Commit 541c8b6f authored by Edlira Nano's avatar Edlira Nano
Browse files

added alignment results to masschroqML

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2256 e4b6dbb4-9209-464b-83f7-6257456c460c
parent a674a79f
......@@ -121,7 +121,7 @@
\def\sitemasschroq{http://pappso.inra.fr/bioinfo/masschroq/}
\def\M{MassChroQ}
\newcommand{\Pa}{\emph{PAPPSO}}
\newcommand{\Mv}{MassChroQ v.1.0}
\newcommand{\Mv}{MassChroQ v.1.2}
\newcommand{\Xp}{\emph{X!Tandem pipeline}}
\newcommand{\mexe}{\texttt{masschroq}}
\newcommand{\ttt}[1]{\texttt{#1}}
......@@ -183,7 +183,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
\begin{htmlonly}
\title{\textbf{\Huge MassChroQ manual}\\
\textbf{First edition for Mass Chromatogram Quantification software v. 1.0}
\textbf{Second edition for Mass Chromatogram Quantification software v. 1.2}
}
\author{Edlira \textsc{Nano}\\
Contributors: Olivier \textsc{Langella}, Beno\^it \textsc{Valot},
......@@ -383,17 +383,18 @@ On the {\M} homepage (\href{\sitemasschroq}{\sitemasschroq}) you can find :
\item masschroq's \href{http://pappso.inra.fr/downloads/masschroq/masschroq.xsd}{schema};
\item Dataset examples of masschroqML input files to {\M} for various
ordinary situations (fractionated sample, isotopic labeled ones, etc);
\item this user manual frequently updated;
\item the code documentation (generated by doxygen);
\item this user manual frequently updated;
\item the latest news and the upcoming features on this project;
\item BibTeX and text entries for MassChroQ citation.
\ei
On the {\M} project page hosted on
\href{https://sourcesup.cru.fr/projects/masschroq/}{SourceSup} you can find :
\bi
\item a \href{https://subversion.cru.fr/masschroq}{subversion repository};
\item a bug tracker;
\item several user and developer forums.
The source code of {\M} contains C++ \emph{Doxygen} documentation, which you can generate and use for development needs.
\ei
\chapter{Installing and running {\M}}\label{running-sec}
......@@ -403,8 +404,8 @@ On the {\M} project page hosted on
\subsection{Linux platforms (32 and 64 bytes)}
\begin{itemize}
\item Debian and Ubuntu: Precompiled binary packages for {\M}
\emph{Hungry Crocklet} version 1.0 are available for
\item Debian and Ubuntu: Precompiled binary packages for all {\M}
versions are available for
\href{http://pappso.inra.fr/downloads/masschroq/masschroq_1.0.1-1_i386.deb
}{32-bit} and
\href{http://pappso.inra.fr/downloads/masschroq/masschroq_1.0.1-1_amd64.deb}{64-bit}
......@@ -527,7 +528,7 @@ To produce a masschroqML input file that also
includes all the identified peptides of your data, you can use the
freely-available
\href{http://pappso.inra.fr/bioinfo/xtandempipeline}{\Xp}. Given a set
of LC-MS runs, this pipeline performs in one shot peptide
of LC-MS runs, this pipeline performs, in one shot, peptide
identification using the \emph{X!Tandem} software, filtering of the
identification results and export to several formats,
one of them being a ready-to-use masschroqML input file.
......
......@@ -2,7 +2,8 @@
<!--
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.
In this version we have added the peak post_matching feature and the alignment results
for the masschroqML result (output) files.
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
......@@ -59,6 +60,7 @@
<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="alignment_result" type="alignment_resultType"/>
<xs:element name="rt" type="rtType"/>
<xs:element name="xic_traces" type="xic_tracesType"/>
<xs:element name="raw_xic" type="raw_xicType"/>
......@@ -71,7 +73,7 @@
<xs:element name="summary" type="summaryType"/>
<xs:element name="execution_time" type="execution_timeType"/>
<xs:complexType name="masschroqType">
<xs:annotation>
<xs:documentation>
......@@ -91,13 +93,27 @@
<xs:element ref="quantification" maxOccurs="1" minOccurs="0"/>
<xs:element ref="results" maxOccurs="1" minOccurs="0"/>
</xs:sequence>
<xs:attribute name="version" type="xs:string">
<xs:attribute name="version">
<xs:annotation>
<xs:documentation>
Version of the current masschroqXML format.
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="type">
<xs:annotation>
<xs:documentation>
Type of the masschroqML file : can be "input" for masschroqML input files
or "output" for output masschroqML result files.
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value="input"></xs:enumeration>
<xs:enumeration value="output"></xs:enumeration>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
</xs:complexType>
<xs:complexType name="rawdataType">
......@@ -1113,6 +1129,7 @@
</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element ref="alignment_result" maxOccurs="1" minOccurs="0"/>
<xs:element ref="data_rt" maxOccurs="1" minOccurs="0"/>
<xs:element ref="quanti_item" maxOccurs="unbounded" minOccurs="0"/>
</xs:sequence>
......@@ -1174,7 +1191,22 @@
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:complexType name="alignment_resultType">
<xs:simpleContent>
<xs:extension base="xs:base64Binary">
<xs:annotation>
<xs:documentation>
The base64 encoded aligned time values of the current msrun. These encoded time values
follow the same organisation as in the .time files : one original retention time followed
by the corresponding aligned one, and so on.
</xs:documentation>
</xs:annotation>
<xs:attributeGroup ref="base64enc_attr_group"/>
</xs:extension>
</xs:simpleContent>
</xs:complexType>
<xs:complexType name="quanti_itemType">
<xs:annotation>
<xs:documentation>
......@@ -1349,13 +1381,12 @@
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="selected" type="xs:boolean">
<xs:attribute name="matched" type="xs:boolean">
<xs:annotation>
<xs:documentation>
Indicates whether this peak has been selected or not. Selected
means retained by the choosen detection method with the
choosen parameters (which are defined in the input file).
</xs:documentation>
Indicates whether this peak has been matched to a quantification item (peptide)
or not (i.e. the item's rt is within the peak boundaries or not).
</xs:documentation>
</xs:annotation>
</xs:attribute>
</xs:complexType>
......
......@@ -33,6 +33,7 @@ QDir MassChroq::tmp_dir;
* it to the system's temporary directory
*/
void
MassChroq::setTmpDir(QString dirName) {
tmp_dir.setPath(dirName);
......
......@@ -93,6 +93,8 @@ class MasschroqWriter : public MonitorBase {
void initialiseOutput();
void printQuantificationData(const std::vector<xicPeak *> * p_v_peak_list);
void printAlignmentResults(const Msrun * msrun);
/// counter for the search items, used to generate unique search xml ids
unsigned int _quanti_item_counter;
......
This diff is collapsed.
......@@ -176,6 +176,8 @@ class Msrun {
const std::vector<mcq_double> getAlignedRetentionTimes() const;
const std::vector<mcq_double> getVectorOfTimeValues() const;
/// begin iterator for _original_rt_set
std::set<mcq_double>::const_iterator begin_original_rt() const {
return (_original_rt_set.begin());
......
......@@ -35,7 +35,6 @@ MsrunSliced::deleteSlicer() {
void
MsrunSliced::setSpectrum(const mcq_double retention_time, spectrum * the_spectrum) {
_slicer->setSpectrumInSlices(retention_time, the_spectrum);
/// very important to delete the old spectrum here, we do not need it anymore
if (the_spectrum != 0) {
delete (the_spectrum);
......
......@@ -174,7 +174,7 @@ void
Slice::setXicVectors(xicBase * ptr_on_xic) {
/// the rt in xics have to be in ascending order, but as we have slept spectra
/// in the order of mzxml parsing into simple vectors, no ordering is guaranteed
/// in our _rt_v vector. Before setting teh xic vectors we sort if necessary,
/// in our _rt_v vector. Before setting the xic vectors we sort if necessary,
/// but we have to sort without loosing the matching rt-> spectra.
vector<mcq_double> * rt_vector = ptr_on_xic->getRetentionTimes();
vector<mcq_double> * intensity_vector = ptr_on_xic->getIntensities();
......
......@@ -969,7 +969,7 @@ MasschroqmlParser::startGnumericResult(const QString output_file) {
}
_p_current_monitor_list->addMonitor(p_results);
return true;
return true;
}
bool
......@@ -991,7 +991,7 @@ bool
MasschroqmlParser::startXhtmltableResult(const QString output_file) {
XhtmltableQuantifResults * p_results;
try {
try {
p_results = new XhtmltableQuantifResults(output_file);
} catch (mcqError error) {
_errorStr = QObject::tr("problem creating xhtmltable output results :\n%1").arg(error.what());
......
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