Adding information about Release 3.2.0, "tubuline squeletique"

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@215 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/doc/xtandem_pipeline.tex

@@ -20,7 +20,7 @@ PAPPSO - \url{http://pappso.inra.fr/}\\
 \includegraphics[width=1cm]{images/pappso.pdf}
 }
 \title{$\X$\\Automated analyses, filtering and export of X!Tandem MS/MS results}
-\date{10 May 2011}
+\date{15 February 2012}
 
 %Modification des entetes et pied de page + marges
 \geometry{top=3cm, bottom=3cm, left=2cm, right=2cm}
@@ -419,5 +419,35 @@ In this case, the column corresponding to the normal and reverse search are indi
 \label{fdr2}
 \end{figure}
 
+\pagebreak
+
+\section{Changelog}
+\subsection{"Tubuline" versions}
+\begin{description}
+  \item[3.2.0] Identification from Mascot dat file can now be imported and filtered. All work as X!Tandem result excepts that protein sequence can not be retrieved : PAI and coverage are absent.\\
+  Correction of FDR calculation from Reverse/Decoy search.
+\end{description}
+
+\subsection{"Kératines" versions}
+\begin{description}
+  \item[3.1.5] Add support of phosphorylation neutral loss and enhanced ETD detection on MS2 spectra.\\
+  Correction of MassChroQ export.
+  \item[3.1.4] Add support for viewving ETD spectra after automatic detection.
+  \item[3.1.3] Corrected bug of xtandem preset. Refine analysis was never start instead refine param is set to yes.\\
+  Adds a new annotated spectrum renderer and bug fix on ODS export.
+  \item[3.1.2] Add export results on Open Document Spreadsheet (.ods) file.\\
+  Correction of bugs (Grouping, PepNovo export, ...).
+  \item[3.1.1] FDR computation are now compatible with reverse option of X!Tandem.
+  \item[3.1.0] Algorithm of grouping have been completly rewritten : 
+  \begin{itemize}
+  \item Older project must be refiltered to be properly grouped.
+  \item Phosphopeptide filtering have been enhanced to correspond to :
+  \begin{itemize}
+    \item SubGroup represents the number of phosphosites
+    \item Group represents the number of phosphoproteins
+  \end{itemize}
+   \item Configuration file have been modified and must be parameter again
+\end{itemize}
+\end{description}
 
 \end{document}

xtandempipeline/src/fr/inra/pappso/xtandempipeline/XtandemPipelineMain.java

@@ -41,8 +41,8 @@ public class XtandemPipelineMain {
 	 * @return
 	 * @return
 	 */
-	static public String version = "3.1.5";
-	static public String versionName = "Kératine Moustachue";
+	static public String version = "3.2.0";
+	static public String versionName = "Tubuline squeletique";
 
 	public static String about = "X!Tandem Pipeline is developped by PAPPSO team (http://pappso.inra.fr) by Benoit Valot and Olivier langella.\n\n"
 			+ "This software is distributed under the terms of the GNU General Public License.\n\n"
@@ -53,20 +53,9 @@ public class XtandemPipelineMain {
 			+ "If a protein is identified by two peptides with an evalue of O.O1, the protein evalue is O.OOO1.\n\n"
 			+ "So, we preconise to put -4 for the protein evalue filter instead of -8.";
 
-	public static String news = "3.1.5 : Add support of phosphorylation neutral loss and enhanced ETD detection on MS2 spectra.\n"
-			+ "Correction of MassChroQ export.\n\n" 
-			+ "3.1.4 : Add support for viewving ETD spectra after automatic detection.\n\n"
-			+ "3.1.3 : Corrected bug of xtandem preset. Refine analysis was never start instead refine param is set to yes\n"
-			+ "Adds a new annotated spectrum renderer and bug fix on ODS export\n\n"
-			+ "3.1.2 : Add export results on Open Document Spreadsheet (.ods) file.\n"
-			+ "Correction of bugs (Grouping, PepNovo export, ...).\n\n"
-			+ "3.1.1 : FDR computation are now compatible with reverse option of X!Tandem.\n\n"
-			+ "3.1.0 : Algorithm of grouping have been completly rewritten : \n"
-			+ "Older project must be refiltered to be properly grouped.\n\n"
-			+ "Phosphopeptide filtering have been enhanced to correspond to :\n"
-			+ "- SubGroup represents the number of phosphosites\n"
-			+ "- Group represents the number of phosphoproteins\n\n"
-			+ "Configuration file have been modified and must be parameter again";
+	public static String news = "3.2.0 : Identification from Mascot dat file can now be imported and filtered."+
+	" All work as X!Tandem result excepts that protein sequence can not be retrieved : PAI and coverage are absent.\n\n"+
+	"Correction of FDR calculation from Reverse/Decoy search.";
 
 	public static void main(String[] args) {