Skip to content
Snippets Groups Projects
Commit b514c2e8 authored by Langella Olivier's avatar Langella Olivier
Browse files

Merge branch 'master' of git+ssh://git.renater.fr:2222/xtandempipeline

parents cc20e093 978d3434
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 238 additions and 72 deletions
CMakeLists.txt
+ 1
− 1
View file @ b514c2e8
...@@ -56,7 +56,7 @@ SET(SOFTWARE_NAME "XTPcpp") ...@@ -56,7 +56,7 @@ SET(SOFTWARE_NAME "XTPcpp")
SET(XTPCPP_VERSION_MAJOR "0") SET(XTPCPP_VERSION_MAJOR "0")
SET(XTPCPP_VERSION_MINOR "2") SET(XTPCPP_VERSION_MINOR "2")
SET(XTPCPP_VERSION_PATCH "23") SET(XTPCPP_VERSION_PATCH "24")
SET(XTPCPP_VERSION "${XTPCPP_VERSION_MAJOR}.${XTPCPP_VERSION_MINOR}.${XTPCPP_VERSION_PATCH}") SET(XTPCPP_VERSION "${XTPCPP_VERSION_MAJOR}.${XTPCPP_VERSION_MINOR}.${XTPCPP_VERSION_PATCH}")
# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non # Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
......
debian/changelog
+ 19
− 0
View file @ b514c2e8
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 xtpcpp (0.2.23-2) stretch; urgency=medium
* fix version number * fix version number
......
src/core/identificationgroup.cpp
+ 16
− 10
View file @ b514c2e8
...@@ -55,14 +55,15 @@ IdentificationGroup::getGroupStore() const ...@@ -55,14 +55,15 @@ IdentificationGroup::getGroupStore() const
} }
pappso::pappso_double 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; pappso::pappso_double nsaf_sum = 0;
for(auto &p_protein_match : _protein_match_list) for(auto &p_protein_match : _protein_match_list)
{ {
if(p_protein_match->getValidationState() >= ValidationState::grouped) 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; return nsaf_sum;
...@@ -130,7 +131,8 @@ unsigned int ...@@ -130,7 +131,8 @@ unsigned int
IdentificationGroup::countDecoyProteinMatch(ValidationState state) const IdentificationGroup::countDecoyProteinMatch(ValidationState state) const
{ {
return std::count_if( 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) { [state](const ProteinMatch *p_protein_match) {
if((p_protein_match->getProteinXtpSp().get()->isDecoy()) && if((p_protein_match->getProteinXtpSp().get()->isDecoy()) &&
(p_protein_match->getValidationState() >= state)) (p_protein_match->getValidationState() >= state))
...@@ -209,7 +211,8 @@ IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const ...@@ -209,7 +211,8 @@ IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const
unsigned int unsigned int
IdentificationGroup::countProteinMatch(ValidationState state) const 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) { [state](const ProteinMatch *p_protein_match) {
if(p_protein_match->getValidationState() >= state) if(p_protein_match->getValidationState() >= state)
{ {
...@@ -302,8 +305,8 @@ IdentificationGroup::addIdentificationDataSourceP( ...@@ -302,8 +305,8 @@ IdentificationGroup::addIdentificationDataSourceP(
IdentificationDataSource *p_identification_source) IdentificationDataSource *p_identification_source)
{ {
addMsRunSp(p_identification_source->getMsRunSp()); addMsRunSp(p_identification_source->getMsRunSp());
auto it = std::find(_id_source_list.begin(), _id_source_list.end(), auto it = std::find(
p_identification_source); _id_source_list.begin(), _id_source_list.end(), p_identification_source);
if(it == _id_source_list.end()) if(it == _id_source_list.end())
{ {
_id_source_list.push_back(p_identification_source); _id_source_list.push_back(p_identification_source);
...@@ -353,7 +356,8 @@ IdentificationGroup::countSubGroup() const ...@@ -353,7 +356,8 @@ IdentificationGroup::countSubGroup() const
void void
IdentificationGroup::collectMhDelta( 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 ValidationState state) const
{ {
std::set<const PeptideEvidence *> peptide_evidence_list; std::set<const PeptideEvidence *> peptide_evidence_list;
...@@ -466,7 +470,9 @@ IdentificationGroup::getProteinFdr(ValidationState state) const ...@@ -466,7 +470,9 @@ IdentificationGroup::getProteinFdr(ValidationState state) const
void void
IdentificationGroup::getSameXicPeptideEvidenceList( IdentificationGroup::getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list, 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)) if(!contains(p_msrun))
return; return;
...@@ -475,8 +481,8 @@ IdentificationGroup::getSameXicPeptideEvidenceList( ...@@ -475,8 +481,8 @@ IdentificationGroup::getSameXicPeptideEvidenceList(
if(p_msrun == p_identification_source->getMsRunSp().get()) if(p_msrun == p_identification_source->getMsRunSp().get())
{ {
p_identification_source->getPeptideEvidenceStore() p_identification_source->getPeptideEvidenceStore()
.getSameXicPeptideEvidenceList(peptide_evidence_list, p_msrun, .getSameXicPeptideEvidenceList(
p_peptide, charge); peptide_evidence_list, p_msrun, p_peptide, charge);
} }
} }
} }
src/core/identificationgroup.h
+ 7
− 3
View file @ b514c2e8
...@@ -62,7 +62,9 @@ class IdentificationGroup ...@@ -62,7 +62,9 @@ class IdentificationGroup
* Warning: this is not NSAF, just a part * Warning: this is not NSAF, just a part
* @param p_msrun_id pointer on the msrun to get NSAF. * @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 /** @brief count groups
* */ * */
...@@ -152,7 +154,8 @@ class IdentificationGroup ...@@ -152,7 +154,8 @@ class IdentificationGroup
* each peptide evidence is only counted once * each peptide evidence is only counted once
*/ */
void collectMhDelta(std::vector<pappso::pappso_double> &delta_list, 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 /** @brief look for a peptide in the same XIC
...@@ -163,7 +166,8 @@ class IdentificationGroup ...@@ -163,7 +166,8 @@ class IdentificationGroup
*/ */
void getSameXicPeptideEvidenceList( void getSameXicPeptideEvidenceList(
std::vector<const PeptideEvidence *> &peptide_evidence_list, 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; unsigned int charge) const;
private: private:
......
src/core/proteinmatch.cpp
+ 81
− 31
View file @ b514c2e8
...@@ -346,7 +346,8 @@ ProteinMatch::countPeptideMatch(ValidationState state) const ...@@ -346,7 +346,8 @@ ProteinMatch::countPeptideMatch(ValidationState state) const
size_t size_t
ProteinMatch::countSequenceLi(ValidationState state, ProteinMatch::countSequenceLi(ValidationState state,
const MsRun *p_msrun_id) const const MsRun *p_msrun_id,
const Label *p_label) const
{ {
// qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__; // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
std::set<QString> sequence_list; std::set<QString> sequence_list;
...@@ -356,13 +357,33 @@ ProteinMatch::countSequenceLi(ValidationState state, ...@@ -356,13 +357,33 @@ ProteinMatch::countSequenceLi(ValidationState state,
{ {
if(p_msrun_id != nullptr) 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() if((peptide_match.getPeptideEvidence()->getMsRunP() ==
->getPeptideXtpSp() p_msrun_id) &&
.get() (peptide_match.getPeptideEvidence()
->getSequenceLi()); ->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 else
...@@ -398,7 +419,8 @@ ProteinMatch::countDistinctMsSamples(ValidationState state) const ...@@ -398,7 +419,8 @@ ProteinMatch::countDistinctMsSamples(ValidationState state) const
unsigned int unsigned int
ProteinMatch::countPeptideMassCharge(ValidationState state, 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; std::set<QString> sequence_list;
for(auto &peptide_match : _peptide_match_list) for(auto &peptide_match : _peptide_match_list)
...@@ -410,19 +432,46 @@ ProteinMatch::countPeptideMassCharge(ValidationState state, ...@@ -410,19 +432,46 @@ ProteinMatch::countPeptideMassCharge(ValidationState state,
// within sample // within sample
if(peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id) if(peptide_match.getPeptideEvidence()->getMsRunP() == sp_msrun_id)
{ {
sequence_list.insert( if(p_label != nullptr)
QString("%1-%2-%3") {
.arg(peptide_match.getPeptideEvidence() if(peptide_match.getPeptideEvidence()
->getPeptideXtpSp() ->getPeptideXtpSp()
.get() .get()
->getNativePeptideP() ->getLabel() == p_label)
->getSequenceLi()) {
.arg(peptide_match.getPeptideEvidence() sequence_list.insert(
->getPeptideXtpSp() QString("%1-%2-%3")
.get() .arg(peptide_match.getPeptideEvidence()
->getNativePeptideP() ->getPeptideXtpSp()
->getMass()) .get()
.arg(peptide_match.getPeptideEvidence()->getCharge())); ->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 else
...@@ -500,7 +549,7 @@ ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const ...@@ -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) for(auto &&peptide_pair : map_sequence_evalue)
{ {
evalue_prot += std::log10(peptide_pair.second); evalue_prot += std::log10(peptide_pair.second);
...@@ -512,7 +561,8 @@ ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const ...@@ -512,7 +561,8 @@ ProteinMatch::getLogEvalue(const MsRun *sp_msrun_id) const
} }
pappso::pappso_double pappso::pappso_double
ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum, 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) if(proto_nsaf_sum == 0)
{ {
...@@ -521,11 +571,11 @@ ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum, ...@@ -521,11 +571,11 @@ ProteinMatch::getNsaf(pappso::pappso_double proto_nsaf_sum,
"Error computing NSAF for protein %1 :\nproto_nsaf_sum is null") "Error computing NSAF for protein %1 :\nproto_nsaf_sum is null")
.arg(this->getProteinXtpSp().get()->getAccession())); .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 pappso::pappso_double
ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id, const Label *p_label) const
{ {
try try
{ {
...@@ -535,8 +585,8 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const ...@@ -535,8 +585,8 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
QObject::tr("protein has no amino acid sequence")); QObject::tr("protein has no amino acid sequence"));
} }
pappso::pappso_double proto_nsaf = pappso::pappso_double proto_nsaf =
(pappso::pappso_double)countSampleScan(ValidationState::validAndChecked, (pappso::pappso_double)countSampleScan(
sp_msrun_id) / ValidationState::validAndChecked, sp_msrun_id, p_label) /
(pappso::pappso_double)_protein_sp.get()->size(); (pappso::pappso_double)_protein_sp.get()->size();
return proto_nsaf; return proto_nsaf;
} }
...@@ -550,13 +600,13 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const ...@@ -550,13 +600,13 @@ ProteinMatch::getProtoNsaf(const MsRun *sp_msrun_id) const
} }
pappso::pappso_double pappso::pappso_double
ProteinMatch::getPAI(const MsRun *sp_msrun_id) const ProteinMatch::getPAI(const MsRun *sp_msrun_id, const Label *p_label) const
{ {
try try
{ {
pappso::pappso_double PAI = pappso::pappso_double PAI =
(pappso::pappso_double)countPeptideMassCharge( (pappso::pappso_double)countPeptideMassCharge(
ValidationState::validAndChecked, sp_msrun_id) / ValidationState::validAndChecked, sp_msrun_id, p_label) /
(pappso::pappso_double)_protein_sp.get()->countTrypticPeptidesForPAI(); (pappso::pappso_double)_protein_sp.get()->countTrypticPeptidesForPAI();
return PAI; return PAI;
} }
...@@ -570,11 +620,11 @@ ProteinMatch::getPAI(const MsRun *sp_msrun_id) const ...@@ -570,11 +620,11 @@ ProteinMatch::getPAI(const MsRun *sp_msrun_id) const
} }
pappso::pappso_double 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 // compute emPAI, Ishihama 2005
pappso::pappso_double value = 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; return value;
} }
......
src/core/proteinmatch.h
+ 12
− 6
View file @ b514c2e8
...@@ -72,7 +72,8 @@ class ProteinMatch ...@@ -72,7 +72,8 @@ class ProteinMatch
* Warning: this is not NSAF, just a part * Warning: this is not NSAF, just a part
* @param p_msrun_id pointer on the msrun to get NSAF. * @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 /** @brief compute NSAF within msrun : normalized spectral abundance factor
* (NSAF) Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing * (NSAF) Florens L., Carozza M. J. C., Swanson S. K., et al. Analyzing
...@@ -84,17 +85,20 @@ class ProteinMatch ...@@ -84,17 +85,20 @@ class ProteinMatch
* @param p_msrun_id pointer on the msrun to get NSAF * @param p_msrun_id pointer on the msrun to get NSAF
* */ * */
pappso::pappso_double getNsaf(pappso::pappso_double proto_nsaf_sum, 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 /** @brief compute Protein Abundance Index (PAI) within sample
* PAI computation (Rappsilber et al. 2002) * 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 /** @brief compute emPAI within sample
* Ishihama 2005 * 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 setProteinXtpSp(ProteinXtpSp protein_sp);
void addPeptideMatch(const PeptideMatch &peptide_match); void addPeptideMatch(const PeptideMatch &peptide_match);
...@@ -162,7 +166,8 @@ class ProteinMatch ...@@ -162,7 +166,8 @@ class ProteinMatch
* @param p_msrun_id count within the specified sample * @param p_msrun_id count within the specified sample
*/ */
size_t countSequenceLi(ValidationState state, 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 /** @brief count distinct peptide+mass+charge
* peptide is the peptide sequence LI (Leucine => Isoleucine) * peptide is the peptide sequence LI (Leucine => Isoleucine)
...@@ -171,7 +176,8 @@ class ProteinMatch ...@@ -171,7 +176,8 @@ class ProteinMatch
* @param p_msrun_id count within the specified sample * @param p_msrun_id count within the specified sample
*/ */
unsigned int countPeptideMassCharge(ValidationState state, 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 /** @brief count distinct MS samples in which the protein is observed
* @param state validation state of peptides to count * @param state validation state of peptides to count
......
src/core/tandem_run/tandemcondorprocess.cpp
+ 3
− 1
View file @ b514c2e8
...@@ -98,7 +98,9 @@ TandemCondorProcess::prepareTemporaryDirectory() ...@@ -98,7 +98,9 @@ TandemCondorProcess::prepareTemporaryDirectory()
{ {
QSettings settings; 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) if(_p_tmp_dir != nullptr)
{ {
delete _p_tmp_dir; delete _p_tmp_dir;
......
src/gui/widgets/automatic_filter_widget/automatic_filter_widget.ui
+ 50
− 2
View file @ b514c2e8
...@@ -6,10 +6,28 @@ ...@@ -6,10 +6,28 @@
<rect> <rect>
<x>0</x> <x>0</x>
<y>0</y> <y>0</y>
<width>533</width> <width>510</width>
<height>300</height> <height>180</height>
</rect> </rect>
</property> </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"> <property name="windowTitle">
<string>Form</string> <string>Form</string>
</property> </property>
...@@ -21,6 +39,12 @@ ...@@ -21,6 +39,12 @@
</property> </property>
<item row="0" column="0"> <item row="0" column="0">
<widget class="QLabel" name="sample_number_label"> <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"> <property name="text">
<string>peptide Evalue</string> <string>peptide Evalue</string>
</property> </property>
...@@ -44,6 +68,12 @@ ...@@ -44,6 +68,12 @@
</item> </item>
<item row="1" column="0"> <item row="1" column="0">
<widget class="QLabel" name="group_number_label"> <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"> <property name="text">
<string>number of peptides per protein</string> <string>number of peptides per protein</string>
</property> </property>
...@@ -61,6 +91,12 @@ ...@@ -61,6 +91,12 @@
</item> </item>
<item row="2" column="0"> <item row="2" column="0">
<widget class="QLabel" name="label"> <widget class="QLabel" name="label">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text"> <property name="text">
<string>overall samples</string> <string>overall samples</string>
</property> </property>
...@@ -75,6 +111,12 @@ ...@@ -75,6 +111,12 @@
</item> </item>
<item row="3" column="0"> <item row="3" column="0">
<widget class="QLabel" name="subgroup_number_label"> <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"> <property name="text">
<string>protein Evalue</string> <string>protein Evalue</string>
</property> </property>
...@@ -98,6 +140,12 @@ ...@@ -98,6 +140,12 @@
</item> </item>
<item row="4" column="0"> <item row="4" column="0">
<widget class="QLabel" name="label_2"> <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"> <property name="text">
<string>protein Evalue (log10)</string> <string>protein Evalue (log10)</string>
</property> </property>
......
src/output/ods/comparbasesheet.cpp
+ 6
− 2
View file @ b514c2e8
...@@ -45,7 +45,10 @@ ComparBaseSheet::ComparBaseSheet(OdsExport *p_ods_export, ...@@ -45,7 +45,10 @@ ComparBaseSheet::ComparBaseSheet(OdsExport *p_ods_export,
_sp_labelling_method = p_project->getLabelingMethodSp(); _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 void
...@@ -174,7 +177,8 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match) ...@@ -174,7 +177,8 @@ ComparBaseSheet::writeProteinMatch(const ProteinMatch *p_protein_match)
{ {
writeComparValue(p_protein_match, writeComparValue(p_protein_match,
ValidationState::validAndChecked, ValidationState::validAndChecked,
msrun_sp.get(),p_label); msrun_sp.get(),
p_label);
if(_first_cell_coordinate.isEmpty()) if(_first_cell_coordinate.isEmpty())
{ {
_first_cell_coordinate = _p_writer->getOdsCellCoordinate(); _first_cell_coordinate = _p_writer->getOdsCellCoordinate();
......
src/output/ods/comparspectrasheet.cpp
+ 42
− 15
View file @ b514c2e8
...@@ -50,7 +50,8 @@ ComparSpectraSheet::writeComparValue(const ProteinMatch *p_protein_match, ...@@ -50,7 +50,8 @@ ComparSpectraSheet::writeComparValue(const ProteinMatch *p_protein_match,
const Label *p_label) const Label *p_label)
{ {
qDebug() << "ComparSpectraSheet::writeComparValue begin"; 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"; qDebug() << "ComparSpectraSheet::writeComparValue end";
} }
...@@ -71,7 +72,7 @@ ComparSequenceSheet::writeComparValue(const ProteinMatch *p_protein_match, ...@@ -71,7 +72,7 @@ ComparSequenceSheet::writeComparValue(const ProteinMatch *p_protein_match,
{ {
qDebug() << "ComparSequenceSheet::writeComparValue begin"; qDebug() << "ComparSequenceSheet::writeComparValue begin";
_p_writer->writeCell( _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"; qDebug() << "ComparSequenceSheet::writeComparValue end";
} }
...@@ -90,7 +91,7 @@ ComparPaiSheet::writeComparValue(const ProteinMatch *p_protein_match, ...@@ -90,7 +91,7 @@ ComparPaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
const Label *p_label) const Label *p_label)
{ {
qDebug() << "ComparPaiSheet::writeComparValue begin"; 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"; qDebug() << "ComparPaiSheet::writeComparValue end";
} }
...@@ -109,7 +110,7 @@ ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match, ...@@ -109,7 +110,7 @@ ComparEmpaiSheet::writeComparValue(const ProteinMatch *p_protein_match,
const Label *p_label) const Label *p_label)
{ {
qDebug() << "ComparEmpaiSheet::writeComparValue begin"; 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"; qDebug() << "ComparEmpaiSheet::writeComparValue end";
} }
...@@ -129,21 +130,47 @@ ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match, ...@@ -129,21 +130,47 @@ ComparNsafSheet::writeComparValue(const ProteinMatch *p_protein_match,
{ {
qDebug() << "ComparNsafSheet::writeComparValue begin"; qDebug() << "ComparNsafSheet::writeComparValue begin";
pappso::pappso_double proto_nsaf_sum = 0; 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( if(_label_list.size() > 0)
std::pair<const MsRun *, pappso::pappso_double>(p_msrun, 0));
if(ret.second == false)
{ {
//"element 'z' already existed"; std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
proto_nsaf_sum = ret.first->second; _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 else
{ {
proto_nsaf_sum = std::pair<std::map<QString, pappso::pappso_double>::iterator, bool> ret =
_p_current_identification_group->computeProtoNsafSum(p_msrun); _map_proto_nsaf_sum_by_msrun.insert(
ret.first->second = proto_nsaf_sum; 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"; qDebug() << "ComparNsafSheet::writeComparValue end";
} }
src/output/ods/comparspectrasheet.h
+ 1
− 1
View file @ b514c2e8
...@@ -104,7 +104,7 @@ class ComparNsafSheet : public ComparBaseSheet ...@@ -104,7 +104,7 @@ class ComparNsafSheet : public ComparBaseSheet
const Label *p_label = nullptr) override; const Label *p_label = nullptr) override;
private: 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 #endif // COMPARSPECTRASHEET_H
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment