Commit 1694ccba authored by Edlira Nano's avatar Edlira Nano
Browse files

removed translation + changed doc

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2097 e4b6dbb4-9209-464b-83f7-6257456c460c
parent 986052fe
...@@ -519,45 +519,7 @@ under CC-BY-SA on the same site at any time before August 1, 2009, ...@@ -519,45 +519,7 @@ under CC-BY-SA on the same site at any time before August 1, 2009,
provided the MMC is eligible for relicensing. provided the MMC is eligible for relicensing.
\begin{center}
{\Large\bf ADDENDUM: How to use this License for your documents\par}
\phantomsection
\addcontentsline{toc}{section}{ADDENDUM: How to use this License for your documents}
\end{center}
To use this License in a document you have written, include a copy of
the License in the document and put the following copyright and the License in the document and put the following copyright and
license notices just after the title page: license notices just after the title page:
\bigskip
\begin{quote}
Copyright \copyright{} YEAR YOUR NAME.
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3
or any later version published by the Free Software Foundation;
with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
A copy of the license is included in the section entitled ``GNU
Free Documentation License''.
\end{quote}
\bigskip
If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts,
replace the ``with \dots\ Texts.'' line with this:
\bigskip
\begin{quote}
with the Invariant Sections being LIST THEIR TITLES, with the
Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.
\end{quote}
\bigskip
If you have Invariant Sections without Cover Texts, or some other
combination of the three, merge those two alternatives to suit the
situation.
If your document contains nontrivial examples of program code, we
recommend releasing these examples in parallel under your choice of
free software license, such as the GNU General Public License,
to permit their use in free software.
%--------------------------------------------------------------------- %---------------------------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
<!--
masschroqML version 1.0 schema (http://pappso/bioinfo/masschroq/)
-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"> <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="masschroq" type="masschroqType"/> <xs:element name="masschroq" type="masschroqType"/>
......
...@@ -38,10 +38,9 @@ LookForPeptideRealRt::getRt(const msRun * pmsrun) const { ...@@ -38,10 +38,9 @@ LookForPeptideRealRt::getRt(const msRun * pmsrun) const {
if ( _p_peptide->isObservedIn(pmsrun) ) { if ( _p_peptide->isObservedIn(pmsrun) ) {
return getRtOnObservedMsrun(pmsrun) ; return getRtOnObservedMsrun(pmsrun) ;
} else { } else {
// else get the mean rt observed in the other msruns for this peptide : // else get the mean rt observed in the other msruns of the group
// getMeanBestRt(_group); ///for this peptide: getMeanBestRt(_group);
// bug :return _rt;
return getMeanRt(); return getMeanRt();
} }
} }
......
...@@ -178,7 +178,7 @@ Peptide::getObservedBestRtForMsRun(const msRun * p_msrun, ...@@ -178,7 +178,7 @@ Peptide::getObservedBestRtForMsRun(const msRun * p_msrun,
mcq_double mcq_double
Peptide::getMeanBestRt(const msRunHashGroup & group) const { Peptide::getMeanBestRt(const msRunHashGroup & group) const {
// stock all the msrun_ids in a set // stock all the msrun_ids this peptide is observed in in a set
std::set<const msRun *> s_msrun; std::set<const msRun *> s_msrun;
std::vector<PeptideObservedIn *> * observed_in_group = std::vector<PeptideObservedIn *> * observed_in_group =
getObservedInGroup(group); getObservedInGroup(group);
......
...@@ -78,7 +78,9 @@ class Utilities { ...@@ -78,7 +78,9 @@ class Utilities {
static const bool isValidSequence(const QString & seq, static const bool isValidSequence(const QString & seq,
const Qt::CaseSensitivity cs); 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); static void replaceLwithI(QString & pep_seq);
/// given a mz and a z, calculate the mh /// given a mz and a z, calculate the mh
......
...@@ -178,7 +178,6 @@ PepParser::processSequence(QString & seq_token) { ...@@ -178,7 +178,6 @@ PepParser::processSequence(QString & seq_token) {
seq_token.remove(not_aaseq); seq_token.remove(not_aaseq);
if (Utilities::isValidSequence(seq_token, Qt::CaseInsensitive)) { if (Utilities::isValidSequence(seq_token, Qt::CaseInsensitive)) {
QString seq_token_upper = seq_token.toUpper(); QString seq_token_upper = seq_token.toUpper();
Utilities::replaceLwithI(seq_token_upper);
return seq_token_upper; return seq_token_upper;
} else { } else {
QString ln; QString ln;
......
...@@ -1313,7 +1313,7 @@ MassChroqHandler::startElement_peptides_in_peptide_list ...@@ -1313,7 +1313,7 @@ MassChroqHandler::startElement_peptides_in_peptide_list
/// this test is not necessary here /// this test is not necessary here
if (rt != -1) { if (rt != -1) {
_p_current_extraction_method->setMz((*itpep)->getMz(*itz)); _p_current_extraction_method->setMz((*itpep)->getMz(*itz));
/// select the peptide/z with the mean rt (mean of all observed /// select the peptide/z with the mean rt (mean of all rt observed
/// values of this peptide in this group) /// values of this peptide in this group)
if (mode == "mean") { if (mode == "mean") {
mz_to_search = new LookForPeptide(*_p_current_extraction_method, mz_to_search = new LookForPeptide(*_p_current_extraction_method,
...@@ -1323,8 +1323,8 @@ MassChroqHandler::startElement_peptides_in_peptide_list ...@@ -1323,8 +1323,8 @@ MassChroqHandler::startElement_peptides_in_peptide_list
_v_p_current_mass_to_look_for.push_back(mz_to_search); _v_p_current_mass_to_look_for.push_back(mz_to_search);
} }
/// in "real_or_mean" mode we select the peptide/z with the /// in "real_or_mean" mode we select the peptide/z with the
/// observed rt of the peptide for each msrun if possible i.e. /// observed/identified rt of the peptide for each msrun if possible
/// if the peptide has been observed in the msrun, otherwise /// (i.e. if the peptide has been identified in the msrun), otherwise
/// with a mean of observed rt-s for the group (as in mean mode) /// with a mean of observed rt-s for the group (as in mean mode)
else { // mode = "real_or_mean" else { // mode = "real_or_mean"
mz_to_search = mz_to_search =
......
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