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PAPPSO
MassChroQ
Commits
5e86a36a
Commit
5e86a36a
authored
Jan 08, 2021
by
Langella Olivier
Browse files
indentation, cleaning debug messages, comments
parent
795d4099
Changes
5
Hide whitespace changes
Inline
Side-by-side
src/lib/quantifications/mapquantirealxic.cpp
View file @
5e86a36a
/** @file src/lib/quantifications/mapquantirealxic.cpp
*/
/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
...
...
@@ -64,7 +66,7 @@ MapQuantiRealXic::operator()(QuantiItemBase *p_currentSearchItem)
{
try
{
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
const
std
::
vector
<
MsMsRtIntensity
>
rt_list
=
p_currentSearchItem
->
getPeptide
()
->
getPeptideRtSp
()
->
getObservedRtList
(
_p_msrun
);
...
...
@@ -90,7 +92,7 @@ MapQuantiRealXic::operator()(QuantiItemBase *p_currentSearchItem)
// rt_list_z.size();
// if (rt_list_z.size() > 0) {
// and it was observed with this charge
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
XicFilterDetectMatchRealRt
filter_detect_match_real_xic
(
p_xic_trace
,
_monitor
,
...
...
@@ -98,24 +100,24 @@ MapQuantiRealXic::operator()(QuantiItemBase *p_currentSearchItem)
_p_detection
,
_quantificator
,
_matching_mode
);
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
pappso
::
MzRange
mass_range
(
p_currentSearchItem
->
getMz
(),
_quantificator
->
getQuantificationMethod
()
->
getLowerPrecision
(),
_quantificator
->
getQuantificationMethod
()
->
getUpperPrecision
());
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
pappso
::
XicCstSPtr
msrun_xic_sp
=
_p_msrun
->
extractXicCstSPtr
(
mass_range
,
rt_list
[
0
].
rt
);
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
if
(
msrun_xic_sp
!=
nullptr
)
{
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
filter_detect_match_real_xic
.
filterDetectQuantify
(
msrun_xic_sp
.
get
(),
&
rt_list
,
p_currentSearchItem
,
_p_msrun
);
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
if
(
p_xic_trace
!=
nullptr
)
{
...
...
@@ -127,7 +129,7 @@ MapQuantiRealXic::operator()(QuantiItemBase *p_currentSearchItem)
}
else
{
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
}
p_currentSearchItem
->
endMsrunQuantification
(
_p_msrun
);
...
...
@@ -136,7 +138,7 @@ MapQuantiRealXic::operator()(QuantiItemBase *p_currentSearchItem)
// this quanti item was not observed with this charge
//}
}
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
}
catch
(
mcqError
&
errorException
)
{
...
...
src/lib/quantifications/mapquantirealxic.h
View file @
5e86a36a
/** @file src/lib/quantifications/mapquantirealxic.h
*/
/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
...
...
src/lib/quantifications/quantificationMethod.cpp
View file @
5e86a36a
...
...
@@ -20,6 +20,7 @@ QuantificationMethod::QuantificationMethod(const QString &xml_id)
_upper_precision_p
=
pappso
::
PrecisionFactory
::
getDaltonInstance
(
_upper_precision
);
}
m_secondChance
=
false
;
}
QuantificationMethod
::
QuantificationMethod
(
const
QuantificationMethod
&
other
)
...
...
@@ -52,8 +53,8 @@ void
QuantificationMethod
::
printInfos
(
QTextStream
&
out
)
const
{
out
<<
"
\t
Quantification method '"
<<
_xml_id
<<
"' parameters : "
<<
endl
;
out
<<
"
\t
xic type : '"
<<
Utilities
::
toString
(
_m_xic_extract_method
)
<<
"'"
<<
endl
;
out
<<
"
\t
xic type : '"
<<
Utilities
::
toString
(
_m_xic_extract_method
)
<<
"'
"
<<
"second chance:"
<<
m_secondChance
<<
endl
;
/*
std::vector<const FilterBase *>::const_iterator it_f;
for (it_f = _v_p_xic_filters.begin();
...
...
src/lib/xic/xicfilterdetectmatchrealrt.cpp
View file @
5e86a36a
/** @file src/lib/xic/xicfilterdetectmatchrealrt.cpp
*/
/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
...
...
@@ -17,9 +19,6 @@
* You should have received a copy of the GNU General Public License
* along with MassChroQ. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
#include
"xicfilterdetectmatchrealrt.h"
#include
"../quanti_items/quantiItemBase.h"
...
...
@@ -33,26 +32,25 @@ XicFilterDetectMatchRealRt::XicFilterDetectMatchRealRt(
McqMatchingMode
matching_mode
)
:
_monitor
(
monitor
)
{
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
_p_detection
=
p_detection
;
_p_xic_filter
=
p_xic_filter
;
_p_quantificator
=
p_quantificator
;
_p_trace
=
p_trace
;
_matching_mode
=
matching_mode
;
qDebug
()
<<
__FILE__
<<
" "
<<
__FUNCTION__
<<
" "
<<
__LINE__
;
qDebug
();
}
XicFilterDetectMatchRealRt
::~
XicFilterDetectMatchRealRt
()
{
qDebug
()
<<
"XicFilterDetectMatchRealRt::~XicFilterDetectMatchRealRt "
<<
this
;
qDebug
()
<<
this
;
}
void
XicFilterDetectMatchRealRt
::
setTracePeak
(
pappso
::
TracePeak
&
xic_peak
)
{
qDebug
()
<<
"
XicFilterDetectMatchRealRt::setXicPeak
begin "
<<
this
;
qDebug
()
<<
" begin "
<<
this
;
if
(
_p_log_peaks
==
nullptr
)
{
...
...
@@ -83,7 +81,7 @@ XicFilterDetectMatchRealRt::setTracePeak(pappso::TracePeak &xic_peak)
{
_p_log_peaks
->
push_back
(
xic_peak
.
makeTracePeakCstSPtr
());
}
qDebug
()
<<
"
XicFilterDetectMatchRealRt::setXicPeak
end "
<<
this
;
qDebug
()
<<
" end "
<<
this
;
}
void
...
...
@@ -94,13 +92,13 @@ XicFilterDetectMatchRealRt::filterDetectQuantify(
const
Msrun
*
p_msrun
)
{
qDebug
()
<<
"
XicFilterDetectMatchRealRt::filterDetectQuantify
begin "
<<
this
;
qDebug
()
<<
" begin "
<<
this
;
if
(
p_origxic
==
nullptr
)
{
throw
mcqError
(
QObject
::
tr
(
"error in "
"XicFilterDetectMatchRealRt::"
"filterDetectQuantify: p_origxic == nullptr"
));
throw
mcqError
(
QObject
::
tr
(
"error in %1 %2 %3: p_origxic == nullptr"
)
.
arg
(
__FILE__
)
.
arg
(
__FUNCTION__
)
.
arg
(
__LINE__
));
}
_peak_counter_map
.
clear
();
...
...
@@ -113,27 +111,25 @@ XicFilterDetectMatchRealRt::filterDetectQuantify(
if
(
_p_xic_filter
!=
nullptr
)
{
qDebug
()
<<
"
XicF
ilter
DetectMatchRealRt::filterDetectQuantify filter
"
<<
p_origxic
->
size
()
<<
" "
<<
newxic
.
size
()
<<
" "
<<
this
;
qDebug
()
<<
"
f
ilter
"
<<
p_origxic
->
size
()
<<
" "
<<
newxic
.
size
()
<<
"
"
<<
this
;
_p_xic_filter
->
filter
(
newxic
);
qDebug
()
<<
"XicFilterDetectMatchRealRt::filterDetectQuantify filter 2 "
<<
newxic
.
size
()
<<
" "
<<
this
;
qDebug
()
<<
" filter 2 "
<<
newxic
.
size
()
<<
" "
<<
this
;
p_xic
=
&
newxic
;
}
// qDebug() << "XicFilterDetectMatch::filterDetectQuantify detect " <<
// _rt_target;
_p_detection
->
detect
(
*
p_xic
,
*
this
);
qDebug
()
<<
"
XicFilterDetectMatchRealRt::filterDetectQuantify
after detect"
qDebug
()
<<
" after detect"
<<
" "
<<
this
;
if
(
_peak_counter_map
.
size
()
>
0
)
{
if
(
_peak_counter_map
.
size
()
==
1
)
{
qDebug
()
<<
"XicFilterDetectMatchRealRt::filterDetectQuantify NO CHOICE "
"_peak_counter_map.size() "
<<
_peak_counter_map
.
size
()
<<
" "
<<
this
;
qDebug
()
<<
" NO CHOICE "
"_peak_counter_map.size() "
<<
_peak_counter_map
.
size
()
<<
" "
<<
this
;
// const pappso::XicPeak * p_peak =
// _peak_counter_map.begin()->first.get();
AlignedXicPeak
aligned_peak
(
*
(
_peak_counter_map
.
begin
()
->
first
.
get
()),
...
...
@@ -166,9 +162,7 @@ XicFilterDetectMatchRealRt::filterDetectQuantify(
else
{
// we have to choose among Xic peaks :/
qDebug
()
<<
"XicFilterDetectMatchRealRt::filterDetectQuantify "
"_peak_counter_map.size() "
<<
_peak_counter_map
.
size
()
<<
" "
<<
this
;
qDebug
()
<<
_peak_counter_map
.
size
()
<<
" "
<<
this
;
auto
it
=
_peak_counter_map
.
begin
();
auto
itend
=
_peak_counter_map
.
end
();
pappso
::
TracePeakCstSPtr
peak_sp
=
it
->
first
;
...
...
@@ -213,9 +207,7 @@ XicFilterDetectMatchRealRt::filterDetectQuantify(
*/
if
(
_p_quantificator
->
getQuantificationMethod
()
->
getSecondChance
())
{
qDebug
()
<<
"XicFilterDetectMatchRealRt::filterDetectQuantify not detected "
<<
" "
<<
this
;
qDebug
()
<<
" "
<<
this
;
_monitor
.
writeMatchedPeak
(
_p_current_msrun
,
_p_current_search_item
,
nullptr
);
...
...
@@ -313,6 +305,5 @@ XicFilterDetectMatchRealRt::filterDetectQuantify(
}
}
qDebug
()
<<
"XicFilterDetectMatchRealRt::filterDetectQuantify end"
<<
" "
<<
this
;
qDebug
()
<<
" "
<<
this
;
}
src/lib/xic/xicfilterdetectmatchrealrt.h
View file @
5e86a36a
/** @file src/lib/xic/xicfilterdetectmatchrealrt.h
*/
/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
...
...
@@ -17,9 +20,6 @@
* You should have received a copy of the GNU General Public License
* along with MassChroQ. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
#pragma once
...
...
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