Commit 8bb7a671 authored by Edlira Nano's avatar Edlira Nano
Browse files

merged post-branching with tunk

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2225 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 85d44675
......@@ -13,6 +13,23 @@ cmake_minimum_required(VERSION 2.6)
PROJECT(masschroq CXX C)
# Project version
SET (MASSCHROQ_MAJOR_VERSION 1)
SET (MASSCHROQ_MINOR_VERSION 2)
SET (MASSCHROQ_PATCH_LEVEL 0)
SET (MASSCHROQ_VERSION
"${MASSCHROQ_MAJOR_VERSION}.${MASSCHROQ_MINOR_VERSION}.${MASSCHROQ_PATCH_LEVEL}")
SET (MASSCHROQ_LIB_NAME "masschroq")
SET (MASSCHROQ_LIB_VERSION "1.0.0")
SET (MASSCHROQ_LIB_SOVERSION "1")
SET (MASSCHROQ_SCHEMA_VERSION "1.1")
SET (MASSCHROQ_SCHEMA_FILE "masschroq-${MASSCHROQ_SCHEMA_VERSION}.xsd")
SET (masschroq_BINARY_DIR "bin")
#SET (CMAKE_INSTALL_SO_NO_EXE "0")
IF (CMAKE_BASE_NAME MATCHES "cl")
SET( WIN32 "true")
ELSE (CMAKE_BASE_NAME MATCHES "cl")
......@@ -41,8 +58,8 @@ if (NOT CMAKE_INSTALL_PREFIX)
SET (CMAKE_INSTALL_PREFIX /usr/local)
endif (NOT CMAKE_INSTALL_PREFIX)
SET(CMAKE_BUILD_TYPE "Release")
#SET(CMAKE_BUILD_TYPE "RelWithDebInfo")
#SET(CMAKE_BUILD_TYPE "Release")
SET(CMAKE_BUILD_TYPE "RelWithDebInfo")
#SET( CMAKE_BUILD_TYPE "Debug")
IF(CMAKE_BUILD_TYPE MATCHES "Release")
......@@ -60,27 +77,18 @@ ENDIF( CMAKE_BUILD_TYPE MATCHES "RelWithDebInfo" )
IF (WIN32)
SET(MASSCHROQ_XSD_DIR ${CMAKE_INSTALL_PREFIX})
SET(MASSCHROQ_XSD ${MASSCHROQ_XSD_DIR}/masschroq.xsd)
SET(MASSCHROQ_XSD_DIR "${CMAKE_INSTALL_PREFIX}")
SET(MASSCHROQ_XSD "${MASSCHROQ_XSD_DIR}/${MASSCHROQ_SCHEMA_FILE}")
#SET(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
ELSE (WIN32)
SET(CMAKE_CXX_FLAGS_DEBUG "-O3 -g -Wall")
SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-O3 -g -Wall")
SET (CMAKE_CXX_FLAGS_RELEASE "-s ${CMAKE_CXX_FLAGS_RELEASE}")
SET(MASSCHROQ_XSD_DIR "${CMAKE_INSTALL_PREFIX}/share/xml/schema")
SET(MASSCHROQ_XSD "${MASSCHROQ_XSD_DIR}/masschroq.xsd")
SET(MASSCHROQ_XSD "${MASSCHROQ_XSD_DIR}/${MASSCHROQ_SCHEMA_FILE}")
ENDIF (WIN32)
SET (MASSCHROQ_VERSION "1.1.1")
#SET (MASSCHROQ_LIB_VERSION "1")
SET (MASSCHROQ_XML_VERSION "1.0")
SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
......@@ -88,21 +96,22 @@ SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "MassChroQ : Mass Chromatogram Quantification")
SET(CPACK_PACKAGE_EXECUTABLES "masschroq")
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "masschroq-${MASSCHROQ_VERSION}")
SET(CPACK_PACKAGE_FILE_NAME "masschroq-${MASSCHROQ_VERSION}-Linux-i686")
SET(CPACK_SYSTEM_NAME "Linux-i686")
SET(CPACK_PACKAGE_FILE_NAME "masschroq-${MASSCHROQ_VERSION}-${CPACK_SYSTEM_NAME}")
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "masschroq ${MASSCHROQ_VERSION}")
SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "masschroq ${MASSCHROQ_VERSION}")
SET(CPACK_PACKAGE_NAME "masschroq")
SET(CPACK_PACKAGE_VENDOR "PAPPSO")
SET(CPACK_PACKAGE_VERSION ${MASSCHROQ_VERSION})
SET(CPACK_RESOURCE_FILE_LICENSE ${masschroq_SOURCE_DIR}/debian/copyright)
#SET(CPACK_RESOURCE_FILE_README ${masschroq_SOURCE_DIR}/README)
SET(CPACK_RESOURCE_FILE_README ${masschroq_SOURCE_DIR}/README)
SET(CPACK_RESOURCE_FILE_WELCOME ${masschroq_SOURCE_DIR}/README)
SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
SET(CPACK_SOURCE_STRIP_FILES "")
SET(CPACK_SYSTEM_NAME "Linux-i686")
SET(CPACK_TOPLEVEL_TAG "Linux-i686")
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "masschroq-${MASSCHROQ_VERSION}")
SET(CPACK_SOURCE_IGNORE_FILES
......@@ -184,9 +193,9 @@ INCLUDE(CPack)
# cause another cmake executable to run. The same process will walk through
# the project's entire directory structure.
add_subdirectory (src)
INSTALL(PROGRAMS src/libmasschroq.so DESTINATION lib)
#INSTALL library libmasschroq is in the src/CMakeLists file
INSTALL(PROGRAMS src/masschroq DESTINATION bin)
INSTALL(FILES doc/schema/masschroq.xsd DESTINATION share/xml/schema)
INSTALL(FILES doc/schema/${MASSCHROQ_SCHEMA_FILE} DESTINATION share/xml/schema)
#INSTALL(FILES doc/man1/masschroq.1.gz DESTINATION share/man/man1)
#INSTALL(FILES doc/manual/masschroq_manual.pdf DESTINATION share/doc/masschroq)
#INSTALL(FILES doc/debian/changelog DESTINATION share/doc/masschroq)
......
......@@ -46,6 +46,4 @@ This installs the masschroq library, binary and manpage in your system
above).
In case of problems with the install procedure you can contact the
developers at <edlira.nano@moulon.inra.fr> or
<olivier.langella@moulon.inra.fr>.
>
\ No newline at end of file
developers at <edlira.nano@moulon.inra.fr> or <olivier.langella@moulon.inra.fr>.
......@@ -135,4 +135,3 @@ quantimscpp (0.0.1-1) intrepid; urgency=low
* Initial release.
-- Olivier Langella <Olivier.Langella@moulon.inra.fr> Fri, 23 Jan 2009 11:18:51 +0200
......@@ -37,7 +37,7 @@
xlink:href="#linearGradient4034"
id="radialGradient4046"
gradientUnits="userSpaceOnUse"
gradientTransform="matrix(1.1036608,-0.00525632,0.00450654,0.94623276,-27.986078,12.321832)"
gradientTransform="matrix(0.92324481,-0.0056018,0.00470472,0.77539747,19.084596,47.201358)"
cx="261.12445"
cy="203.64244"
fx="261.12445"
......@@ -52,8 +52,8 @@
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
inkscape:zoom="1.979899"
inkscape:cx="238.14089"
inkscape:cy="213.49542"
inkscape:cx="300.03506"
inkscape:cy="193.29237"
inkscape:document-units="px"
inkscape:current-layer="layer1"
showgrid="false"
......@@ -76,7 +76,7 @@
<dc:format>image/svg+xml</dc:format>
<dc:type
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
<dc:title></dc:title>
<dc:title />
</cc:Work>
</rdf:RDF>
</metadata>
......
<?xml version="1.0" encoding="UTF-8"?>
<!--
masschroqML version 1.0 schema (http://pappso/bioinfo/masschroq/)
masschroqML version 1.1 schema (http://pappso/bioinfo/masschroq/).
Retro compatibility with older masschroq schemas and versions is assured.
In this version we have added the peak post_matching feature.
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
......@@ -49,13 +51,12 @@
<xs:element name="mzrt_value" type="mzrt_valueType"/>
<xs:element name="mzrt" type="mzrtType"/>
<xs:element name="quantify" type="quantifyType"/>
<xs:element name="peptides_in_peptide_list"
type="peptides_in_peptide_listType"/>
<xs:element name="peptides_in_peptide_list" type="peptides_in_peptide_listType"/>
<xs:element name="mz_list" type="xs:string"/>
<xs:element name="mzrt_list" type="mzrt_listType"/>
<xs:element name="results" type="resultsType"/>
<xs:element name="result" type="resultType"/>
<xs:element name="search" type="searchType"/>
<xs:element name="quanti_item" type="quanti_itemType"/>
<xs:element name="data" type="dataType"/>
<xs:element name="data_rt" type="data_rtType"/>
<xs:element name="rt" type="rtType"/>
......@@ -65,7 +66,8 @@
<xs:element name="filtered_xic_intensity" type="filtered_xic_intensityType"/>
<xs:element name="xic_peaks" type="xic_peaksType"/>
<xs:element name="peak" type="peakType"/>
<xs:element name="quantification_data" type="quantification_dataType"/>
<xs:element name="quantification_data" type="quantification_dataType"/>
<xs:element name="post_matching_data" type="post_matching_dataType"/>
<xs:element name="summary" type="summaryType"/>
<xs:element name="execution_time" type="execution_timeType"/>
......@@ -995,19 +997,28 @@
<xs:attribute name="mode" use="required">
<xs:annotation>
<xs:documentation>
Peptide quantification mode, among :
- real_or_mean mode : if the peptide is observed in a MS data
file we use its observed values for the quantification; if not
we use the mean of all other observed values in the group for
this peptide;
- mean mode : we always use the mean of the observed values
through the entire group for the quantification of this peptide.
Peptide peak matching mode : once a peak is detected for an identified pepride, we check
that the peptide's RT is within the range of this peak's RT. The following are peptide's
RT computation modes:
- real_or_mean mode : if the peptide is observed in an MS run
we use its observed RT value for the peak matching; if not
we use the mean of all the other observed RT values in the group
being quantified for this peptide;
- mean mode : we always use the mean of the observed RT values of this peptide
in the group being quantified;
- post_matching : peaks are first matched as in the real mode (real observed RT values).
During the first peak matching we keep the not matched peaks. Once quantification is
finished in the group, we perform a post matching match : the previously non matched
peaks are rematched with a better, recomputed peptide's RT. This recomputed RT takes
into account the best RT-s (i.e. the RT-s corresponding to the max intensity) of this
peptide in the previously matched peaks.
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="real_or_mean"></xs:enumeration>
<xs:enumeration value="mean"></xs:enumeration>
<xs:enumeration value="post_matching"></xs:enumeration>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
......@@ -1070,6 +1081,7 @@
</xs:annotation>
<xs:sequence>
<xs:element ref="data" maxOccurs="unbounded" minOccurs="1"/>
<xs:element ref="post_matching_data" maxOccurs="1" minOccurs="0"/>
</xs:sequence>
<xs:attribute name="quantify_id" type="xs:IDREF" use="required">
<xs:annotation>
......@@ -1081,6 +1093,18 @@
</xs:attribute>
</xs:complexType>
<xs:complexType name="post_matching_dataType">
<xs:annotation>
<xs:documentation>
If peak post-matching has been performed (quantification mode=post_matching)
the post matched peak results will be put in this block.
</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element ref="data" maxOccurs="unbounded" minOccurs="1"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="dataType">
<xs:annotation>
<xs:documentation>
......@@ -1090,9 +1114,9 @@
</xs:annotation>
<xs:sequence>
<xs:element ref="data_rt" maxOccurs="1" minOccurs="0"/>
<xs:element ref="search" maxOccurs="unbounded" minOccurs="0"/>
<xs:element ref="quanti_item" maxOccurs="unbounded" minOccurs="0"/>
</xs:sequence>
<xs:attribute name="id" type="xs:IDREF" use="required">
<xs:attribute name="id_ref" type="xs:IDREF" use="required">
<xs:annotation>
<xs:documentation>
The unique xml id of the msrun data_file (previously defined) that
......@@ -1151,10 +1175,10 @@
</xs:simpleContent>
</xs:complexType>
<xs:complexType name="searchType">
<xs:complexType name="quanti_itemType">
<xs:annotation>
<xs:documentation>
Contains the quantification results for a searched item (a peptide,
Contains the quantification results for a quantification item (a peptide,
an mz value or an (mz,rt) values).
</xs:documentation>
</xs:annotation>
......@@ -1166,28 +1190,35 @@
<xs:attribute name="id" type="xs:ID" use="required">
<xs:annotation>
<xs:documentation>
Unique xml id for this search item.
Unique xml id for this quantification item.
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="item_id" type="xs:IDREF">
<xs:attribute name="item_id_ref" type="xs:IDREF">
<xs:annotation>
<xs:documentation>
References the xml id of this quanti item (ex pep0 for a peptide).
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="z" type="xs:integer">
<xs:annotation>
<xs:documentation>
References the xml id of this searched item (ex pep0 for a peptide).
If this quanti_item is a peptide, references its charge value.
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="mz" type="xs:double">
<xs:annotation>
<xs:documentation>
References the mz value of this mz or mz/rt searched item.
References the mz value of this mz or mz/rt quanti item.
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="rt" type="xs:double">
<xs:annotation>
<xs:documentation>
References the rt value of this mz/rt searched item.
References the rt value of this mz/rt quanti item.
</xs:documentation>
</xs:annotation>
</xs:attribute>
......@@ -1196,7 +1227,7 @@
<xs:complexType name="xic_tracesType">
<xs:annotation>
<xs:documentation>
Contains the xic traces of this searched item (raw xics +
Contains the xic traces of this quantification item (raw xics +
filtered xics + all detected peaks + selected peaks) encoded
in base64.
</xs:documentation>
......@@ -1212,7 +1243,7 @@
<xs:complexType name="raw_xicType">
<xs:annotation>
<xs:documentation>
Contains the raw xic of the searched item, i.e. the intensity and
Contains the raw xic of the quantified item, i.e. the intensity and
the retention time arrays encoded in base64.
</xs:documentation>
</xs:annotation>
......@@ -1332,7 +1363,7 @@
<xs:complexType name="quantification_dataType">
<xs:annotation>
<xs:documentation>
Contains the quantification data for this search item.
Contains the quantification data for this quantified item.
</xs:documentation>
</xs:annotation>
<xs:attribute name="mz" type="xs:double" use="required">
......
......@@ -11,23 +11,33 @@ INCLUDE( ${QT_USE_FILE} )
SET(MASSCHROQ_LIB_SRCS
./lib/mcq_error.h
./lib/share/utilities.cpp
./lib/peptides/protein.cpp
./lib/peptides/peptide.cpp
./lib/peptides/peptide_isotope.cpp
./lib/peptides/peptide_observed_in.cpp
./lib/peptides/peptide_list.cpp
./lib/peptides/isotope_label.cpp
./lib/quanti_items/quantiItemBase.cpp
./lib/quanti_items/quantiItemMzRt.cpp
./lib/quanti_items/quantiItemPeptide.cpp
./lib/msrun/spectrum.cpp
./lib/msrun/precursor.cpp
./lib/msrun/msrun.cpp
./lib/msrun/msrun_sliced.cpp
./lib/msrun/msrun_classic.cpp
./lib/msrun/slicer.cpp
./lib/msrun/slice.cpp
./lib/mass_chroq.cpp
./lib/share/utilities.cpp
./lib/msrun/slicer.cpp
./lib/msrun/msrun_sliced.cpp
./lib/msrun/ms_run_hash_group.cpp
./lib/msrun/spectrum.cpp
./lib/msrun/precursor.cpp
./lib/look_for/lookForBase.cpp
./lib/look_for/lookForMzRt.cpp
./lib/look_for/lookForPeptide.cpp
./lib/look_for/lookForPeptideRealRt.cpp
./lib/quantifications/quantificationMethod.cpp
./lib/quantificator.cpp
./lib/mass_chroq.cpp
./lib/peak_matching/peakMatcher.cpp
./lib/detections/peak_detection_moulon.cpp
./lib/detections/peak_detection_base.cpp
......@@ -71,13 +81,6 @@ SET(MASSCHROQ_LIB_SRCS
./lib/monitors/tsv_mzrt_xics.cpp
./lib/monitors/masschroqWriter.cpp
./lib/peptides/protein.cpp
./lib/peptides/peptide.cpp
./lib/peptides/peptide_isotope.cpp
./lib/peptides/peptide_observed_in.cpp
./lib/peptides/peptide_list.cpp
./lib/peptides/isotope_label.cpp
./reporters/ReporterConsole.cpp
)
......@@ -153,17 +156,25 @@ IF (WIN32)
${SAXLIB_SRCS} ${OBIWARP_SRCS})
TARGET_LINK_LIBRARIES(masschroq ${QT_LIBRARIES})
ELSE (WIN32)
ADD_LIBRARY(masschroq SHARED ${MASSCHROQ_LIB_SRCS}
ADD_LIBRARY(${MASSCHROQ_LIB_NAME} SHARED ${MASSCHROQ_LIB_SRCS}
${SAXLIB_SRCS} ${OBIWARP_SRCS})
SET_TARGET_PROPERTIES(${MASSCHROQ_LIB_NAME} PROPERTIES
VERSION ${MASSCHROQ_LIB_VERSION}
SOVERSION ${MASSCHROQ_LIB_SOVERSION}
)
ADD_EXECUTABLE(masschroq_main main.cpp)
TARGET_LINK_LIBRARIES(masschroq_main masschroq ${QT_LIBRARIES})
TARGET_LINK_LIBRARIES(masschroq_main ${MASSCHROQ_LIB_NAME} ${QT_LIBRARIES})
SET_TARGET_PROPERTIES(masschroq_main PROPERTIES OUTPUT_NAME masschroq)
ENDIF(WIN32)
INSTALL(TARGETS ${MASSCHROQ_LIB_NAME} LIBRARY DESTINATION lib)
# if lib quanti is graphical
#TARGET_LINK_LIBRARIES(masschroq libmasschroq ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
......@@ -171,7 +182,7 @@ ENDIF(WIN32)
#TARGET_LINK_LIBRARIES(viewxic libmasschroq ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
#ADD_EXECUTABLE(visualqms visualqms.cpp ${VIEWXIC_SRCS} ${VIEWXIC_MOC_SRCS} ${SAXLIB_SRCS} ${OBIWARP_SRCS})
#ADD_EXECUTABLE(visualqms visualqms.cpp ${VIEWXIC_SRCS} ${VIEWXIC_MOC_SRCS} ${SAXLIB_SRCS} ${OBWARP_SRCS})
#TARGET_LINK_LIBRARIES(visualqms libmasschroq ${QT_LIBRARIES} ${Qwt5_Qt4_LIBRARY})
#ADD_EXECUTABLE(align_mzxml align_mzxml.cpp ${MASSCHROQLIB_SRCS} ${SAXLIB_SRCS} ${OBIWARP_SRCS})
......
......@@ -3,7 +3,7 @@
#cmakedefine MASSCHROQ_VERSION "@MASSCHROQ_VERSION@"
#cmakedefine MASSCHROQ_XSD "@MASSCHROQ_XSD@"
#cmakedefine MASSCHROQ_XML_VERSION "@MASSCHROQ_XML_VERSION@"
#cmakedefine MASSCHROQ_SCHEMA_VERSION "@MASSCHROQ_SCHEMA_VERSION@"
#define QT_V_4_5 0x040500
#define QT_V_4_6 0x040600
......
......@@ -15,6 +15,11 @@ peakDetectionBase::peakDetectionBase() {
peakDetectionBase::~peakDetectionBase() {
}
const mcq_double
peakDetectionBase::get_coeff_detect_range() const {
return coeff_detect_range;
}
const QString
peakDetectionBase::printInfos() const {
QString infos;
......@@ -27,7 +32,7 @@ std::vector<xicPeak *> *
peakDetectionBase::newDetectedPeaks(const xicBase & xic) const {
const Msrun * p_msrun(xic.getMsRun());
const LookForBase & mz_lookfor(*xic.getMzSelection());
QuantiItemBase quanti_item(*xic.getQuantiItem());
const std::vector<mcq_double> * p_v_rt(xic.getConstRetentionTimes());
const std::vector<mcq_double> * p_v_intensity(xic.getConstIntensities());
......@@ -35,34 +40,12 @@ peakDetectionBase::newDetectedPeaks(const xicBase & xic) const {
throw mcqError("Error in peakDetectionBase::newDetectedPeaks :\n rt and signal intensity vectors must have the same size.");
}
// detect all peaks
vector<xicPeak *> * v_peaks = this->privNewDetectedPeaks(mz_lookfor,
vector<xicPeak *> * v_peaks = this->privNewDetectedPeaks(quanti_item,
p_msrun,
p_v_rt,
p_v_intensity);
_p_monitor->setAllPeaks(v_peaks);
// filter the peaks (retain only the ones we are looking for)
mcq_double rt_to_look_for = mz_lookfor.getRt(p_msrun);
if (rt_to_look_for != -1) {
vector<xicPeak *> * peak_list = new vector<xicPeak *> ;
for (unsigned int i(0); i < v_peaks->size(); ++i) {
// getRt doi etre aligné
if ((*v_peaks)[i]->contains_rt(rt_to_look_for,
coeff_detect_range)) {
peak_list->push_back((*v_peaks)[i]);
} else {
delete (*v_peaks)[i];
}
}
delete v_peaks;
return (peak_list);
} else {
return v_peaks;
}
return v_peaks;
}
void
......@@ -132,8 +115,3 @@ void peakDetectionBase::test() {
printvf(*p_v_average);
}
void
peakDetectionBase::setMonitor(MonitorBase & monitor) {
_p_monitor = &monitor;
}
......@@ -33,7 +33,6 @@
#include "../peak/xic_peak.h"
#include "../mcq_error.h"
#include "../filters/filter_base.h"
#include "../monitors/monitorBase.h"
using namespace std;
......@@ -54,15 +53,15 @@ class peakDetectionBase {
std::vector<xicPeak *> * newDetectedPeaks(const xicBase & xic) const;
void setMonitor(MonitorBase & monitor);
const mcq_double get_coeff_detect_range() const;
void test();
protected:
/// pure virtual method that detects and returns a vector of xicPeak-s
virtual std::vector<xicPeak *> * privNewDetectedPeaks
(const LookForBase mz_lookfor,
(const QuantiItemBase mz_quanti_item,
const Msrun * p_msrun,
const std::vector<mcq_double> * p_v_rt,
const std::vector<mcq_double> * p_v_intensity) const = 0;
......@@ -74,9 +73,6 @@ class peakDetectionBase {
mcq_double coeff_detect_range;
/// Peak's monitor
MonitorBase * _p_monitor;
};
#endif /* PEAK_DETECTION_BASE_H_ */
......@@ -28,7 +28,7 @@ peakDetectionMoulon::printInfos(QTextStream & out) const {
std::vector<xicPeak *> *
peakDetectionMoulon::privNewDetectedPeaks
(const LookForBase mz_lookfor,
(QuantiItemBase mz_lookfor,
const Msrun * p_msrun,
const std::vector<mcq_double> * p_v_rt,
const std::vector<mcq_double> * p_v_intensity) const {
......
......@@ -69,7 +69,7 @@ public:
protected:
virtual std::vector<xicPeak *> *
privNewDetectedPeaks(const LookForBase mz_lookfor,
privNewDetectedPeaks(QuantiItemBase mz_lookfor,
const Msrun * p_msrun,
const std::vector<mcq_double> * p_v_rt,
const std::vector<mcq_double> * p_v_intensity) const;
......
......@@ -32,7 +32,7 @@ void peakDetectionZivy::printInfos(QTextStream & out) const {
std::vector<xicPeak *> *
peakDetectionZivy::privNewDetectedPeaks
(const LookForBase mz_lookfor,
(QuantiItemBase quanti_item,
const Msrun * p_msrun,
const std::vector<mcq_double> * p_v_rt,
const std::vector<mcq_double> * p_v_intensity) const
......@@ -89,7 +89,7 @@ peakDetectionZivy::privNewDetectedPeaks
}
// there is a peak here ! case
else if (v_minmax[i] > v_minmax[i + 1]) {
xicPeak * tmp_peak = new xicPeak(mz_lookfor, p_msrun);
xicPeak * tmp_peak = new xicPeak(quanti_item, p_msrun);
unsigned int begin_peak;
unsigned int end_peak;
findPeakRangeWalkingFromMax(&begin_peak, &end_peak, i, v_minmax);
......
......@@ -65,7 +65,7 @@ class peakDetectionZivy : public peakDetectionBase {
protected:
virtual std::vector<xicPeak *> *
privNewDetectedPeaks(const LookForBase mz_lookfor,
privNewDetectedPeaks(QuantiItemBase quanti_item,
const Msrun * p_msrun,
const std::vector<mcq_double> * p_v_rt,
const std::vector<mcq_double> * p_v_intensity) const;
......
/**
* \file selection_mz_rt.cpp
* \date 30 sept. 2009
* \author: Olivier Langella
*/
#include "lookForMzRt.h"
LookForMzRt::LookForMzRt(const XicExtractionMethodBase & extraction_method,
const msRunHashGroup & group,
mcq_double rt) :
LookForBase(extraction_method, group),
_rt(rt)
{
}
/// copy constructor
LookForMzRt::LookForMzRt(const LookForMzRt & look_for) :
LookForBase(look_for) {
_rt = look_for._rt;
}
LookForMzRt::~LookForMzRt() {
// TODO Auto-generated destructor stub
}
void
LookForMzRt::printInfos(ostream & out) const {