Commit f99a5aaa authored by Langella Olivier's avatar Langella Olivier
Browse files

new peptide view column

parent b0b5499b
...@@ -15,6 +15,9 @@ Build-Depends: debhelper-compat (= 12), ...@@ -15,6 +15,9 @@ Build-Depends: debhelper-compat (= 12),
libgrantlee5-dev, libgrantlee5-dev,
librdata-dev (>= 0~20210223+git-85757dc6), librdata-dev (>= 0~20210223+git-85757dc6),
docbook-to-man, docbook-to-man,
daps,
fonts-ebgaramond,
fonts-ebgaramond-extra,
doxygen doxygen
Standards-Version: 4.5.0 Standards-Version: 4.5.0
Homepage: http://pappso.inra.fr/bioinfo Homepage: http://pappso.inra.fr/bioinfo
......
...@@ -39,5 +39,5 @@ STYLEROOT="xslt" ...@@ -39,5 +39,5 @@ STYLEROOT="xslt"
#PROFOS="" #PROFOS=""
#PROFVENDOR="" #PROFVENDOR=""
FOP_CMD_OPTIONS="-c /home/rusconi/devel/xtpcpp/development/doc/user-manual/fop.xconf" FOP_CMD_OPTIONS="-c /home/langella/developpement/git/xtandempipeline/doc/user-manual/fop.xconf"
<!ENTITY VERSION "0.4.27"> <!ENTITY VERSION "0.4.28">
...@@ -33,7 +33,7 @@ ...@@ -33,7 +33,7 @@
#include <pappsomspp/psm/deepprot/deepprotenum.h> #include <pappsomspp/psm/deepprot/deepprotenum.h>
#include "../../core/labeling/label.h" #include "../../core/labeling/label.h"
#include "../../utils/utils.h" #include "../../utils/utils.h"
#include <pappsomspp/exception/exceptionnotfound.h>
PeptideTableModel::PeptideTableModel(PeptideListWindow *parent) PeptideTableModel::PeptideTableModel(PeptideListWindow *parent)
: QAbstractTableModel(parent) : QAbstractTableModel(parent)
...@@ -163,7 +163,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent [[maybe_unused]]) const ...@@ -163,7 +163,7 @@ PeptideTableModel::rowCount(const QModelIndex &parent [[maybe_unused]]) const
int int
PeptideTableModel::columnCount(const QModelIndex &parent [[maybe_unused]]) const PeptideTableModel::columnCount(const QModelIndex &parent [[maybe_unused]]) const
{ {
return 49; return 50;
} }
QVariant QVariant
PeptideTableModel::headerData(int section, PeptideTableModel::headerData(int section,
...@@ -286,6 +286,20 @@ PeptideTableModel::data(const QModelIndex &index, int role) const ...@@ -286,6 +286,20 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
.getPeptideEvidence() .getPeptideEvidence()
->getScanNumber()); ->getScanNumber());
break; break;
case(std::int8_t)PeptideListColumn::spectrum_index:
try
{
return QVariant(
(quint32)_p_protein_match->getPeptideMatchList()
.at(row)
.getPeptideEvidence()
->getSpectrumIndex());
}
catch(pappso::ExceptionNotFound &notfound)
{
// no spectrum index
}
break;
case(std::int8_t)PeptideListColumn::rtmin: case(std::int8_t)PeptideListColumn::rtmin:
return QVariant( return QVariant(
(qreal)(_p_protein_match->getPeptideMatchList() (qreal)(_p_protein_match->getPeptideMatchList()
...@@ -564,40 +578,60 @@ PeptideTableModel::data(const QModelIndex &index, int role) const ...@@ -564,40 +578,60 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
break; break;
case(std::int8_t)PeptideListColumn::deepprot_match_type: case(std::int8_t)PeptideListColumn::deepprot_match_type:
return pappso::DeepProtEnumStr::toString( {
(pappso::DeepProtMatchType)_p_protein_match QVariant param(
->getPeptideMatchList() _p_protein_match->getPeptideMatchList()
.at(row) .at(row)
.getPeptideEvidence() .getPeptideEvidence()
->getParam(PeptideEvidenceParam::deepprot_match_type) ->getParam(PeptideEvidenceParam::deepprot_match_type));
.toUInt()); if(param.isNull())
return QString();
return pappso::DeepProtEnumStr::toString(
(pappso::DeepProtMatchType)param.toUInt());
}
break; break;
case(std::int8_t)PeptideListColumn::deepprot_status: case(std::int8_t)PeptideListColumn::deepprot_status:
return pappso::DeepProtEnumStr::toString( {
(pappso::DeepProtPeptideCandidateStatus)_p_protein_match QVariant param(
->getPeptideMatchList() _p_protein_match->getPeptideMatchList()
.at(row) .at(row)
.getPeptideEvidence() .getPeptideEvidence()
->getParam( ->getParam(PeptideEvidenceParam::
PeptideEvidenceParam::deepprot_peptide_candidate_status) deepprot_peptide_candidate_status));
.toUInt()); if(param.isNull())
return QString();
return pappso::DeepProtEnumStr::toString(
(pappso::DeepProtPeptideCandidateStatus)param.toUInt());
}
break; break;
case(std::int8_t)PeptideListColumn::deepprot_mass_delta: case(std::int8_t)PeptideListColumn::deepprot_mass_delta:
return _p_protein_match->getPeptideMatchList() {
.at(row) QVariant param(
.getPeptideEvidence() _p_protein_match->getPeptideMatchList()
->getParam(PeptideEvidenceParam::deepprot_mass_delta) .at(row)
.toDouble(); .getPeptideEvidence()
->getParam(PeptideEvidenceParam::deepprot_mass_delta));
if(param.isNull())
return QString();
return param.toDouble();
}
break; break;
case(std::int8_t)PeptideListColumn::deepprot_delta_positions: case(std::int8_t)PeptideListColumn::deepprot_delta_positions:
return _p_protein_match->getPeptideMatchList() {
.at(row) QVariant param(
.getPeptideEvidence() _p_protein_match->getPeptideMatchList()
->getParam(PeptideEvidenceParam::deepprot_delta_positions); .at(row)
.getPeptideEvidence()
->getParam(
PeptideEvidenceParam::deepprot_delta_positions));
if(param.isNull())
return QString();
return param;
}
break; break;
} }
} }
...@@ -609,7 +643,7 @@ PeptideTableModel::data(const QModelIndex &index, int role) const ...@@ -609,7 +643,7 @@ PeptideTableModel::data(const QModelIndex &index, int role) const
void void
PeptideTableModel::onPeptideDataChanged() PeptideTableModel::onPeptideDataChanged()
{ {
qDebug() << "PeptideTableModel::onPeptideDataChanged begin " << rowCount(); qDebug() << "begin " << rowCount();
emit layoutAboutToBeChanged(); emit layoutAboutToBeChanged();
emit layoutChanged(); emit layoutChanged();
} }
...@@ -623,7 +657,7 @@ PeptideTableModel::getPeptideListColumn(std::int8_t column) ...@@ -623,7 +657,7 @@ PeptideTableModel::getPeptideListColumn(std::int8_t column)
const QString const QString
PeptideTableModel::getTitle(PeptideListColumn column) PeptideTableModel::getTitle(PeptideListColumn column)
{ {
qDebug() << "PeptideTableModel::getTitle begin "; qDebug() << " begin ";
return PeptideTableModel::getTitle((std::int8_t)column); return PeptideTableModel::getTitle((std::int8_t)column);
// qDebug() << "ProteinTableModel::getTitle end "; // qDebug() << "ProteinTableModel::getTitle end ";
} }
...@@ -658,6 +692,9 @@ PeptideTableModel::getTitle(std::int8_t column) ...@@ -658,6 +692,9 @@ PeptideTableModel::getTitle(std::int8_t column)
case(std::int8_t)PeptideListColumn::scan: case(std::int8_t)PeptideListColumn::scan:
return "scan"; return "scan";
break; break;
case(std::int8_t)PeptideListColumn::spectrum_index:
return "index";
break;
case(std::int8_t)PeptideListColumn::rtmin: case(std::int8_t)PeptideListColumn::rtmin:
return "RT min"; return "RT min";
break; break;
...@@ -822,6 +859,9 @@ PeptideTableModel::getDescription(std::int8_t column) ...@@ -822,6 +859,9 @@ PeptideTableModel::getDescription(std::int8_t column)
case(std::int8_t)PeptideListColumn::scan: case(std::int8_t)PeptideListColumn::scan:
return "scan number"; return "scan number";
break; break;
case(std::int8_t)PeptideListColumn::spectrum_index:
return "spectrum index";
break;
case(std::int8_t)PeptideListColumn::rtmin: case(std::int8_t)PeptideListColumn::rtmin:
return "retention time in minutes"; return "retention time in minutes";
break; break;
...@@ -990,7 +1030,7 @@ PeptideTableModel::getColumnWidth(int column) ...@@ -990,7 +1030,7 @@ PeptideTableModel::getColumnWidth(int column)
bool bool
PeptideTableModel::hasColumn(PeptideListColumn column) PeptideTableModel::hasColumn(PeptideListColumn column)
{ {
if((std::int8_t)column < 24) if((std::int8_t)column < 25)
{ {
return true; return true;
} }
......
...@@ -38,53 +38,54 @@ enum class PeptideListColumn : std::int8_t ...@@ -38,53 +38,54 @@ enum class PeptideListColumn : std::int8_t
engine = 2, engine = 2,
sample = 3, sample = 3,
scan = 4, scan = 4,
rtmin = 5, spectrum_index = 5, ///< spectrum index
rt = 6, rtmin = 6,
charge = 7, rt = 7,
experimental_mz = 8, charge = 8,
sequence_nter = 9, experimental_mz = 9,
sequence = 10, sequence_nter = 10,
sequence_cter = 11, sequence = 11,
modifs = 12, sequence_cter = 12,
label = 13, modifs = 13,
start = 14, label = 14,
length = 15, start = 15,
used = 16, length = 16,
subgroups = 17, used = 17,
Evalue = 18, subgroups = 18,
qvalue = 19, Evalue = 19,
experimental_mhplus = 20, qvalue = 20,
theoretical_mhplus = 21, experimental_mhplus = 21,
delta_mhplus = 22, theoretical_mhplus = 22,
delta_ppm = 23, delta_mhplus = 23,
peptide_prophet_probability = 24, ///< no PSI MS description delta_ppm = 24,
peptide_inter_prophet_probability = 25, ///< no PSI MS description peptide_prophet_probability = 25, ///< no PSI MS description
tandem_hyperscore = 26, ///< X!Tandem hyperscore MS:1001331 peptide_inter_prophet_probability = 26, ///< no PSI MS description
mascot_score = 27, ///< PSI-MS MS:1001171 mascot:score 56.16 tandem_hyperscore = 27, ///< X!Tandem hyperscore MS:1001331
mascot_score = 28, ///< PSI-MS MS:1001171 mascot:score 56.16
mascot_expectation_value = mascot_expectation_value =
28, ///< PSI-MS MS:1001172 mascot:expectation value 2.42102904673618e-006 29, ///< PSI-MS MS:1001172 mascot:expectation value 2.42102904673618e-006
omssa_evalue = 29, ///< MS:1001328 "OMSSA E-value." [PSI:PI] omssa_evalue = 30, ///< MS:1001328 "OMSSA E-value." [PSI:PI]
omssa_pvalue = 30, ///< MS:1001329 "OMSSA p-value." [PSI:PI] omssa_pvalue = 31, ///< MS:1001329 "OMSSA p-value." [PSI:PI]
msgfplus_raw = 31, ///< MS:1002049 "MS-GF raw score." [PSI:PI] msgfplus_raw = 32, ///< MS:1002049 "MS-GF raw score." [PSI:PI]
msgfplus_denovo = 32, ///< MS:1002050 "MS-GF de novo score." [PSI:PI] msgfplus_denovo = 33, ///< MS:1002050 "MS-GF de novo score." [PSI:PI]
msgfplus_energy = 33, ///< MS:1002051 "MS-GF energy score." [PSI:PI] msgfplus_energy = 34, ///< MS:1002051 "MS-GF energy score." [PSI:PI]
msgfplus_SpecEValue = 34, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI] msgfplus_SpecEValue = 35, ///< MS:1002052 "MS-GF spectral E-value." [PSI:PI]
msgfplus_EValue = 35, ///< MS:1002053 "MS-GF E-value." [PSI:PI] msgfplus_EValue = 36, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
msgfplus_isotope_error = 36, ///< MS:1002053 "MS-GF E-value." [PSI:PI] msgfplus_isotope_error = 37, ///< MS:1002053 "MS-GF E-value." [PSI:PI]
comet_xcorr = 37, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI] comet_xcorr = 38, ///< MS:1002252 "The Comet result 'XCorr'." [PSI:PI]
comet_deltacn = 38, ///< MS:1002253 "The Comet result 'DeltaCn'." [PSI:PI] comet_deltacn = 39, ///< MS:1002253 "The Comet result 'DeltaCn'." [PSI:PI]
comet_deltacnstar = comet_deltacnstar =
39, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI] 40, ///< MS:1002254 "The Comet result 'DeltaCnStar'." [PSI:PI]
comet_spscore = 40, ///< MS:1002255 "The Comet result 'SpScore'." [PSI:PI] comet_spscore = 41, ///< MS:1002255 "The Comet result 'SpScore'." [PSI:PI]
comet_sprank = 41, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI] comet_sprank = 42, ///< MS:1002256 "The Comet result 'SpRank'." [PSI:PI]
comet_expectation_value = comet_expectation_value =
42, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI] 43, ///< MS:1002257 "The Comet result 'Expectation value'." [PSI:PI]
deepprot_original_count = 43, ///< number of matched peaks before specfit deepprot_original_count = 44, ///< number of matched peaks before specfit
deepprot_fitted_count = 44, ///< number of matched peaks after specfit deepprot_fitted_count = 45, ///< number of matched peaks after specfit
deepprot_match_type = 45, ///< DeepProt spectrum match type deepprot_match_type = 46, ///< DeepProt spectrum match type
deepprot_status = 46, ///< DeepProt PSM status deepprot_status = 47, ///< DeepProt PSM status
deepprot_mass_delta = 47, ///< DeepProt mass delta deepprot_mass_delta = 48, ///< DeepProt mass delta
deepprot_delta_positions = 48, ///< DeepProt mass delta positions deepprot_delta_positions = 49, ///< DeepProt mass delta positions
}; };
class PeptideListWindow; class PeptideListWindow;
......
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