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Commit 6b256679 authored by Langella Olivier's avatar Langella Olivier
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Peptide prophet column display

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src/core/peptideevidence.h
+ 157
− 148
View file @ 6b256679
...@@ -2,31 +2,33 @@ ...@@ -2,31 +2,33 @@
* \file utils/peptideevidence.h * \file utils/peptideevidence.h
* \date 18/11/2017 * \date 18/11/2017
* \author Olivier Langella * \author Olivier Langella
* \brief peptide evidence : a peptide sequence + spectrum + identification engine evaluation (psm) * \brief peptide evidence : a peptide sequence + spectrum + identification
* engine evaluation (psm)
*/ */
/******************************************************************************* /*******************************************************************************
* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>. * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
* *
* This file is part of XTPcpp. * This file is part of XTPcpp.
* *
* XTPcpp is free software: you can redistribute it and/or modify * XTPcpp is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by * it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or * the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version. * (at your option) any later version.
* *
* XTPcpp is distributed in the hope that it will be useful, * XTPcpp is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of * but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details. * GNU General Public License for more details.
* *
* You should have received a copy of the GNU General Public License * You should have received a copy of the GNU General Public License
* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>. * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
* *
* Contributors: * Contributors:
* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
******************************************************************************/ *implementation
******************************************************************************/
#ifndef PEPTIDEEVIDENCE_H #ifndef PEPTIDEEVIDENCE_H
#define PEPTIDEEVIDENCE_H #define PEPTIDEEVIDENCE_H
...@@ -46,132 +48,139 @@ typedef std::shared_ptr<PeptideEvidence> PeptideEvidenceSp; ...@@ -46,132 +48,139 @@ typedef std::shared_ptr<PeptideEvidence> PeptideEvidenceSp;
class PeptideEvidence class PeptideEvidence
{ {
public : public:
PeptideEvidence(MsRun * msrunid_sp, unsigned int scan); PeptideEvidence(MsRun *msrunid_sp, unsigned int scan);
PeptideEvidence(const PeptideEvidence & other); PeptideEvidence(const PeptideEvidence &other);
std::size_t getHashSampleScan() const; std::size_t getHashSampleScan() const;
std::size_t getHashPeptideMassSample() const; std::size_t getHashPeptideMassSample() const;
PeptideEvidenceSp makePeptideEvidenceSp() const; PeptideEvidenceSp makePeptideEvidenceSp() const;
void setRetentionTime(pappso::pappso_double rt); void setRetentionTime(pappso::pappso_double rt);
void setEvalue(pappso::pappso_double evalue); void setEvalue(pappso::pappso_double evalue);
/** @brief get experimental mass of this peptide /** @brief get experimental mass of this peptide
* @return the computed mass given the precursor measured mass and the deduced peptide charge * @return the computed mass given the precursor measured mass and the deduced
*/ * peptide charge
pappso::pappso_double getExperimentalMass() const; */
pappso::pappso_double getExperimentalMass() const;
/** @brief get experimental MH+ of this peptide
* @return getExperimentalMass + MHPLUS /** @brief get experimental MH+ of this peptide
*/ * @return getExperimentalMass + MHPLUS
pappso::pappso_double getExperimentalMhplus() const; */
pappso::pappso_double getExperimentalMhplus() const;
/** @brief get experimental mz of this peptide
* @return the real mass measured (precuror mass) by the spectrometer /** @brief get experimental mz of this peptide
*/ * @return the real mass measured (precuror mass) by the spectrometer
pappso::pappso_double getExperimentalMz() const; */
pappso::pappso_double getExperimentalMz() const;
/** @brief set experimental mass of this peptide
* @arg exp_mass the computed mass given the precursor measured mass and the deduced peptide charge /** @brief set experimental mass of this peptide
*/ * @arg exp_mass the computed mass given the precursor measured mass and the
void setExperimentalMass(pappso::pappso_double exp_mass); * deduced peptide charge
*/
void setExperimentalMass(pappso::pappso_double exp_mass);
/** \brief set specific parameter value
*/ /** \brief set specific parameter value
virtual void setParam(PeptideEvidenceParam param, const QVariant& value); */
/** \brief get specific parameter value virtual void setParam(PeptideEvidenceParam param, const QVariant &value);
*/ /** \brief get specific parameter value
virtual const QVariant getParam(PeptideEvidenceParam param) const; */
virtual const QVariant getParam(PeptideEvidenceParam param) const;
const std::map<PeptideEvidenceParam, QVariant> & getParamList() const;
const std::map<PeptideEvidenceParam, QVariant> &getParamList() const;
void setCharge(unsigned int charge);
void setPeptideXtpSp (PeptideXtpSp peptide); void setCharge(unsigned int charge);
void setIdentificationDataSource(IdentificationDataSource* identification_source); void setPeptideXtpSp(PeptideXtpSp peptide);
void
setIdentificationDataSource(IdentificationDataSource *identification_source);
/** @brief sets the identification engine
* by default, this is the identification engine of the datasource
*/ /** @brief sets the identification engine
void setIdentificationEngine(IdentificationEngine identification_engine); * by default, this is the identification engine of the datasource
*/
/** @brief get the identification engine void setIdentificationEngine(IdentificationEngine identification_engine);
* by default, this is the identification engine of the datasource
*/ /** @brief get the identification engine
IdentificationEngine getIdentificationEngine() const; * by default, this is the identification engine of the datasource
*/
void setChecked(bool arg1); IdentificationEngine getIdentificationEngine() const;
bool isChecked() const;
bool isValid() const; void setChecked(bool arg1);
bool isValidAndChecked() const; bool isChecked() const;
bool isGrouped() const; bool isValid() const;
bool isValidAndChecked() const;
const MsRun * getMsRunP() const; bool isGrouped() const;
IdentificationDataSource* getIdentificationDataSource () const;
unsigned int getScan() const; const MsRun *getMsRunP() const;
pappso::pappso_double getRetentionTime() const; IdentificationDataSource *getIdentificationDataSource() const;
unsigned int getCharge() const; unsigned int getScan() const;
const PeptideXtpSp & getPeptideXtpSp() const; pappso::pappso_double getRetentionTime() const;
pappso::pappso_double getEvalue() const; unsigned int getCharge() const;
const PeptideXtpSp &getPeptideXtpSp() const;
void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide); pappso::pappso_double getEvalue() const;
const pappso::GrpPeptideSp & getGrpPeptideSp() const;
void setGrpPeptideSp(const pappso::GrpPeptideSp &sp_grp_peptide);
/** @brief validate or invalidate peptides and proteins based automatic filters and manual checks const pappso::GrpPeptideSp &getGrpPeptideSp() const;
* */
void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters); /** @brief validate or invalidate peptides and proteins based automatic
* filters and manual checks
/** @brief get delta between theoretical mhplus mass and mhplus experimental mass * */
* mhplus experimental mass - theoretical mhplus mass void updateAutomaticFilters(
*/ const AutomaticFilterParameters &automatic_filter_parameters);
pappso::mz getDeltaMass() const;
/** @brief get delta between theoretical mhplus mass and mhplus experimental
/** @brief get delta in ppm between theoretical mhplus mass and mhplus experimental mass * mass mhplus experimental mass - theoretical mhplus mass
* @return mhplus experimental mass - theoretical mhplus mass */
*/ pappso::mz getDeltaMass() const;
pappso::mz getPpmDeltaMass() const;
/** @brief get delta in ppm between theoretical mhplus mass and mhplus
/** @brief get theoretical (not observed) m/z based on peptide composition and charge * experimental mass
* @return theoretical mz mass * @return mhplus experimental mass - theoretical mhplus mass
*/ */
pappso::mz getTheoreticalMz() const; pappso::mz getPpmDeltaMass() const;
ValidationState getValidationState() const; /** @brief get theoretical (not observed) m/z based on peptide composition and
* charge
/** @brief tells if this peptide contains a protein position * @return theoretical mz mass
* the position is the amino acid position on the protein sequence (starts from 0) */
* */ pappso::mz getTheoreticalMz() const;
bool containsPosition(unsigned int position) const;
ValidationState getValidationState() const;
private :
static std::hash<std::string> _hash_fn; /** @brief tells if this peptide contains a protein position
MsRun * _msrunid_sp; * the position is the amino acid position on the protein sequence (starts
unsigned int _scan=0; * from 0)
size_t _hash_sample_scan; * */
pappso::GrpPeptideSp _sp_grp_peptide; bool containsPosition(unsigned int position) const;
PeptideXtpSp _peptide_sp;
pappso::pappso_double _rt; private:
pappso::pappso_double _evalue=0; static std::hash<std::string> _hash_fn;
pappso::pappso_double _exp_mass; MsRun *_msrunid_sp;
unsigned int _charge; unsigned int _scan = 0;
IdentificationDataSource* _p_identification_source = nullptr; size_t _hash_sample_scan;
std::map<PeptideEvidenceParam, QVariant> _params; pappso::GrpPeptideSp _sp_grp_peptide;
PeptideXtpSp _peptide_sp;
/** @brief manually checked by user (true by default) pappso::pappso_double _rt;
*/ pappso::pappso_double _evalue = 0;
bool _checked = true; pappso::pappso_double _exp_mass;
unsigned int _charge;
/** @brief automatic filter result (false by default) IdentificationDataSource *_p_identification_source = nullptr;
*/ std::map<PeptideEvidenceParam, QVariant> _params;
bool _proxy_valid = false;
/** @brief manually checked by user (true by default)
/** @brief the search/identification engine that found this evidence */
*/ bool _checked = true;
IdentificationEngine _identification_engine;
/** @brief automatic filter result (false by default)
*/
bool _proxy_valid = false;
/** @brief the search/identification engine that found this evidence
*/
IdentificationEngine _identification_engine;
}; };
#endif // PEPTIDEEVIDENCE_H #endif // PEPTIDEEVIDENCE_H
src/gui/peptide_list_view/peptidetablemodel.cpp
+ 45
− 8
View file @ 6b256679
...@@ -56,13 +56,28 @@ PeptideTableModel::setProteinMatch(ProteinMatch *p_protein_match) ...@@ -56,13 +56,28 @@ PeptideTableModel::setProteinMatch(ProteinMatch *p_protein_match)
// QModelIndex bottomRight = createIndex(rowCount(),columnCount()); // QModelIndex bottomRight = createIndex(rowCount(),columnCount());
std::set<PeptideListColumn> engine_columns; std::set<PeptideListColumn> engine_columns;
bool first = true;
for(auto &&peptide_match : _p_protein_match->getPeptideMatchList()) for(auto &&peptide_match : _p_protein_match->getPeptideMatchList())
{ {
if(first)
{
QVariant var = peptide_match.getPeptideEvidence()->getParam(
PeptideEvidenceParam::peptide_prophet_probability);
if(!var.isNull())
{
}
var = peptide_match.getPeptideEvidence()->getParam(
PeptideEvidenceParam::peptide_inter_prophet_probability);
if(!var.isNull())
{
}
first = false;
}
IdentificationEngine engine = IdentificationEngine engine =
peptide_match.getPeptideEvidence()->getIdentificationEngine(); peptide_match.getPeptideEvidence()->getIdentificationEngine();
if(engine == IdentificationEngine::XTandem) if(engine == IdentificationEngine::XTandem)
{ {
engine_columns.insert(PeptideListColumn::hyperscore); engine_columns.insert(PeptideListColumn::tandem_hyperscore);
} }
else if(engine == IdentificationEngine::mascot) else if(engine == IdentificationEngine::mascot)
{ {
...@@ -95,7 +110,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent) const ...@@ -95,7 +110,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent) const
int int
PeptideTableModel::columnCount(const QModelIndex &parent) const PeptideTableModel::columnCount(const QModelIndex &parent) const
{ {
return 23; return 33;
} }
QVariant QVariant
PeptideTableModel::headerData(int section, Qt::Orientation orientation, PeptideTableModel::headerData(int section, Qt::Orientation orientation,
...@@ -333,7 +348,7 @@ PeptideTableModel::data(const QModelIndex &index, int role) const ...@@ -333,7 +348,7 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
.getPeptideEvidence() .getPeptideEvidence()
->getPpmDeltaMass()); ->getPpmDeltaMass());
break; break;
case(std::int8_t)PeptideListColumn::hyperscore: case(std::int8_t)PeptideListColumn::tandem_hyperscore:
return _p_protein_match->getPeptideMatchList() return _p_protein_match->getPeptideMatchList()
.at(row) .at(row)
.getPeptideEvidence() .getPeptideEvidence()
...@@ -345,11 +360,25 @@ PeptideTableModel::data(const QModelIndex &index, int role) const ...@@ -345,11 +360,25 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
.getPeptideEvidence() .getPeptideEvidence()
->getParam(PeptideEvidenceParam::mascot_score); ->getParam(PeptideEvidenceParam::mascot_score);
break; break;
case(std::int8_t)PeptideListColumn::peptide_prophet_probability:
return _p_protein_match->getPeptideMatchList()
.at(row)
.getPeptideEvidence()
->getParam(
PeptideEvidenceParam::peptide_prophet_probability);
break;
case(std::int8_t)
PeptideListColumn::peptide_inter_prophet_probability:
return _p_protein_match->getPeptideMatchList()
.at(row)
.getPeptideEvidence()
->getParam(
PeptideEvidenceParam::peptide_inter_prophet_probability);
break;
} }
} }
return QString("Row%1, Column%2") return QString();
.arg(index.row() + 1)
.arg(index.column() + 1);
} }
return QVariant(); return QVariant();
} }
...@@ -454,11 +483,15 @@ PeptideTableModel::getTitle(std::int8_t column) ...@@ -454,11 +483,15 @@ PeptideTableModel::getTitle(std::int8_t column)
case(std::int8_t)PeptideListColumn::delta_ppm: case(std::int8_t)PeptideListColumn::delta_ppm:
return "delta ppm"; return "delta ppm";
break; break;
case(std::int8_t)PeptideListColumn::hyperscore: case(std::int8_t)PeptideListColumn::tandem_hyperscore:
return "hyperscore"; return "hyperscore";
break; break;
case(std::int8_t)PeptideListColumn::mascot_score: case(std::int8_t)PeptideListColumn::mascot_score:
return "mascot score"; return "mascot score";
case(std::int8_t)PeptideListColumn::peptide_prophet_probability:
return "Prophet probability";
case(std::int8_t)PeptideListColumn::peptide_inter_prophet_probability:
return "Inter prophet probability";
} }
return ""; return "";
} }
...@@ -537,11 +570,15 @@ PeptideTableModel::getDescription(std::int8_t column) ...@@ -537,11 +570,15 @@ PeptideTableModel::getDescription(std::int8_t column)
return "peptide mass difference in ppm between observed mass and " return "peptide mass difference in ppm between observed mass and "
"theoretical mass"; "theoretical mass";
break; break;
case(std::int8_t)PeptideListColumn::hyperscore: case(std::int8_t)PeptideListColumn::tandem_hyperscore:
return "X!Tandem hyperscore"; return "X!Tandem hyperscore";
break; break;
case(std::int8_t)PeptideListColumn::mascot_score: case(std::int8_t)PeptideListColumn::mascot_score:
return "Mascot ion score"; return "Mascot ion score";
case(std::int8_t)PeptideListColumn::peptide_prophet_probability:
return "Peptide prophet probability";
case(std::int8_t)PeptideListColumn::peptide_inter_prophet_probability:
return "Peptide inter prophet probability";
} }
return ""; return "";
} }
......
src/gui/peptide_list_view/peptidetablemodel.h
+ 34
− 23
View file @ 6b256679
...@@ -34,29 +34,40 @@ ...@@ -34,29 +34,40 @@
enum class PeptideListColumn : std::int8_t enum class PeptideListColumn : std::int8_t
{ {
checked = 0, ///< manual checked checked = 0, ///< manual checked
peptide_grouping_id = 1, ///< manual checked peptide_grouping_id = 1, ///< manual checked
engine = 2, engine = 2,
sample = 3, sample = 3,
scan = 4, scan = 4,
rtmin = 5, rtmin = 5,
rt = 6, rt = 6,
charge = 7, charge = 7,
experimental_mz = 8, experimental_mz = 8,
sequence = 9, sequence = 9,
modifs = 10, modifs = 10,
label = 11, label = 11,
start = 12, start = 12,
length = 13, length = 13,
used = 14, used = 14,
subgroups = 15, subgroups = 15,
Evalue = 16, Evalue = 16,
experimental_mhplus = 17, experimental_mhplus = 17,
theoretical_mhplus = 18, theoretical_mhplus = 18,
delta_mhplus = 19, delta_mhplus = 19,
delta_ppm = 20, delta_ppm = 20,
hyperscore = 21, peptide_prophet_probability = 21, ///< no PSI MS description
mascot_score = 22 peptide_inter_prophet_probability = 22, ///< no PSI MS description
tandem_hyperscore = 23, ///< X!Tandem hyperscore MS:1001331
mascot_score = 24, ///< PSI-MS MS:1001171 mascot:score 56.16
mascot_expectation_value =
25, ///< PSI-MS MS:1001172 mascot:expectation value 2.42102904673618e-006
omssa_evalue = 26, ///< MS:1001328 "OMSSA E-value." [PSI:PI]
omssa_pvalue = 27, ///< MS:1001329 "OMSSA p-value." [PSI:PI]
msgfplus_raw = 28, ///< MS:1002049 "MS-GF raw score." [PSI:PI]
msgfplus_denovo = 29, ///< MS:1002050 "MS-GF de novo score." [PSI:PI]
msgfplus_energy = 30, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
msgfplus_SpecEValue = 31, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI]
msgfplus_EValue = 32, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
}; };
class PeptideListWindow; class PeptideListWindow;
......
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