diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index 27f8b2bffae35a4840eac8daab8a70b09efb1ab5..c1657579f7f7a3cfce484ef56628b5485645e23a 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -812,7 +812,7 @@ ProteinMatch::collectPeptideEvidences(
QString
ProteinMatch::getFlankingNterRegion(const PeptideMatch &peptide_match,
- int orig_length)
+ int orig_length) const
{
int length = orig_length;
int start = peptide_match.getStart() - length;
@@ -836,7 +836,7 @@ ProteinMatch::getFlankingNterRegion(const PeptideMatch &peptide_match,
QString
ProteinMatch::getFlankingCterRegion(const PeptideMatch &peptide_match,
- int orig_length)
+ int orig_length) const
{
int start = peptide_match.getStop();
int max = getProteinXtpSp().get()->getSequence().size();
diff --git a/src/core/proteinmatch.h b/src/core/proteinmatch.h
index b8fb3b6dcd7564d8a9857dc272fdbc0acb0b027a..218deeffeb92897cd55e2298f3cf7290846d9f96 100644
--- a/src/core/proteinmatch.h
+++ b/src/core/proteinmatch.h
@@ -188,13 +188,15 @@ class ProteinMatch
* @param peptide_match the peptide from which we want flanking region
* @param length size of the protein flanking region
*/
- QString getFlankingNterRegion(const PeptideMatch &peptide_match, int length);
+ QString getFlankingNterRegion(const PeptideMatch &peptide_match,
+ int length) const;
/** @brief get the flanking protein sequence at the Cter side of the peptide
* @param peptide_match the peptide from which we want flanking region
* @param length size of the protein flanking region
*/
- QString getFlankingCterRegion(const PeptideMatch &peptide_match, int length);
+ QString getFlankingCterRegion(const PeptideMatch &peptide_match,
+ int length) const;
protected:
void setGroupingExperiment(GroupingExperiment *p_grp_experiment);
diff --git a/src/output/ods/peptidepossheet.cpp b/src/output/ods/peptidepossheet.cpp
index 9918513ab2ae6008b353b0a3e6410612ee4c1a42..4b66f6ab557585933ddf06fc014824cef7dfb5ea 100644
--- a/src/output/ods/peptidepossheet.cpp
+++ b/src/output/ods/peptidepossheet.cpp
@@ -82,12 +82,14 @@ PeptidePosSheet::writeHeaders(IdentificationGroup *p_ident)
_p_writer->writeCell("Protein ID");
_p_writer->writeCell("accession");
_p_writer->writeCell("description");
- _p_writer->writeCell("Peptide ID");
- _p_writer->writeCell("Sequence");
- _p_writer->writeCell("Modifs");
- _p_writer->writeCell("Start");
+ writeCellHeader(PeptideListColumn::peptide_grouping_id);
+ writeCellHeader(PeptideListColumn::sequence_nter);
+ writeCellHeader(PeptideListColumn::sequence);
+ writeCellHeader(PeptideListColumn::sequence_cter);
+ writeCellHeader(PeptideListColumn::modifs);
+ writeCellHeader(PeptideListColumn::start);
_p_writer->writeCell("Stop");
- _p_writer->writeCell("MH+ theo");
+ writeCellHeader(PeptideListColumn::theoretical_mhplus);
}
void
@@ -121,8 +123,12 @@ PeptidePosSheet::writeBestPeptideMatch(const ProteinMatch *p_protein_match,
p_protein_match->getProteinXtpSp().get()->getDescription());
_p_writer->writeCell(
p_peptide_evidence->getGrpPeptideSp().get()->getGroupingId());
+ _p_writer->writeCell(
+ p_protein_match->getFlankingNterRegion(peptide_match, 1));
_p_writer->writeCell(
p_peptide_evidence->getPeptideXtpSp().get()->getSequence());
+ _p_writer->writeCell(
+ p_protein_match->getFlankingCterRegion(peptide_match, 1));
_p_writer->writeCell(
p_peptide_evidence->getPeptideXtpSp().get()->getModifString());
_p_writer->writeCell(peptide_match.getStart() + 1);
@@ -149,7 +155,8 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
}
std::sort(
- protein_match_list.begin(), protein_match_list.end(),
+ protein_match_list.begin(),
+ protein_match_list.end(),
[](const ProteinMatch *a, const ProteinMatch *b) {
unsigned int agroup = a->getGrpProteinSp().get()->getGroupNumber();
unsigned int asubgroup = a->getGrpProteinSp().get()->getSubGroupNumber();
@@ -174,7 +181,8 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
continue;
peptide_match_list.push_back(peptide_match);
}
- std::sort(peptide_match_list.begin(), peptide_match_list.end(),
+ std::sort(peptide_match_list.begin(),
+ peptide_match_list.end(),
[](const PeptideMatch &a, const PeptideMatch &b) {
unsigned int arank =
a.getPeptideEvidence()->getGrpPeptideSp().get()->getRank();
@@ -231,3 +239,14 @@ PeptidePosSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
_p_writer->writeLine();
qDebug() << "PeptidePosSheet::writeIdentificationGroup end";
}
+
+
+void
+PeptidePosSheet::writeCellHeader(PeptideListColumn column)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << (std::int8_t)column;
+ _p_writer->setCellAnnotation(PeptideTableModel::getDescription(column));
+ _p_writer->writeCell(PeptideTableModel::getTitle(column));
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}
diff --git a/src/output/ods/peptidepossheet.h b/src/output/ods/peptidepossheet.h
index a7b32bf8cfc34ea6a970f7abc372fb21d37ceaf1..83b55fa34819009f2e48b703032be4b190efd082 100644
--- a/src/output/ods/peptidepossheet.h
+++ b/src/output/ods/peptidepossheet.h
@@ -37,11 +37,13 @@
#include <odsstream/calcwriterinterface.h>
#include "../../core/proteinmatch.h"
#include "odsexport.h"
+#include "../../gui/peptide_list_view/peptidetablemodel.h"
class PeptidePosSheet
{
public:
- PeptidePosSheet(OdsExport *p_ods_export, CalcWriterInterface *p_writer,
+ PeptidePosSheet(OdsExport *p_ods_export,
+ CalcWriterInterface *p_writer,
const Project *p_project);
private:
@@ -50,6 +52,8 @@ class PeptidePosSheet
void writeBestPeptideMatch(const ProteinMatch *p_protein_match,
const PeptideMatch &peptide_match);
+ void writeCellHeader(PeptideListColumn column);
+
private:
OdsExport *_p_ods_export;
const Project *_p_project;
diff --git a/src/output/ods/proteinsheet.cpp b/src/output/ods/proteinsheet.cpp
index 70fc14d52dc9e2f845dfa35bcca583a9dfd809e5..87111d39110be0d4c80ea7fc340577f46e22b837 100644
--- a/src/output/ods/proteinsheet.cpp
+++ b/src/output/ods/proteinsheet.cpp
@@ -58,10 +58,11 @@ ProteinSheet::ProteinSheet(OdsExport *p_ods_export,
void
ProteinSheet::writeCellHeader(ProteinListColumn column)
{
- qDebug() << "ProteinSheet::writeCellHeader begin " << (std::int8_t)column;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
+ << (std::int8_t)column;
_p_writer->setCellAnnotation(ProteinTableModel::getDescription(column));
_p_writer->writeCell(ProteinTableModel::getTitle(column));
- qDebug() << "ProteinSheet::writeCellHeader end";
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
void
@@ -141,7 +142,8 @@ ProteinSheet::writeIdentificationGroup(IdentificationGroup *p_ident)
std::vector<const ProteinMatch *> protein_match_list =
group_pair.second.get()->getProteinMatchList();
- std::sort(protein_match_list.begin(), protein_match_list.end(),
+ std::sort(protein_match_list.begin(),
+ protein_match_list.end(),
[](const ProteinMatch *a, const ProteinMatch *b) {
return a->getGrpProteinSp().get()->getGroupingId() <
b->getGrpProteinSp().get()->getGroupingId();