diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7610046a2f658cede84029dac73ffddb01e8e3b1..c7b3d38b6231842329e6405d44ef770159f75d78 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -56,7 +56,7 @@ SET(SOFTWARE_NAME "XTPcpp")
SET(XTPCPP_VERSION_MAJOR "0")
SET(XTPCPP_VERSION_MINOR "2")
-SET(XTPCPP_VERSION_PATCH "23")
+SET(XTPCPP_VERSION_PATCH "24")
SET(XTPCPP_VERSION "${XTPCPP_VERSION_MAJOR}.${XTPCPP_VERSION_MINOR}.${XTPCPP_VERSION_PATCH}")
# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
diff --git a/debian/changelog b/debian/changelog
index 4a3532ef71dacfd9d6ccf847b6d4cf4db57caf66..79f15f937399ff70e0b5526c728a6d9e9d58154e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,22 @@
+xtpcpp (0.2.24-3) stretch; urgency=medium
+
+ * fix for temporary directory under condor
+
+ -- Olivier Langella <olivier.langella@u-psud.fr> Mon, 29 Oct 2018 11:14:33 +0100
+
+xtpcpp (0.2.24-2) stretch; urgency=medium
+
+ * ODS output fix
+
+ -- Olivier Langella <olivier.langella@u-psud.fr> Fri, 19 Oct 2018 16:57:33 +0200
+
+xtpcpp (0.2.24-1) stretch; urgency=medium
+
+ * new compar ODS output dedicated to labeled experiments
+ * SEVERE bug fix concerning protein Evalue computation (reported by T. Balliau)
+
+ -- Olivier Langella <olivier.langella@u-psud.fr> Fri, 19 Oct 2018 16:13:10 +0200
+
xtpcpp (0.2.23-2) stretch; urgency=medium
* fix version number
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index 1f805b5e69e38909f4ea7352164ff997acafc84f..5063f0bfb48c297b92f89bb4156a96be14dce68a 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -55,14 +55,15 @@ IdentificationGroup::getGroupStore() const
}
pappso::pappso_double
-IdentificationGroup::computeProtoNsafSum(const MsRun *p_msrun_id) const
+IdentificationGroup::computeProtoNsafSum(const MsRun *p_msrun_id,
+ const Label *p_label) const
{
pappso::pappso_double nsaf_sum = 0;
for(auto &p_protein_match : _protein_match_list)
{
if(p_protein_match->getValidationState() >= ValidationState::grouped)
{
- nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id);
+ nsaf_sum += p_protein_match->getProtoNsaf(p_msrun_id, p_label);
}
}
return nsaf_sum;
@@ -130,7 +131,8 @@ unsigned int
IdentificationGroup::countDecoyProteinMatch(ValidationState state) const
{
return std::count_if(
- _protein_match_list.begin(), _protein_match_list.end(),
+ _protein_match_list.begin(),
+ _protein_match_list.end(),
[state](const ProteinMatch *p_protein_match) {
if((p_protein_match->getProteinXtpSp().get()->isDecoy()) &&
(p_protein_match->getValidationState() >= state))
@@ -209,7 +211,8 @@ IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const
unsigned int
IdentificationGroup::countProteinMatch(ValidationState state) const
{
- return std::count_if(_protein_match_list.begin(), _protein_match_list.end(),
+ return std::count_if(_protein_match_list.begin(),
+ _protein_match_list.end(),
[state](const ProteinMatch *p_protein_match) {
if(p_protein_match->getValidationState() >= state)
{
@@ -302,8 +305,8 @@ IdentificationGroup::addIdentificationDataSourceP(
IdentificationDataSource *p_identification_source)
{
addMsRunSp(p_identification_source->getMsRunSp());
- auto it = std::find(_id_source_list.begin(), _id_source_list.end(),
- p_identification_source);
+ auto it = std::find(
+ _id_source_list.begin(), _id_source_list.end(), p_identification_source);
if(it == _id_source_list.end())
{
_id_source_list.push_back(p_identification_source);
@@ -353,7 +356,8 @@ IdentificationGroup::countSubGroup() const
void
IdentificationGroup::collectMhDelta(
- std::vector<pappso::pappso_double> &delta_list, pappso::PrecisionUnit unit,
+ std::vector<pappso::pappso_double> &delta_list,
+ pappso::PrecisionUnit unit,
ValidationState state) const
{
std::set<const PeptideEvidence *> peptide_evidence_list;
@@ -466,7 +470,9 @@ IdentificationGroup::getProteinFdr(ValidationState state) const
void
IdentificationGroup::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide, unsigned int charge) const
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
+ unsigned int charge) const
{
if(!contains(p_msrun))
return;
@@ -475,8 +481,8 @@ IdentificationGroup::getSameXicPeptideEvidenceList(
if(p_msrun == p_identification_source->getMsRunSp().get())
{
p_identification_source->getPeptideEvidenceStore()
- .getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun,
- p_peptide, charge);
+ .getSameXicPeptideEvidenceList(
+ peptide_evidence_list, p_msrun, p_peptide, charge);
}
}
}
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 43e03e2bd4e5088115bd930ce990c92ba2220bda..7ec739ac5d3fa153e57d3be3d5ca1954ec90aca2 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -62,7 +62,9 @@ class IdentificationGroup
* Warning: this is not NSAF, just a part
* @param p_msrun_id pointer on the msrun to get NSAF.
* */
- pappso::pappso_double computeProtoNsafSum(const MsRun *p_msrun_id) const;
+ pappso::pappso_double
+ computeProtoNsafSum(const MsRun *p_msrun_id,
+ const Label *p_label = nullptr) const;
/** @brief count groups
* */
@@ -152,7 +154,8 @@ class IdentificationGroup
* each peptide evidence is only counted once
*/
void collectMhDelta(std::vector<pappso::pappso_double> &delta_list,
- pappso::PrecisionUnit unit, ValidationState state) const;
+ pappso::PrecisionUnit unit,
+ ValidationState state) const;
/** @brief look for a peptide in the same XIC
@@ -163,7 +166,8 @@ class IdentificationGroup
*/
void getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list,
- const MsRun *p_msrun, const PeptideXtp *p_peptide,
+ const MsRun *p_msrun,
+ const PeptideXtp *p_peptide,
unsigned int charge) const;
private:
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 360b897c17a0d312713d8df99b9bced28ea3cba9..700dedd321de85960ea1f91b585aa68343a54d89 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -346,7 +346,8 @@ ProteinMatch::countPeptideMatch(ValidationState state) const
size_t
ProteinMatch::countSequenceLi(ValidationState state,
- const MsRun *p_msrun_id) const
+ const MsRun *p_msrun_id,
+ const Label *p_label) const
{
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
std::set<QString> sequence_list;
@@ -356,13 +357,33 @@ ProteinMatch::countSequenceLi(ValidationState state,
{
if(p_msrun_id != nullptr)
{
- // within sample
- if(peptide_match.getPeptideEvidence()->getMsRunP() == p_msrun_id)
+
+ if(p_label != nullptr)
{
- sequence_list.insert(peptide_match.getPeptideEvidence()
- ->getPeptideXtpSp()
- .get()
- ->getSequenceLi());
+ if((peptide_match.getPeptideEvidence()->getMsRunP() ==
+ p_msrun_id) &&
+ (peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getLabel() == p_label))
+ {
+ sequence_list.insert(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi());
+ }
+ }
+ else
+ {
+ // within sample
+ if(peptide_match.getPeptideEvidence()->getMsRunP() ==
+ p_msrun_id)
+ {
+ sequence_list.insert(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getSequenceLi());
+ }
}
}
else
@@ -398,7 +419,8 @@ ProteinMatch::countDistinctMsSamples(ValidationState state) const
unsigned int
ProteinMatch::countPeptideMassCharge(ValidationState state,
- const MsRun *sp_msrun_id) const
+ const MsRun *sp_msrun_id,
+ const Label *p_label) const
{
std::set<QString> sequence_list;
for(auto &peptide_match : _peptide_match_list)
@@ -410,19 +432,46 @@ ProteinMatch::countPeptideMassCharge(ValidationState state,
// within sample
if(peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id)
{
- sequence_list.insert(
- QString("%1-%2-%3")
- .arg(peptide_match.getPeptideEvidence()
- ->getPeptideXtpSp()
- .get()
- ->getNativePeptideP()
- ->getSequenceLi())
- .arg(peptide_match.getPeptideEvidence()
- ->getPeptideXtpSp()
- .get()
- ->getNativePeptideP()
- ->getMass())
- .arg(peptide_match.getPeptideEvidence()->getCharge()));
+ if(p_label != nullptr)
+ {
+ if(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getLabel() == p_label)
+ {
+ sequence_list.insert(
+ QString("%1-%2-%3")
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getSequenceLi())
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getMass())
+ .arg(peptide_match.getPeptideEvidence()
+ ->getCharge()));
+ }
+ }
+ else
+ {
+ sequence_list.insert(
+ QString("%1-%2-%3")
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getSequenceLi())
+ .arg(peptide_match.getPeptideEvidence()
+ ->getPeptideXtpSp()
+ .get()
+ ->getNativePeptideP()
+ ->getMass())
+ .arg(
+ peptide_match.getPeptideEvidence()->getCharge()));
+ }
}
}
else
@@ -500,7 +549,7 @@ ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const
}
}
- pappso::pappso_double evalue_prot = 1;
+ pappso::pappso_double evalue_prot = 0;
for(auto &&peptide_pair : map_sequence_evalue)
{
evalue_prot += std::log10(peptide_pair.second);
@@ -512,7 +561,8 @@ ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const
}
pappso::pappso_double
ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
- const MsRun *p_msrun_id) const
+ const MsRun *p_msrun_id,
+ const Label *p_label) const
{
if(proto_nsaf_sum == 0)
{
@@ -521,11 +571,11 @@ ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
"Error computing NSAF for protein %1 :\nproto_nsaf_sum is null")
.arg(this->getProteinXtpSp().get()->getAccession()));
}
- return (getProtoNsaf(p_msrun_id) / proto_nsaf_sum);
+ return (getProtoNsaf(p_msrun_id, p_label) / proto_nsaf_sum);
}
pappso::pappso_double
-ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
+ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id, const Label *p_label) const
{
try
{
@@ -535,8 +585,8 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
QObject::tr("protein has no amino acid sequence"));
}
pappso::pappso_double proto_nsaf =
- (pappso::pappso_double)countSampleScan(ValidationState::validAndChecked,
- sp_msrun_id) /
+ (pappso::pappso_double)countSampleScan(
+ ValidationState::validAndChecked, sp_msrun_id, p_label) /
(pappso::pappso_double)_protein_sp.get()->size();
return proto_nsaf;
}
@@ -550,13 +600,13 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
}
pappso::pappso_double
-ProteinMatch::getPAI(const MsRun *sp_msrun_id) const
+ProteinMatch::getPAI(const MsRun *sp_msrun_id, const Label *p_label) const
{
try
{
pappso::pappso_double PAI =
(pappso::pappso_double)countPeptideMassCharge(
- ValidationState::validAndChecked, sp_msrun_id) /
+ ValidationState::validAndChecked, sp_msrun_id, p_label) /
(pappso::pappso_double)_protein_sp.get()->countTrypticPeptidesForPAI();
return PAI;
}
@@ -570,11 +620,11 @@ ProteinMatch::getPAI(const MsRun *sp_msrun_id) const
}
pappso::pappso_double
-ProteinMatch::getEmPAI(const MsRun *sp_msrun_id) const
+ProteinMatch::getEmPAI(const MsRun *sp_msrun_id, const Label *p_label) const
{
// compute emPAI, Ishihama 2005
pappso::pappso_double value =
- std::pow(10.0, getPAI(sp_msrun_id)) - (pappso::pappso_double)1.0;
+ std::pow(10.0, getPAI(sp_msrun_id, p_label)) - (pappso::pappso_double)1.0;
return value;
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 7bb8efd81901c8eaaaf7cc5188d6fc205b843cfd..33ff923c7b481ad6c3bef43deb3483b020b73522 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -72,7 +72,8 @@ class ProteinMatch
* Warning: this is not NSAF, just a part
* @param p_msrun_id pointer on the msrun to get NSAF.
* */
- pappso::pappso_double getProtoNsaf(const MsRun *p_msrun_id) const;
+ pappso::pappso_double getProtoNsaf(const MsRun *p_msrun_id,
+ const Label *p_label = nullptr) const;
/** @brief compute NSAF within msrun : normalized spectral abundance factor
* (NSAF) Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing
@@ -84,17 +85,20 @@ class ProteinMatch
* @param p_msrun_id pointer on the msrun to get NSAF
* */
pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum,
- const MsRun *p_msrun_id) const;
+ const MsRun *p_msrun_id,
+ const Label *p_label = nullptr) const;
/** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002)
* */
- pappso::pappso_double getPAI(const MsRun *sp_msrun_id = nullptr) const;
+ pappso::pappso_double getPAI(const MsRun *sp_msrun_id = nullptr,
+ const Label *p_label = nullptr) const;
/** @brief compute emPAI within sample
* Ishihama 2005
* */
- pappso::pappso_double getEmPAI(const MsRun *sp_msrun_id = nullptr) const;
+ pappso::pappso_double getEmPAI(const MsRun *sp_msrun_id = nullptr,
+ const Label *p_label = nullptr) const;
void setProteinXtpSp(ProteinXtpSp protein_sp);
void addPeptideMatch(const PeptideMatch &peptide_match);
@@ -162,7 +166,8 @@ class ProteinMatch
* @param p_msrun_id count within the specified sample
*/
size_t countSequenceLi(ValidationState state,
- const MsRun *p_msrun_id = nullptr) const;
+ const MsRun *p_msrun_id = nullptr,
+ const Label *p_label = nullptr) const;
/** @brief count distinct peptide+mass+charge
* peptide is the peptide sequence LI (Leucine => Isoleucine)
@@ -171,7 +176,8 @@ class ProteinMatch
* @param p_msrun_id count within the specified sample
*/
unsigned int countPeptideMassCharge(ValidationState state,
- const MsRun *sp_msrun_id = nullptr) const;
+ const MsRun *sp_msrun_id = nullptr,
+ const Label *p_label = nullptr) const;
/** @brief count distinct MS samples in which the protein is observed
* @param state validation state of peptides to count
diff --git a/src/core/tandem_run/tandemcondorprocess.cpp b/src/core/tandem_run/tandemcondorprocess.cpp
index 79b22eebc724c5cdc08c1ae2d6e9fba6dcef2f41..f05d317dbac15f1ed33f33824d314f5c05331c27 100644
--- a/src/core/tandem_run/tandemcondorprocess.cpp
+++ b/src/core/tandem_run/tandemcondorprocess.cpp
@@ -98,7 +98,9 @@ TandemCondorProcess::prepareTemporaryDirectory()
{
QSettings settings;
- QString condor_tmp_dir = QString("%1/xtpcpp");
+ QString condor_tmp_dir =
+ QString("%1/xtpcpp")
+ .arg(settings.value("condor/tmp_dir", "/tmp").toString());
if(_p_tmp_dir != nullptr)
{
delete _p_tmp_dir;
diff --git a/src/gui/widgets/automatic_filter_widget/automatic_filter_widget.ui b/src/gui/widgets/automatic_filter_widget/automatic_filter_widget.ui
index 4611c3aa163279f4cafd596d0316c16d2576d6e3..ec90cfb4088fba249c58b44418f2d1abca38a372 100644
--- a/src/gui/widgets/automatic_filter_widget/automatic_filter_widget.ui
+++ b/src/gui/widgets/automatic_filter_widget/automatic_filter_widget.ui
@@ -6,10 +6,28 @@
<rect>
<x>0</x>
<y>0</y>
- <width>533</width>
- <height>300</height>
+ <width>510</width>
+ <height>180</height>
</rect>
</property>
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="minimumSize">
+ <size>
+ <width>0</width>
+ <height>180</height>
+ </size>
+ </property>
+ <property name="baseSize">
+ <size>
+ <width>0</width>
+ <height>180</height>
+ </size>
+ </property>
<property name="windowTitle">
<string>Form</string>
</property>
@@ -21,6 +39,12 @@
</property>
<item row="0" column="0">
<widget class="QLabel" name="sample_number_label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
<string>peptide Evalue</string>
</property>
@@ -44,6 +68,12 @@
</item>
<item row="1" column="0">
<widget class="QLabel" name="group_number_label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
<string>number of peptides per protein</string>
</property>
@@ -61,6 +91,12 @@
</item>
<item row="2" column="0">
<widget class="QLabel" name="label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
<string>overall samples</string>
</property>
@@ -75,6 +111,12 @@
</item>
<item row="3" column="0">
<widget class="QLabel" name="subgroup_number_label">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
<string>protein Evalue</string>
</property>
@@ -98,6 +140,12 @@
</item>
<item row="4" column="0">
<widget class="QLabel" name="label_2">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
<property name="text">
<string>protein Evalue (log10)</string>
</property>
diff --git a/src/output/ods/comparbasesheet.cpp b/src/output/ods/comparbasesheet.cpp
index 627e1c7229a7f4fcef149b786fcbdd78e59c3d95..3c7bfaa5533bc635701407f3559d173a051862d2 100644
--- a/src/output/ods/comparbasesheet.cpp
+++ b/src/output/ods/comparbasesheet.cpp
@@ -45,7 +45,10 @@ ComparBaseSheet::ComparBaseSheet(OdsExport *p_ods_export,
_sp_labelling_method = p_project->getLabelingMethodSp();
- _label_list = _sp_labelling_method.get()->getLabelList();
+ if(_sp_labelling_method.get() != nullptr)
+ {
+ _label_list = _sp_labelling_method.get()->getLabelList();
+ }
}
void
@@ -174,7 +177,8 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match)
{
writeComparValue(p_protein_match,
ValidationState::validAndChecked,
- msrun_sp.get(),p_label);
+ msrun_sp.get(),
+ p_label);
if(_first_cell_coordinate.isEmpty())
{
_first_cell_coordinate = _p_writer->getOdsCellCoordinate();
diff --git a/src/output/ods/comparspectrasheet.cpp b/src/output/ods/comparspectrasheet.cpp
index 2a94fe0fad05ac23eecd7e7e7391c08445b949ae..b9ee4cc32c6eb1f6d0e503358be87e0935e9f503 100644
--- a/src/output/ods/comparspectrasheet.cpp
+++ b/src/output/ods/comparspectrasheet.cpp
@@ -50,7 +50,8 @@ ComparSpectraSheet::writeComparValue(const ProteinMatch *p_protein_match,
const Label *p_label)
{
qDebug() << "ComparSpectraSheet::writeComparValue begin";
- _p_writer->writeCell(p_protein_match->countSampleScan(state, p_msrun,p_label));
+ _p_writer->writeCell(
+ p_protein_match->countSampleScan(state, p_msrun, p_label));
qDebug() << "ComparSpectraSheet::writeComparValue end";
}
@@ -71,7 +72,7 @@ ComparSequenceSheet::writeComparValue(const ProteinMatch *p_protein_match,
{
qDebug() << "ComparSequenceSheet::writeComparValue begin";
_p_writer->writeCell(
- (unsigned int)p_protein_match->countSequenceLi(state, p_msrun));
+ (unsigned int)p_protein_match->countSequenceLi(state, p_msrun, p_label));
qDebug() << "ComparSequenceSheet::writeComparValue end";
}
@@ -90,7 +91,7 @@ ComparPaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
const Label *p_label)
{
qDebug() << "ComparPaiSheet::writeComparValue begin";
- _p_writer->writeCell(p_protein_match->getPAI(p_msrun));
+ _p_writer->writeCell(p_protein_match->getPAI(p_msrun, p_label));
qDebug() << "ComparPaiSheet::writeComparValue end";
}
@@ -109,7 +110,7 @@ ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
const Label *p_label)
{
qDebug() << "ComparEmpaiSheet::writeComparValue begin";
- _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun));
+ _p_writer->writeCell(p_protein_match->getEmPAI(p_msrun, p_label));
qDebug() << "ComparEmpaiSheet::writeComparValue end";
}
@@ -129,21 +130,47 @@ ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
{
qDebug() << "ComparNsafSheet::writeComparValue begin";
pappso::pappso_double proto_nsaf_sum = 0;
- std::pair<std::map<const MsRun *, pappso::pappso_double>::iterator, bool>
- ret = _map_proto_nsaf_sum_by_msrun.insert(
- std::pair<const MsRun *, pappso::pappso_double>(p_msrun, 0));
- if(ret.second == false)
+
+ if(_label_list.size() > 0)
{
- //"element 'z' already existed";
- proto_nsaf_sum = ret.first->second;
+ std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
+ _map_proto_nsaf_sum_by_msrun.insert(
+ std::pair<QString, pappso::pappso_double>(
+ QString("%1--%2").arg(p_msrun->getXmlId()).arg(p_label->getXmlId()),
+ 0));
+ if(ret.second == false)
+ {
+ //"element 'z' already existed";
+ proto_nsaf_sum = ret.first->second;
+ }
+ else
+ {
+ proto_nsaf_sum = _p_current_identification_group->computeProtoNsafSum(
+ p_msrun, p_label);
+ ret.first->second = proto_nsaf_sum;
+ }
+
+ _p_writer->writeCell(
+ p_protein_match->getNsaf(proto_nsaf_sum, p_msrun, p_label));
}
else
{
- proto_nsaf_sum =
- _p_current_identification_group->computeProtoNsafSum(p_msrun);
- ret.first->second = proto_nsaf_sum;
+ std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
+ _map_proto_nsaf_sum_by_msrun.insert(
+ std::pair<QString, pappso::pappso_double>(p_msrun->getXmlId(), 0));
+ if(ret.second == false)
+ {
+ //"element 'z' already existed";
+ proto_nsaf_sum = ret.first->second;
+ }
+ else
+ {
+ proto_nsaf_sum =
+ _p_current_identification_group->computeProtoNsafSum(p_msrun);
+ ret.first->second = proto_nsaf_sum;
+ }
+
+ _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum, p_msrun));
}
-
- _p_writer->writeCell(p_protein_match->getNsaf(proto_nsaf_sum, p_msrun));
qDebug() << "ComparNsafSheet::writeComparValue end";
}
diff --git a/src/output/ods/comparspectrasheet.h b/src/output/ods/comparspectrasheet.h
index 737af6c1eab249560020dbae9a0b40a2f45facf7..d129f71f728bd408dc887d27843dbf7720014a28 100644
--- a/src/output/ods/comparspectrasheet.h
+++ b/src/output/ods/comparspectrasheet.h
@@ -104,7 +104,7 @@ class ComparNsafSheet : public ComparBaseSheet
const Label *p_label = nullptr) override;
private:
- std::map<const MsRun *, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
+ std::map<QString, pappso::pappso_double> _map_proto_nsaf_sum_by_msrun;
};
#endif // COMPARSPECTRASHEET_H