.h
@@ -109,7 +109,8 @@ class MsIdentificationTableModel : public QAbstractTableModel
private:
static int getColumnWidth(int column);
- QVariant getMsRunStatisticsFollowingFormat(MsRunSp msrun_sp, MsRunStatistics column) const;
+ QVariant getMsRunStatisticsFollowingFormat(MsRunSp msrun_sp,
+ MsRunStatistics column) const;
private:
std::vector<IdentificationDataSourceSp> m_identificationDataSourceSpList;
diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
index 4d3b8432..b47dc86c 100644
--- a/src/input/pepxmlsaxhandler.cpp
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -332,7 +332,7 @@ PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
//<alternative_protein protein="sp|P46784|RS10B_YEAST" protein_descr="40S
// ribosomal protein S10-B OS=Saccharomyces cerevisiae (strain ATCC 204508
-// \
+// \
//S288c) GN=RPS10B PE=1 SV=1" num_tol_term="2" peptide_prev_aa="K"
// peptide_next_aa="N"/>
bool
diff --git a/src/utils/types.h b/src/utils/types.h
index 4fcc17bb..83206f04 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -88,8 +88,7 @@ enum class PeptideEvidenceParam : std::int8_t
comet_sprank = 18, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI]
comet_expectation_value =
19, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI]
- pappso_qvalue =
- 20, ///< q-value computed with FDR = decoy / (decoy + target)
+ pappso_qvalue = 20, ///< q-value computed with FDR = decoy / (decoy + target)
};
--
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