removed translation + changed doc

git-svn-id: https://subversion.renater.fr/masschroq/trunk@2097 e4b6dbb4-9209-464b-83f7-6257456c460c

masschroq/doc/masschroq_v1_user_manual/fdl.tex

@@ -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.
 
 
-\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
 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.
-
 %---------------------------------------------------------------------

masschroq/doc/schema/masschroq.xsd

 <?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:element name="masschroq" type="masschroqType"/>

masschroq/src/lib/look_for/lookForPeptideRealRt.cpp

@@ -38,10 +38,9 @@ LookForPeptideRealRt::getRt(const msRun * pmsrun) const {
   if ( _p_peptide->isObservedIn(pmsrun) ) {
     return getRtOnObservedMsrun(pmsrun) ; 
   } else {
-    // else get the mean rt observed in the other msruns for this peptide :
-    // getMeanBestRt(_group);
+    // else get the mean rt observed in the other msruns of the group
+    ///for this peptide: getMeanBestRt(_group);
     
-    // bug :return _rt;
     return getMeanRt();
   }
 }

masschroq/src/lib/peptides/peptide.cpp

@@ -178,7 +178,7 @@ Peptide::getObservedBestRtForMsRun(const msRun * p_msrun,
 
 mcq_double 
 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::vector<PeptideObservedIn *> * observed_in_group = 
     getObservedInGroup(group);

masschroq/src/lib/share/utilities.h

@@ -78,7 +78,9 @@ class Utilities {
   
   static const 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

masschroq/src/pepfileparser/pepParser.cpp

@@ -178,7 +178,6 @@ PepParser::processSequence(QString & seq_token) {
   seq_token.remove(not_aaseq);
   if (Utilities::isValidSequence(seq_token, Qt::CaseInsensitive)) {
     QString seq_token_upper = seq_token.toUpper();
-    Utilities::replaceLwithI(seq_token_upper);
     return seq_token_upper;
   } else {
     QString ln;

masschroq/src/saxhandlers/mass_chroq_handler.cpp

@@ -1313,7 +1313,7 @@ MassChroqHandler::startElement_peptides_in_peptide_list
 	  /// this test is not necessary here
 	  if (rt != -1) {
 	    _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)
 	    if (mode == "mean") {
 	      mz_to_search = new LookForPeptide(*_p_current_extraction_method,
@@ -1323,8 +1323,8 @@ MassChroqHandler::startElement_peptides_in_peptide_list
 	      _v_p_current_mass_to_look_for.push_back(mz_to_search);
 	    } 
 	    /// in "real_or_mean" mode we select the peptide/z with the 
-	    /// observed rt of the peptide for each msrun if possible i.e. 
-	    /// if the peptide has been observed in the msrun, otherwise 
+	    /// observed/identified rt of the peptide for each msrun if possible 
+	    /// (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) 
 	    else { // mode = "real_or_mean"
 	      mz_to_search =