From 5654a80333d793a61c20e1928de30d0dbaf728a9 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Tue, 13 Jun 2017 22:15:22 +0200
Subject: [PATCH] build ptm island with specific modifications on specific
amino acids
---
src/CMakeLists.txt | 8 ++---
src/grouping/ptm/ptmgroupingexperiment.cpp | 34 +++++++++++++++-------
src/grouping/ptm/ptmgroupingexperiment.h | 7 ++++-
3 files changed, 33 insertions(+), 16 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f2b16461..2367b510 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -27,11 +27,11 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
-FIND_PACKAGE( Pappsomspp REQUIRED )
-# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+#FIND_PACKAGE( Pappsomspp REQUIRED )
+ SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
-# SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
-# SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
+ SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
+ SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake_modules)
diff --git a/src/grouping/ptm/ptmgroupingexperiment.cpp b/src/grouping/ptm/ptmgroupingexperiment.cpp
index b92db88d..5b157218 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.cpp
+++ b/src/grouping/ptm/ptmgroupingexperiment.cpp
@@ -63,8 +63,8 @@ PtmGroupingExperiment::PtmGroupingExperiment()
*/
//phospho :
- _modification_list.push_back(pappso::AaModification::getInstance("MOD:00696"));
- _modification_list.push_back(pappso::AaModification::getInstance("MOD:00704"));
+ _modification_list.push_back({pappso::AaModification::getInstance("MOD:00696"), {}});
+ _modification_list.push_back({pappso::AaModification::getInstance("MOD:00704"), {'S','T'}});
}
PtmGroupingExperiment::~PtmGroupingExperiment()
@@ -73,7 +73,7 @@ PtmGroupingExperiment::~PtmGroupingExperiment()
}
const std::vector<PtmIslandSp> & PtmGroupingExperiment::getPtmIslandList() const {
- return _ptm_island_list;
+ return _ptm_island_list;
}
void PtmGroupingExperiment::numbering() {
@@ -150,21 +150,33 @@ std::vector< PtmIslandSp > PtmGroupingExperiment::mergePeptideMatchPtmIslandList
}
- unsigned int PtmGroupingExperiment::countPeptideMatchPtm(const PeptideMatch* p_peptide_match)const {
- unsigned int number=0;
- for (pappso::AaModificationP modification: _modification_list) {
- number += p_peptide_match->getPeptideXtpSp().get()->getNumberOfModification(modification);
+unsigned int PtmGroupingExperiment::countPeptideMatchPtm(const PeptideMatch* p_peptide_match)const {
+ unsigned int number=0;
+ for (const ModificationAndAa & modification: _modification_list) {
+ if (modification.aa_list.size() == 0) {
+ number += p_peptide_match->getPeptideXtpSp().get()->getNumberOfModification(modification.modification);
+ }
+ else {
+ number += p_peptide_match->getPeptideXtpSp().get()->countModificationOnAa(modification.modification, modification.aa_list);
}
- return number;
}
+ return number;
+}
std::vector<unsigned int> PtmGroupingExperiment::getPtmPositions(const ProteinMatch * protein_match) const {
std::vector<unsigned int> position_list;
for (PeptideMatch * p_peptide_match: protein_match->getPeptideMatchList(_peptide_validation_state)) {
unsigned int start = p_peptide_match->getStart();
- for (pappso::AaModificationP modification: _modification_list) {
- for (unsigned int position : p_peptide_match->getPeptideXtpSp().get()->getModificationPositionList(modification)) {
- position_list.push_back(start+position);
+ for (const ModificationAndAa & modification: _modification_list) {
+ if (modification.aa_list.size() == 0) {
+ for (unsigned int position : p_peptide_match->getPeptideXtpSp().get()->getModificationPositionList(modification.modification)) {
+ position_list.push_back(start+position);
+ }
+ }
+ else {
+ for (unsigned int position : p_peptide_match->getPeptideXtpSp().get()->getModificationPositionList(modification.modification, modification.aa_list)) {
+ position_list.push_back(start+position);
+ }
}
}
}
diff --git a/src/grouping/ptm/ptmgroupingexperiment.h b/src/grouping/ptm/ptmgroupingexperiment.h
index a8002b37..bcc97954 100644
--- a/src/grouping/ptm/ptmgroupingexperiment.h
+++ b/src/grouping/ptm/ptmgroupingexperiment.h
@@ -36,6 +36,11 @@
#include "ptmislandsubgroup.h"
#include "ptmislandgroup.h"
+struct ModificationAndAa {
+ pappso::AaModificationP modification;
+ std::vector<char> aa_list;
+};
+
class PtmGroupingExperiment
{
public:
@@ -58,7 +63,7 @@ private:
void addPtmIsland(PtmIslandSp ptm_island);
void numbering();
private:
- std::list<pappso::AaModificationP> _modification_list;
+ std::list<ModificationAndAa> _modification_list;
ValidationState _peptide_validation_state = ValidationState::validAndChecked;
std::vector<PtmIslandSp> _ptm_island_list;
std::vector<PtmIslandSubgroupSp> _ptm_island_subgroup_list;
--
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