From 4efc081002828034f231390a95598838df9a67bd Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Fri, 7 Apr 2017 19:28:23 +0200
Subject: [PATCH] FDR computation OK
---
src/core/identificationgroup.cpp | 21 +++++++++++++++++
src/core/identificationgroup.h | 8 ++++++-
src/core/peptidematch.cpp | 11 +++++++++
src/core/peptidematch.h | 2 ++
src/core/proteinmatch.cpp | 31 +++++++++++++++++++++-----
src/core/proteinmatch.h | 3 +++
src/gui/project_view/projectwindow.cpp | 6 +++--
src/utils/types.h | 1 +
8 files changed, 75 insertions(+), 8 deletions(-)
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index a2c3f253a..df013590e 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -42,6 +42,17 @@ IdentificationGroup::~IdentificationGroup()
}
+unsigned int IdentificationGroup::countDecoyPeptideMatch(ValidationState state) const {
+ unsigned int i=0;
+ for (auto & p_protein_match : _protein_match_list) {
+ if (p_protein_match->getValidationState() == state) {
+ if (p_protein_match->getProteinXtpSp().get()->isDecoy()) {
+ i+=p_protein_match->countPeptideMatch(state);
+ }
+ }
+ }
+ return i;
+}
unsigned int IdentificationGroup::countDecoyProtein(ValidationState state) const {
unsigned int i=0;
for (auto & p_protein_match : _protein_match_list) {
@@ -67,6 +78,16 @@ unsigned int IdentificationGroup::countDecoyProtein(ValidationState state) const
return i;
}
+unsigned int IdentificationGroup::countPeptideMatch(ValidationState state) const {
+ unsigned int i=0;
+ for (auto & p_protein_match : _protein_match_list) {
+ if (p_protein_match->getValidationState() == state) {
+ i+=p_protein_match->countPeptideMatch(state);
+ }
+ }
+ return i;
+}
+
unsigned int IdentificationGroup::countProtein(ValidationState state) const {
unsigned int i=0;
if (state == ValidationState::grouped) {
diff --git a/src/core/identificationgroup.h b/src/core/identificationgroup.h
index 767f8cc25..3eaf8565c 100644
--- a/src/core/identificationgroup.h
+++ b/src/core/identificationgroup.h
@@ -74,7 +74,13 @@ public:
unsigned int countProtein(ValidationState state) const;
/** @brief count decoy proteins
* */
- unsigned int countDecoyProtein(ValidationState state) const;
+ unsigned int countDecoyProtein(ValidationState state) const;
+ /** @brief count peptide match
+ * */
+ unsigned int countPeptideMatch(ValidationState state) const;
+ /** @brief count decoy peptide match
+ * */
+ unsigned int countDecoyPeptideMatch(ValidationState state) const;
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
diff --git a/src/core/peptidematch.cpp b/src/core/peptidematch.cpp
index c95a4d48e..81706face 100644
--- a/src/core/peptidematch.cpp
+++ b/src/core/peptidematch.cpp
@@ -69,6 +69,17 @@ void PeptideMatch::setChecked(bool arg1) {
_checked = arg1;
}
+ValidationState PeptideMatch::getValidationState() const {
+ if (isValid()) {
+ return ValidationState::valid;
+ } else if (isValidAndChecked()) {
+ return ValidationState::validAndChecked;
+ } else if (isGrouped()) {
+ return ValidationState::grouped;
+ }
+ return ValidationState::notValid;
+}
+
bool PeptideMatch::isValid() const {
return _proxy_valid;
}
diff --git a/src/core/peptidematch.h b/src/core/peptidematch.h
index bd150ed5c..a9f67e112 100644
--- a/src/core/peptidematch.h
+++ b/src/core/peptidematch.h
@@ -75,6 +75,8 @@ public :
/** @brief get delta between theoretical mhplus mass and mhplus experimental mass
*/
pappso::mz getDeltaMass() const;
+
+ ValidationState getValidationState() const;
private :
MsRun * _msrunid_sp;
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 0df923cc2..792634523 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -43,7 +43,16 @@ ProteinMatch::~ProteinMatch()
it++;
}
}
-
+ValidationState ProteinMatch::getValidationState() const {
+ if (isValid()) {
+ return ValidationState::valid;
+ } else if (isValidAndChecked()) {
+ return ValidationState::validAndChecked;
+ } else if (isGrouped()) {
+ return ValidationState::grouped;
+ }
+ return ValidationState::notValid;
+}
bool ProteinMatch::contains(PeptideMatch * peptide_match) const {
if (peptide_match == nullptr) return false;
for (auto & p_peptide_match : _peptide_match_list) {
@@ -166,6 +175,18 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
return _sp_grp_protein;
}
+
+unsigned int ProteinMatch::countPeptideMatch(ValidationState state) const {
+ return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [state](const PeptideMatch * p_peptide_match) {
+ if (p_peptide_match->getValidationState() == state) {
+ return true;
+ }
+ else {
+ return false;
+ }
+ });
+}
+
size_t ProteinMatch::countValidSpectrum()const {
return std::count_if (_peptide_match_list.begin(), _peptide_match_list.end(), [](const PeptideMatch * p_peptide_match) {
return (p_peptide_match->isValid());
@@ -312,7 +333,7 @@ const QString ProteinMatch::getHtmlSequence(PeptideMatch * peptide_match_to_loca
}
else {
sequence_html.append(QString("</span>"));
- i--;
+ i--;
break;
}
}
@@ -323,9 +344,9 @@ const QString ProteinMatch::getHtmlSequence(PeptideMatch * peptide_match_to_loca
i++;
for (; i < prot_size; i++) {
if (highlight_bool[i]) {
- i--;
- break;
- }
+ i--;
+ break;
+ }
if(cover_bool[i]) {
sequence_html.append(sequence[i]);
}
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index 3044d8d70..b2501074d 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -75,6 +75,9 @@ public:
bool isValidAndChecked() const;
bool isGrouped() const;
+ ValidationState getValidationState() const;
+ unsigned int countPeptideMatch(ValidationState state) const;
+
/** @brief count valid spectrums
* */
size_t countValidSpectrum()const;
diff --git a/src/gui/project_view/projectwindow.cpp b/src/gui/project_view/projectwindow.cpp
index f2a57aa78..f9c63fed0 100644
--- a/src/gui/project_view/projectwindow.cpp
+++ b/src/gui/project_view/projectwindow.cpp
@@ -151,9 +151,11 @@ void ProjectWindow::computeFdr(ValidationState state) {
pappso::pappso_double total_peptide=0;
pappso::pappso_double false_peptide=0;
for (IdentificationGroup * identification_group : _project_sp.get()->getIdentificationGroupList()) {
- //total_peptide += identification_group->countPeptideMatch(state);
- //false_peptide += identification_group->countDecoyPeptideMatch(state);
+ total_peptide += identification_group->countPeptideMatch(state);
+ false_peptide += identification_group->countDecoyPeptideMatch(state);
}
+ qDebug() << "ProjectWindow::computeFdr false_peptide=" <<false_peptide;
+ qDebug() << "ProjectWindow::computeFdr total_peptide=" <<total_peptide;
ui->peptide_fdr_label->setText(QString("%1 %").arg(false_peptide/total_peptide));
}
diff --git a/src/utils/types.h b/src/utils/types.h
index e3cbf9b1c..c87465c67 100644
--- a/src/utils/types.h
+++ b/src/utils/types.h
@@ -51,6 +51,7 @@ enum class MzFormat {
*/
enum class ValidationState {
+ notValid,///< notValid : automatic filter validation failed
valid, ///< valid : automatic filter validation passed
validAndChecked, ///< validAndChecked : automatic filter validation passed + manual checking
grouped, ///< grouped : automatic filter validation passed + manual checking + grouped
--
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