Commit 479c0d99 authored by Langella Olivier's avatar Langella Olivier
Browse files

bunch of warnings fixed

parent 99bd37a1
......@@ -283,7 +283,7 @@ AlignmentMs2::getOldRtSetForMsrun(const Msrun *p_msrun) const
/// given an ms-level 1 rt (oldRt), by linear interpolation on the given
/// deltaRt points, calculate the best corresponding deltaRt
const mcq_double
mcq_double
AlignmentMs2::getDeltaRtForOldRt(
mcq_double oldRt, std::map<mcq_double, mcq_double> bestRt_deltaRt) const
{
......
......@@ -131,7 +131,7 @@ class AlignmentMs2 : public AlignmentBase
mcq_double last_key,
mcq_double last_value) const;
const mcq_double
mcq_double
getDeltaRtForOldRt(mcq_double oldRt,
std::map<mcq_double, mcq_double> bestRt_deltaRt) const;
......
......@@ -19,7 +19,7 @@
MasschroqWriter::MasschroqWriter(const QString &in_filename,
const QString &out_filename,
const bool with_traces)
const bool with_traces [[maybe_unused]])
: _quanti_item_counter(0),
_input_filename(in_filename),
_enc_precision(64),
......
......@@ -329,7 +329,7 @@ Msrun::write_time_values() const
(i.e. an old alignment has been charged) or if an alignment has occurred
during this process.
*/
const bool
bool
Msrun::hasBeenAligned() const
{
return (!_map_aligned_rt.empty());
......
......@@ -130,7 +130,7 @@ class Msrun
(i.e. an old alignment has been charged) or if an alignment has occurred
during this process.
*/
const bool hasBeenAligned() const;
bool hasBeenAligned() const;
/**
clears the alignment effects on this Ms-run. We need to call this method
......
......@@ -112,7 +112,8 @@ AlignedPeakCollectionOnDisk::add(const Msrun *p_current_msrun,
}
void
AlignedPeakCollectionOnDisk::clear(const Msrun *p_current_msrun)
AlignedPeakCollectionOnDisk::clear(const Msrun *p_current_msrun
[[maybe_unused]])
{
_tmp_aligned_peak_list.clear();
}
......
......@@ -60,7 +60,7 @@ class IsotopeLabelModification
void setPappsoModification(pappso::AaModificationP modification);
const pappso::AaModificationP
pappso::AaModificationP
getPappsoModification() const
{
return _pappso_modification;
......
......@@ -74,7 +74,7 @@ class QuantiItemBase
virtual pappso::PeptideNaturalIsotopeAverageSp
getPeptideNaturalIsotopeAverageSp() const;
virtual const mcq_double
virtual mcq_double
getRt() const
{
return -1;
......@@ -114,15 +114,18 @@ class QuantiItemBase
const pappso::pappso_double &getMz() const;
virtual PeptideRtSp getPeptideRtSp() const;
virtual void
storeAlignedXicPeakForPostMatching(const Msrun *p_current_msrun,
AlignedXicPeakSp &xic_peak_sp){};
virtual void
clearAlignedXicPeakForPostMatching(const Msrun *p_current_msrun){};
virtual void doPostMatching(MonitorSpeedInterface &_p_monitor_speed){};
virtual void storeAlignedXicPeakForPostMatching(const Msrun *p_current_msrun
[[maybe_unused]],
AlignedXicPeakSp &xic_peak_sp
[[maybe_unused]]){};
virtual void clearAlignedXicPeakForPostMatching(const Msrun *p_current_msrun
[[maybe_unused]]){};
virtual void doPostMatching(MonitorSpeedInterface &_p_monitor_speed
[[maybe_unused]]){};
/** \brief signal of the end of quantification on this MSrun*/
virtual void endMsrunQuantification(const Msrun *p_current_msrun){};
virtual void endMsrunQuantification(const Msrun *p_current_msrun
[[maybe_unused]]){};
protected:
virtual CalcWriterInterface *
......
......@@ -20,7 +20,7 @@ QuantiItemMzRt::~QuantiItemMzRt()
{
}
const mcq_double
mcq_double
QuantiItemMzRt::getRt() const
{
return (_rt);
......
......@@ -52,7 +52,7 @@ class QuantiItemMzRt : public QuantiItemBase
* peptide+z+isotopenumber**/
virtual const QString getMzId() const override;
virtual const mcq_double getRt() const override;
virtual mcq_double getRt() const override;
protected:
mcq_double _rt;
......
......@@ -210,7 +210,7 @@ Utilities::newVectorByApplyingWindowsOperation(
return (new_vector);
}
const bool
bool
Utilities::isValidSequence(const QString &sequence, Qt::CaseSensitivity cs)
{
QRegExp match_aaseq("^[A,R,N,D,C,E,Q,G,H,I,L,K,M,F,P,S,T,W,Y,V]*$", cs);
......@@ -223,7 +223,7 @@ Utilities::replaceLwithI(QString &pep_seq)
pep_seq.replace(QString("L"), QString("I"));
}
const Duration
Duration
Utilities::getDurationFromDates(const QDateTime &date_begin,
const QDateTime &date_end)
{
......@@ -248,38 +248,38 @@ Utilities::getDurationFromDates(const QDateTime &date_begin,
return ret_vector;
}
const int
int
Utilities::getDaysFromDuration(const Duration &d)
{
return d.at(0);
}
const int
int
Utilities::getHoursFromDuration(const Duration &d)
{
return d.at(1);
}
const int
int
Utilities::getMinutesFromDuration(const Duration &d)
{
return d.at(2);
}
const int
int
Utilities::getSecondsFromDuration(const Duration &d)
{
return d.at(3);
}
const bool
bool
Utilities::isSorted(const std::vector<mcq_double> &v)
{
return (adjacent_find(v.begin(), v.end(), std::greater<mcq_double>()) ==
v.end());
}
const int
int
Utilities::random_pivot(const int first, const int last)
{
srand(time(NULL));
......
......@@ -73,35 +73,34 @@ class Utilities
/// verify if a given amino-acid sequence is valid
static const bool isValidSequence(const QString &seq,
const Qt::CaseSensitivity cs);
static bool isValidSequence(const QString &seq, const Qt::CaseSensitivity cs);
/// Replace Leucine with Isoleucine amino-acid in a sequence
/// Not used in MassChroQ v 1.0.1 anymore
static void replaceLwithI(QString &pep_seq);
/// given a mz and a z, calculate the mh
static const mcq_double mz2mh(const mcq_double mz, const unsigned int charge);
static mcq_double mz2mh(const mcq_double mz, const unsigned int charge);
/// given a mh and a z, calculate the mz
static const mcq_double mh2mz(const mcq_double mh, const unsigned int charge);
static mcq_double mh2mz(const mcq_double mh, const unsigned int charge);
static const Duration getDurationFromDates(const QDateTime &date_begin,
const QDateTime &date_end);
static Duration getDurationFromDates(const QDateTime &date_begin,
const QDateTime &date_end);
static const int getDaysFromDuration(const Duration &d);
static int getDaysFromDuration(const Duration &d);
static const int getHoursFromDuration(const Duration &d);
static int getHoursFromDuration(const Duration &d);
static const int getMinutesFromDuration(const Duration &d);
static int getMinutesFromDuration(const Duration &d);
static const int getSecondsFromDuration(const Duration &d);
static int getSecondsFromDuration(const Duration &d);
static const bool isSorted(const std::vector<mcq_double> &v);
static bool isSorted(const std::vector<mcq_double> &v);
/// given two integers first and last, returns a random integer between first
/// and last
static const int random_pivot(const int first, const int last);
static int random_pivot(const int first, const int last);
/// double_quicksort sorts vector v1 using a quicksort algorithm, but also
/// sorts vector v2
......
......@@ -44,13 +44,12 @@ MasschroqmlParser::~MasschroqmlParser()
}
bool
MasschroqmlParser::startElement(const QString &namespaceURI,
const QString &localName,
MasschroqmlParser::startElement(const QString &namespaceURI [[maybe_unused]],
const QString &localName [[maybe_unused]],
const QString &qName,
const QXmlAttributes &attributes)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< qName;
qDebug() << qName;
_tag_stack.push_back(qName);
bool is_ok = true;
......@@ -257,12 +256,11 @@ MasschroqmlParser::startElement(const QString &namespaceURI,
}
bool
MasschroqmlParser::endElement(const QString &namespaceURI,
const QString &localName,
MasschroqmlParser::endElement(const QString &namespaceURI [[maybe_unused]],
const QString &localName [[maybe_unused]],
const QString &qName)
{
qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
<< qName;
qDebug() << qName;
bool is_ok = true;
try
{
......@@ -1122,7 +1120,8 @@ MasschroqmlParser::startElement_smoothing(const QXmlAttributes &attributes)
/// <detection_zivy>
bool
MasschroqmlParser::startElement_detection_zivy(const QXmlAttributes &attributes)
MasschroqmlParser::startElement_detection_zivy(const QXmlAttributes &attributes
[[maybe_unused]])
{
msp_current_detection_zivy =
std::make_shared<pappso::TraceDetectionZivy>(0, 2, 3, 1000, 100);
......@@ -1217,7 +1216,7 @@ MasschroqmlParser::endElement_detection_threshold_on_min()
/// <detection_moulon>
bool
MasschroqmlParser::startElement_detection_moulon(
const QXmlAttributes &attributes)
const QXmlAttributes &attributes [[maybe_unused]])
{
msp_current_detection_moulon =
std::make_shared<pappso::TraceDetectionMoulon>(0, 100, 10);
......@@ -1313,7 +1312,7 @@ MasschroqmlParser::endElement_quantification_method()
/// <quantification_results>
bool
MasschroqmlParser::startElement_quantification_results(
const QXmlAttributes &attributes)
const QXmlAttributes &attributes [[maybe_unused]])
{
return true;
}
......
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