xtandempipeline_3.3.3-1

CMakeLists.txt

@@ -47,7 +47,7 @@ cmake_minimum_required(VERSION 2.6)
 
 SET(CPACK_PACKAGE_VERSION_MAJOR "3")
 SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "2")
+SET(CPACK_PACKAGE_VERSION_PATCH "3")
 
 SET (XTANDEMPIPELINE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
 

debian/changelog

+xtandempipeline (3.3.3-1) wheezy; urgency=low
+
+  * bug fixed int the peptide_pos tab output (in expert mode)
+
+ -- Olivier Langella <Olivier.Langella@moulon.inra.fr>  Mon, 24 Nov 2014 13:35:02 +0100
+
 xtandempipeline (3.3.2-8) wheezy; urgency=low
 
   * bug fix creating protein accession, HTCondor real job completed

doc/xtandem_pipeline.tex

@@ -12,6 +12,8 @@
 \newcommand{\xtp}{\textbf{X!TandemPipeline}}
 \newcommand{\xt}{\textbf{X!Tandem}}
 \newcommand{\mhplus} {$MH^{+}$}
+\newcommand{\version}{3.3.3}
+\newcommand{\nickname}{Myosine Anabolisée}
 
 %\usepackage{enumitem}
 %\setdescription{labelsep=\textwidth}
@@ -21,7 +23,7 @@
 PAPPSO - \url{http://pappso.inra.fr/}\\
 \includegraphics[width=1cm]{images/pappso}
 }
-\title{\xtp\ 3.3.2 (Myosine Chargée)\\validating, filtering and grouping MSMS identifications}
+\title{\xtp\ \version\ (\nickname)\\validating, filtering and grouping MSMS identifications}
 \date{21 October 2014}
 
 %Modification des entetes et pied de page + marges
@@ -710,27 +712,30 @@ In this case, the column corresponding to the normal and reverse search are indi
 \section{Changelog}
 \subsection{"Myosine" branch}
 \begin{description}
-  \item[3.3.2] Better performances. New ODS output featuring complete summary of MS identification runs. Updated documentation.
-  \item[3.3.1] Better performances. Problems concerning the PAI computation by
+  \item[3.3.3 Myosine Anabolisée] New XML parser giving better informations to the users (line number, column number, filename containing errors). Better support
+  for high performance clusters throught HTCondor. BUG FIX in the ``peptide pos'' tab of the spreadsheet output in expert mode : 
+  only the first protein in each subgroup was displayed.
+  \item[3.3.2 Myosine Chargée] Better performances. New ODS output featuring complete summary of MS identification runs. Updated documentation.
+  \item[3.3.1 Myosine Famélique] Better performances. Problems concerning the PAI computation by
   samples are fixed. Updated documentation.
-  \item[3.3.0] Grouping of sub-group has been changed for better performances and to fix over-grouping on large datasets (thanks to M. Blein)\\
+  \item[3.3.0 Myosine Rachitique] Grouping of sub-group has been changed for better performances and to fix over-grouping on large datasets (thanks to M. Blein)\\
  If you have a very large dataset, we recommand to reload xtandem results to fix errors.
 \end{description}
 
 \subsection{"Tubuline" branch}
 \begin{description}
- \item[3.2.2] Corrected report of input parameter on X!Tandem output result (thanks to T. Greko).
- \item[3.2.1] Add new X!Tandem paramaters for multiple search of modifications in one analyse and calculation can now be performed on z > 3.
- \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.\\
+ \item[3.2.2 Tubuline Étayée] Corrected report of input parameter on X!Tandem output result (thanks to T. Greko).
+ \item[3.2.1 Tubuline Étayée] Add new X!Tandem paramaters for multiple search of modifications in one analyse and calculation can now be performed on z > 3.
+ \item[3.2.0 Tubuline Squelettique] 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{"Kératine" branch}
 \begin{description}
-  \item[3.1.5] Add support of phosphorylation neutral loss and enhanced ETD detection on MS2 spectra.\\
+  \item[3.1.5 Kératine Moustachue] 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.\\
+  \item[3.1.4 Kératine Poilue] Add support for viewving ETD spectra after automatic detection.
+  \item[3.1.3 Kératine Chevelue] 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, ...).

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

@@ -41,8 +41,8 @@ public class XtandemPipelineMain {
 	 * @return
 	 * @return
 	 */
-	static public String version = "3.3.2";
-	static public String versionName = "Myosine Chargée";
+	static public String version = "3.3.3";
+	static public String versionName = "Myosine Anabolisée";
 
 	public static String about = "X!Tandem Pipeline is developped by PAPPSO team (http://pappso.inra.fr).\n\n"
 			+ "This software is distributed under the terms of the GNU General Public License.\n\n"
@@ -52,7 +52,7 @@ public class XtandemPipelineMain {
 
 	// public static String news =
 	// "3.3.1 : Start and stop peptide positions added in exported spreadsheet files (ODS or CSV)";
-	public static String news = "3.3.2 : new output reports, unique identifiers for proteins and peptides, lots of structural modifications";
+	public static String news = "3.3.3 : new XML parser with better error reports, HTCondor jobs support, BUG FIXED in the spreadsheet expert output : the peptide_pos tab now displays all peptides of all proteins (not just the first of each subgroup)";
 
 	public static void main(String[] args) {
 

src/fr/inra/pappso/xtandempipeline/output/SpreadSheets/OdsPeptidePosOutput.java

@@ -25,7 +25,6 @@ package fr.inra.pappso.xtandempipeline.output.SpreadSheets;
 
 import java.io.IOException;
 import java.io.OutputStream;
-import java.util.HashSet;
 
 import javax.xml.datatype.DatatypeConfigurationException;
 import javax.xml.stream.XMLStreamException;
@@ -148,7 +147,8 @@ public class OdsPeptidePosOutput {
 				for (SubGroup sg : group.getSubGroupSet().getSubGroupList()) {
 
 					int k = 0;
-					HashSet<PeptideMass> uniquePepMass = new HashSet<PeptideMass>();
+					// HashSet<PeptideMass> uniquePepMass = new
+					// HashSet<PeptideMass>();
 
 					for (HashSampleScanSetProt hashProt : sg
 							.getHashSampleScanSetProtList()) {
@@ -159,10 +159,10 @@ public class OdsPeptidePosOutput {
 								.get_peptide_order_inclus_redon()) {
 							PeptideMass pepMass = pepMassSet
 									.getInstance(peptide);
-							if (uniquePepMass.add(pepMass)) {
-								this.writeOnePeptideMassPerProt(ident, group,
-										sg, k, pepMass, hashProt, peptide);
-							}
+							// if (uniquePepMass.add(pepMass)) {
+							this.writeOnePeptideMassPerProt(ident, group, sg,
+									k, pepMass, hashProt, peptide);
+							// }
 
 						}
 					}