From 6b256679fc67c59b0c41918f87be60598b4a92fe Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Thu, 21 Jun 2018 18:14:00 +0200
Subject: [PATCH] Peptide prophet column display
---
src/core/peptideevidence.h | 305 +++++++++---------
.../peptide_list_view/peptidetablemodel.cpp | 53 ++-
src/gui/peptide_list_view/peptidetablemodel.h | 57 ++--
3 files changed, 236 insertions(+), 179 deletions(-)
diff --git a/src/core/peptideevidence.h b/src/core/peptideevidence.h
index acda0872c..490aec2b7 100644
--- a/src/core/peptideevidence.h
+++ b/src/core/peptideevidence.h
@@ -2,31 +2,33 @@
* \file utils/peptideevidence.h
* \date 18/11/2017
* \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>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef PEPTIDEEVIDENCE_H
#define PEPTIDEEVIDENCE_H
@@ -46,132 +48,139 @@ typedef std::shared_ptr<PeptideEvidence> PeptideEvidenceSp;
class PeptideEvidence
{
-public :
- PeptideEvidence(MsRun * msrunid_sp, unsigned int scan);
- PeptideEvidence(const PeptideEvidence & other);
- std::size_t getHashSampleScan() const;
- std::size_t getHashPeptideMassSample() const;
-
- PeptideEvidenceSp makePeptideEvidenceSp() const;
-
- void setRetentionTime(pappso::pappso_double rt);
- void setEvalue(pappso::pappso_double evalue);
-
- /** @brief get experimental mass of this peptide
- * @return the computed mass given the precursor measured mass and the deduced peptide charge
- */
- pappso::pappso_double getExperimentalMass() const;
-
- /** @brief get experimental MH+ of this peptide
- * @return getExperimentalMass + MHPLUS
- */
- pappso::pappso_double getExperimentalMhplus() const;
-
- /** @brief get experimental mz of this peptide
- * @return the real mass measured (precuror mass) by the spectrometer
- */
- 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
- */
- void setExperimentalMass(pappso::pappso_double exp_mass);
-
-
-
- /** \brief set specific parameter value
- */
- virtual void setParam(PeptideEvidenceParam param, const QVariant& value);
- /** \brief get specific parameter value
- */
- virtual const QVariant getParam(PeptideEvidenceParam param) const;
-
- const std::map<PeptideEvidenceParam, QVariant> & getParamList() const;
-
-
- void setCharge(unsigned int charge);
- void setPeptideXtpSp (PeptideXtpSp peptide);
- void setIdentificationDataSource(IdentificationDataSource* identification_source);
-
-
- /** @brief sets the identification engine
- * by default, this is the identification engine of the datasource
- */
- void setIdentificationEngine(IdentificationEngine identification_engine);
-
- /** @brief get the identification engine
- * by default, this is the identification engine of the datasource
- */
- IdentificationEngine getIdentificationEngine() const;
-
- void setChecked(bool arg1);
- bool isChecked() const;
- bool isValid() const;
- bool isValidAndChecked() const;
- bool isGrouped() const;
-
- const MsRun * getMsRunP() const;
- IdentificationDataSource* getIdentificationDataSource () const;
- unsigned int getScan() const;
- pappso::pappso_double getRetentionTime() const;
- unsigned int getCharge() const;
- const PeptideXtpSp & getPeptideXtpSp() const;
- pappso::pappso_double getEvalue() const;
-
- void setGrpPeptideSp(const pappso::GrpPeptideSp & sp_grp_peptide);
- const pappso::GrpPeptideSp & getGrpPeptideSp() const;
-
- /** @brief validate or invalidate peptides and proteins based automatic filters and manual checks
- * */
- void updateAutomaticFilters(const AutomaticFilterParameters & automatic_filter_parameters);
-
- /** @brief get delta between theoretical mhplus mass and mhplus experimental mass
- * mhplus experimental mass - theoretical mhplus mass
- */
- pappso::mz getDeltaMass() const;
-
- /** @brief get delta in ppm between theoretical mhplus mass and mhplus experimental mass
- * @return mhplus experimental mass - theoretical mhplus mass
- */
- pappso::mz getPpmDeltaMass() const;
-
- /** @brief get theoretical (not observed) m/z based on peptide composition and charge
- * @return theoretical mz mass
- */
- pappso::mz getTheoreticalMz() const;
-
- ValidationState getValidationState() const;
-
- /** @brief tells if this peptide contains a protein position
- * the position is the amino acid position on the protein sequence (starts from 0)
- * */
- bool containsPosition(unsigned int position) const;
-
-private :
- static std::hash<std::string> _hash_fn;
- MsRun * _msrunid_sp;
- unsigned int _scan=0;
- size_t _hash_sample_scan;
- pappso::GrpPeptideSp _sp_grp_peptide;
- PeptideXtpSp _peptide_sp;
- pappso::pappso_double _rt;
- pappso::pappso_double _evalue=0;
- pappso::pappso_double _exp_mass;
- unsigned int _charge;
- IdentificationDataSource* _p_identification_source = nullptr;
- std::map<PeptideEvidenceParam, QVariant> _params;
-
- /** @brief manually checked by user (true by default)
- */
- bool _checked = true;
-
- /** @brief automatic filter result (false by default)
- */
- bool _proxy_valid = false;
-
- /** @brief the search/identification engine that found this evidence
- */
- IdentificationEngine _identification_engine;
+ public:
+ PeptideEvidence(MsRun *msrunid_sp, unsigned int scan);
+ PeptideEvidence(const PeptideEvidence &other);
+ std::size_t getHashSampleScan() const;
+ std::size_t getHashPeptideMassSample() const;
+
+ PeptideEvidenceSp makePeptideEvidenceSp() const;
+
+ void setRetentionTime(pappso::pappso_double rt);
+ void setEvalue(pappso::pappso_double evalue);
+
+ /** @brief get experimental mass of this peptide
+ * @return the computed mass given the precursor measured mass and the deduced
+ * peptide charge
+ */
+ pappso::pappso_double getExperimentalMass() const;
+
+ /** @brief get experimental MH+ of this peptide
+ * @return getExperimentalMass + MHPLUS
+ */
+ pappso::pappso_double getExperimentalMhplus() const;
+
+ /** @brief get experimental mz of this peptide
+ * @return the real mass measured (precuror mass) by the spectrometer
+ */
+ 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
+ */
+ void setExperimentalMass(pappso::pappso_double exp_mass);
+
+
+ /** \brief set specific parameter value
+ */
+ virtual void setParam(PeptideEvidenceParam param, const QVariant &value);
+ /** \brief get specific parameter value
+ */
+ virtual const QVariant getParam(PeptideEvidenceParam param) const;
+
+ const std::map<PeptideEvidenceParam, QVariant> &getParamList() const;
+
+
+ void setCharge(unsigned int charge);
+ void setPeptideXtpSp(PeptideXtpSp peptide);
+ void
+ setIdentificationDataSource(IdentificationDataSource *identification_source);
+
+
+ /** @brief sets the identification engine
+ * by default, this is the identification engine of the datasource
+ */
+ void setIdentificationEngine(IdentificationEngine identification_engine);
+
+ /** @brief get the identification engine
+ * by default, this is the identification engine of the datasource
+ */
+ IdentificationEngine getIdentificationEngine() const;
+
+ void setChecked(bool arg1);
+ bool isChecked() const;
+ bool isValid() const;
+ bool isValidAndChecked() const;
+ bool isGrouped() const;
+
+ const MsRun *getMsRunP() const;
+ IdentificationDataSource *getIdentificationDataSource() const;
+ unsigned int getScan() const;
+ pappso::pappso_double getRetentionTime() const;
+ unsigned int getCharge() const;
+ const PeptideXtpSp &getPeptideXtpSp() const;
+ pappso::pappso_double getEvalue() const;
+
+ void setGrpPeptideSp(const pappso::GrpPeptideSp &sp_grp_peptide);
+ const pappso::GrpPeptideSp &getGrpPeptideSp() const;
+
+ /** @brief validate or invalidate peptides and proteins based automatic
+ * filters and manual checks
+ * */
+ void updateAutomaticFilters(
+ const AutomaticFilterParameters &automatic_filter_parameters);
+
+ /** @brief get delta between theoretical mhplus mass and mhplus experimental
+ * mass mhplus experimental mass - theoretical mhplus mass
+ */
+ pappso::mz getDeltaMass() const;
+
+ /** @brief get delta in ppm between theoretical mhplus mass and mhplus
+ * experimental mass
+ * @return mhplus experimental mass - theoretical mhplus mass
+ */
+ pappso::mz getPpmDeltaMass() const;
+
+ /** @brief get theoretical (not observed) m/z based on peptide composition and
+ * charge
+ * @return theoretical mz mass
+ */
+ pappso::mz getTheoreticalMz() const;
+
+ ValidationState getValidationState() const;
+
+ /** @brief tells if this peptide contains a protein position
+ * the position is the amino acid position on the protein sequence (starts
+ * from 0)
+ * */
+ bool containsPosition(unsigned int position) const;
+
+ private:
+ static std::hash<std::string> _hash_fn;
+ MsRun *_msrunid_sp;
+ unsigned int _scan = 0;
+ size_t _hash_sample_scan;
+ pappso::GrpPeptideSp _sp_grp_peptide;
+ PeptideXtpSp _peptide_sp;
+ pappso::pappso_double _rt;
+ pappso::pappso_double _evalue = 0;
+ pappso::pappso_double _exp_mass;
+ unsigned int _charge;
+ IdentificationDataSource *_p_identification_source = nullptr;
+ std::map<PeptideEvidenceParam, QVariant> _params;
+
+ /** @brief manually checked by user (true by default)
+ */
+ bool _checked = true;
+
+ /** @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
diff --git a/src/gui/peptide_list_view/peptidetablemodel.cpp b/src/gui/peptide_list_view/peptidetablemodel.cpp
index c6daa2cc4..b028f6b30 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.cpp
+++ b/src/gui/peptide_list_view/peptidetablemodel.cpp
@@ -56,13 +56,28 @@ PeptideTableModel::setProteinMatch(ProteinMatch *p_protein_match)
// QModelIndex bottomRight = createIndex(rowCount(),columnCount());
std::set<PeptideListColumn> engine_columns;
+ bool first = true;
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 =
peptide_match.getPeptideEvidence()->getIdentificationEngine();
if(engine == IdentificationEngine::XTandem)
{
- engine_columns.insert(PeptideListColumn::hyperscore);
+ engine_columns.insert(PeptideListColumn::tandem_hyperscore);
}
else if(engine == IdentificationEngine::mascot)
{
@@ -95,7 +110,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent) const
int
PeptideTableModel::columnCount(const QModelIndex &parent) const
{
- return 23;
+ return 33;
}
QVariant
PeptideTableModel::headerData(int section, Qt::Orientation orientation,
@@ -333,7 +348,7 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
.getPeptideEvidence()
->getPpmDeltaMass());
break;
- case(std::int8_t)PeptideListColumn::hyperscore:
+ case(std::int8_t)PeptideListColumn::tandem_hyperscore:
return _p_protein_match->getPeptideMatchList()
.at(row)
.getPeptideEvidence()
@@ -345,11 +360,25 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
.getPeptideEvidence()
->getParam(PeptideEvidenceParam::mascot_score);
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")
- .arg(index.row() + 1)
- .arg(index.column() + 1);
+ return QString();
}
return QVariant();
}
@@ -454,11 +483,15 @@ PeptideTableModel::getTitle(std::int8_t column)
case(std::int8_t)PeptideListColumn::delta_ppm:
return "delta ppm";
break;
- case(std::int8_t)PeptideListColumn::hyperscore:
+ case(std::int8_t)PeptideListColumn::tandem_hyperscore:
return "hyperscore";
break;
case(std::int8_t)PeptideListColumn::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 "";
}
@@ -537,11 +570,15 @@ PeptideTableModel::getDescription(std::int8_t column)
return "peptide mass difference in ppm between observed mass and "
"theoretical mass";
break;
- case(std::int8_t)PeptideListColumn::hyperscore:
+ case(std::int8_t)PeptideListColumn::tandem_hyperscore:
return "X!Tandem hyperscore";
break;
case(std::int8_t)PeptideListColumn::mascot_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 "";
}
diff --git a/src/gui/peptide_list_view/peptidetablemodel.h b/src/gui/peptide_list_view/peptidetablemodel.h
index 85c719227..549aa3378 100644
--- a/src/gui/peptide_list_view/peptidetablemodel.h
+++ b/src/gui/peptide_list_view/peptidetablemodel.h
@@ -34,29 +34,40 @@
enum class PeptideListColumn : std::int8_t
{
- checked = 0, ///< manual checked
- peptide_grouping_id = 1, ///< manual checked
- engine = 2,
- sample = 3,
- scan = 4,
- rtmin = 5,
- rt = 6,
- charge = 7,
- experimental_mz = 8,
- sequence = 9,
- modifs = 10,
- label = 11,
- start = 12,
- length = 13,
- used = 14,
- subgroups = 15,
- Evalue = 16,
- experimental_mhplus = 17,
- theoretical_mhplus = 18,
- delta_mhplus = 19,
- delta_ppm = 20,
- hyperscore = 21,
- mascot_score = 22
+ checked = 0, ///< manual checked
+ peptide_grouping_id = 1, ///< manual checked
+ engine = 2,
+ sample = 3,
+ scan = 4,
+ rtmin = 5,
+ rt = 6,
+ charge = 7,
+ experimental_mz = 8,
+ sequence = 9,
+ modifs = 10,
+ label = 11,
+ start = 12,
+ length = 13,
+ used = 14,
+ subgroups = 15,
+ Evalue = 16,
+ experimental_mhplus = 17,
+ theoretical_mhplus = 18,
+ delta_mhplus = 19,
+ delta_ppm = 20,
+ peptide_prophet_probability = 21, ///< no PSI MS description
+ 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;
--
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