From f2ff0d905b05cf531abe817e2de63fc663c93f2b Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Mon, 13 May 2013 10:48:18 +0200
Subject: [PATCH] subversion repository imported into git with wommand : git
svn clone https://langella@subversion.renater.fr/xtandempipeline -T trunk -b
branches -t tags
all files in subdirectory xtandempipeline moved to the git root.
subdirectory xtandempipeline removed
---
xtandempipeline/.classpath => .classpath | 0
xtandempipeline/.project => .project | 0
.../org.eclipse.jdt.core.prefs | 0
xtandempipeline/CMakeLists.txt => CMakeLists.txt | 0
xtandempipeline/COPYING => COPYING | 0
xtandempipeline/README => README | 0
xtandempipeline/build.xml => build.xml | 0
xtandempipeline/build.xml.cmake => build.xml.cmake | 0
...build_ubuntu.xml.cmake => build_ubuntu.xml.cmake | 0
{xtandempipeline/debian => debian}/changelog | 0
{xtandempipeline/debian => debian}/compat | 0
{xtandempipeline/debian => debian}/control | 0
{xtandempipeline/debian => debian}/copyright | 0
{xtandempipeline/debian => debian}/rules | 0
{xtandempipeline/doc => doc}/Xtandem_batch.pdf | Bin
{xtandempipeline/doc => doc}/Xtandem_batch.tex | 0
{xtandempipeline/doc => doc}/Xtandem_parser.pdf | Bin
{xtandempipeline/doc => doc}/Xtandem_parser.tex | 0
{xtandempipeline/doc => doc}/animation.svg | 0
.../doc => doc}/files/dat/FtorfncmO.dat | 0
.../files/dat/modificationConversion.txt | 0
{xtandempipeline/doc => doc}/files/xpip/xpip.xsd | 0
.../doc => doc}/files/xpip/xpip_sample.xml | 0
.../doc => doc}/images/batch_acceuil.png | Bin
.../doc => doc}/images/batch_process.png | Bin
.../doc => doc}/images/batch_process.xcf | Bin
.../doc => doc}/images/batch_terminal.png | Bin
.../doc => doc}/images/batch_xml_search.png | Bin
{xtandempipeline/doc => doc}/images/pappso.pdf | Bin
.../doc => doc}/images/tandem_analysis.png | Bin
.../doc => doc}/images/tandem_comparaison.pdf | Bin
.../doc => doc}/images/tandem_comparaison.png | Bin
.../doc => doc}/images/tandem_configuration.png | Bin
.../doc => doc}/images/tandem_export.png | Bin
{xtandempipeline/doc => doc}/images/tandem_fdr.png | Bin
.../doc => doc}/images/tandem_filter.png | Bin
.../doc => doc}/images/tandem_parameter.png | Bin
.../doc => doc}/images/tandem_peptide.pdf | Bin
.../doc => doc}/images/tandem_peptide.png | Bin
.../doc => doc}/images/tandem_principal.png | Bin
{xtandempipeline/doc => doc}/images/tandem_prot.pdf | Bin
{xtandempipeline/doc => doc}/images/tandem_prot.png | Bin
.../doc => doc}/images/window_peptide.png | Bin
.../doc => doc}/images/window_peptide_detail.png | Bin
.../doc => doc}/images/window_protein.png | Bin
.../doc => doc}/images/window_protein_detail.png | Bin
{xtandempipeline/doc => doc}/logo.svg | 0
{xtandempipeline/doc => doc}/xtandem_pipeline.pdf | Bin
{xtandempipeline/doc => doc}/xtandem_pipeline.tex | 0
{xtandempipeline/lib => lib}/PPClient.jar | Bin
.../lib => lib}/batik/batik-anim-1.7.jar | Bin
.../lib => lib}/batik/batik-awt-util-1.7.jar | Bin
.../lib => lib}/batik/batik-bridge-1.7.jar | Bin
.../lib => lib}/batik/batik-codec-1.7.jar | Bin
.../lib => lib}/batik/batik-css-1.7.jar | Bin
.../lib => lib}/batik/batik-dom-1.7.jar | Bin
.../lib => lib}/batik/batik-ext-1.7.jar | Bin
.../lib => lib}/batik/batik-gvt-1.7.jar | Bin
.../lib => lib}/batik/batik-parser-1.7.jar | Bin
.../lib => lib}/batik/batik-script-1.7.jar | Bin
.../lib => lib}/batik/batik-svg-dom-1.7.jar | Bin
.../lib => lib}/batik/batik-svggen-1.7.jar | Bin
.../lib => lib}/batik/batik-transcoder-1.7.jar | Bin
.../lib => lib}/batik/batik-util-1.7.jar | Bin
.../lib => lib}/batik/batik-xml-1.7.jar | Bin
.../lib => lib}/cxf-common-utilities-2.2.4.jar | Bin
.../lib => lib}/http/commons-codec-1.2.jar | Bin
.../lib => lib}/http/commons-httpclient-3.1.jar | Bin
.../lib => lib}/http/commons-logging-1.0.4.jar | Bin
{xtandempipeline/lib => lib}/javacsv.jar | Bin
{xtandempipeline/lib => lib}/libodsstream.jar | Bin
{xtandempipeline/lib => lib}/libproteomicsvg.jar | Bin
{xtandempipeline/lib => lib}/log4j-1.2.jar | Bin
{xtandempipeline/lib => lib}/mascotdatfile-3.3.jar | Bin
{xtandempipeline/lib => lib}/ods2csv.jar | Bin
.../lib => lib}/swt/swt-cocoa-macosx-x86.jar | Bin
.../lib => lib}/swt/swt-cocoa-macosx-x86_64.jar | Bin
.../lib => lib}/swt/swt-gtk-linux-x86.jar | Bin
.../lib => lib}/swt/swt-gtk-linux-x86_64.jar | Bin
.../lib => lib}/swt/swt-win32-windows-x86.jar | Bin
.../lib => lib}/swt/swt-win32-windows-x86_64.jar | Bin
{xtandempipeline/lib => lib}/xalan-2.6.0.jar | Bin
{xtandempipeline/lib => lib}/xercesImpl-2.9.1.jar | Bin
{xtandempipeline/lib => lib}/xml-apis-1.3.04.jar | Bin
.../lib => lib}/xml-apis-ext-1.3.04.jar | Bin
.../applications/xtandempipeline.desktop.cmake | 0
.../xtandempipeline_online.desktop.cmake | 0
{xtandempipeline/share => share}/classpath | 0
.../mime/packages/xtandempipeline.xml | 0
.../xtandempipeline/xtandempipeline.jnlp | 0
.../xtandempipeline/xtandempipeline.jnlp.cmake | 0
.../xtandempipeline/xtandempipeline.sh.cmake | 0
.../xtandempipeline/xtandempipeline_icon.svg | 0
.../xtandempipeline/xtandempipeline_xpip.svg | 0
.../src => src}/conf/log4j.linux.properties | 0
.../src => src}/conf/log4j.windows.properties | 0
.../src => src}/conf/release/log4j.linux.properties | 0
.../conf/release/log4j.windows.properties | 0
.../xtandempipeline/MsException/GuiException.java | 0
.../xtandempipeline/MsException/MSMSException.java | 0
.../xtandempipeline/MsException/StopException.java | 0
.../pappso/xtandempipeline/XtandemPipelineMain.java | 0
.../xtandempipeline/XtandemPipelineSession.java | 0
.../pappso/xtandempipeline/class_msms/Database.java | 0
.../xtandempipeline/class_msms/DatabaseSet.java | 0
.../xtandempipeline/class_msms/Identification.java | 0
.../IdentificationDataFile.java | 0
.../IdentificationDataSource.java | 0
.../IdentificationDataSourceSet.java | 0
.../IdentificationMascotFile.java | 0
.../IdentificationProticPortSource.java | 0
.../IdentificationXtandemFile.java | 0
.../xtandempipeline/class_msms/MapDb/Peptide.java | 0
.../class_msms/MapDb/PeptideStore.java | 0
.../pappso/xtandempipeline/class_msms/Match.java | 0
.../xtandempipeline/class_msms/MatchList.java | 0
.../pappso/xtandempipeline/class_msms/Modifs.java | 0
.../xtandempipeline/class_msms/ModifsList.java | 0
.../pappso/xtandempipeline/class_msms/MsRun.java | 0
.../pappso/xtandempipeline/class_msms/MsRunSet.java | 0
.../xtandempipeline/class_msms/PhosphoIsland.java | 0
.../class_msms/PhosphoIslandSet.java | 0
.../pappso/xtandempipeline/class_msms/Protein.java | 0
.../pappso/xtandempipeline/class_msms/config.java | 0
.../xtandempipeline/class_msms/fdr_count.java | 0
.../xtandempipeline/class_msms/xtandem_param.java | 0
.../filter_print/FilterGroupFromFastaDatabase.java | 0
.../filter_print/calculation_base_peptide.java | 0
.../filter_print/calculation_base_protein.java | 0
.../filter_print/calculation_peptide_fdr.java | 0
.../calculation_peptide_fdr_distribution.java | 0
.../calculation_peptide_mh_deviation.java | 0
.../filter_print/calculation_protein_fdr.java | 0
.../calculation_protein_fdr_distribution.java | 0
.../xtandempipeline/filter_print/filter_base.java | 0
.../filter_index_and_order_match_scan.java | 0
.../filter_print/filter_isotopic_modifs.java | 0
.../filter_print/filter_peptide_evalue.java | 0
.../filter_print/filter_peptide_redondancy.java | 0
.../filter_print/filter_phospho_peptide.java | 0
.../filter_print/filter_protein_evalue.java | 0
.../filter_print/filter_protein_evalue_to.java | 0
.../filter_recalcul_protein_evalue.java | 0
.../filter_print/filter_unique_peptide_number.java | 0
.../filter_unique_peptide_number_to.java | 0
.../xtandempipeline/filter_print/printOdsBase.java | 0
.../xtandempipeline/filter_print/print_base.java | 0
.../xtandempipeline/filter_print/print_fasta.java | 0
.../filter_print/print_fasta_to_group.java | 0
.../filter_print/print_fasta_to_subgroup.java | 0
.../filter_print/print_ods_compar.java | 0
.../filter_print/print_ods_compar_phospho.java | 0
.../filter_print/print_ods_peptide_list.java | 0
.../print_ods_peptide_list_to_phosphopeptide.java | 0
.../filter_print/print_ods_protein_to_combined.java | 0
.../filter_print/print_ods_protein_to_indiv.java | 0
.../print_ods_protein_to_phosphopeptide.java | 0
.../xtandempipeline/filter_print/print_pepnovo.java | 0
.../filter_print/swt_table_base.java | 0
.../filter_print/swt_table_peptide.java | 0
.../filter_print/swt_table_protein.java | 0
.../xtandempipeline/grouping/AlgoGrouping.java | 0
.../xtandempipeline/grouping/AlgoGroupingBase.java | 0
.../grouping/AlgoGroupingPhospho.java | 0
.../inra/pappso/xtandempipeline/grouping/Group.java | 0
.../pappso/xtandempipeline/grouping/GroupSet.java | 0
.../xtandempipeline/grouping/HashKey4Groups.java | 0
.../xtandempipeline/grouping/HashKey4GroupsSet.java | 0
.../xtandempipeline/grouping/HashPeptide.java | 0
.../xtandempipeline/grouping/HashPeptideSet.java | 0
.../xtandempipeline/grouping/HashProtein.java | 0
.../xtandempipeline/grouping/HashProteinSet.java | 0
.../xtandempipeline/grouping/HashSampleScan.java | 0
.../xtandempipeline/grouping/HashSampleScanSet.java | 0
.../grouping/HashSampleScanSetPhospho.java | 0
.../grouping/HashSampleScanSetProt.java | 0
.../pappso/xtandempipeline/grouping/SubGroup.java | 0
.../xtandempipeline/grouping/SubGroupSet.java | 0
.../grouping/interfaces/GrpMsSample.java | 0
.../grouping/interfaces/GrpPeptide.java | 0
.../grouping/interfaces/GrpPhosphoModif.java | 0
.../grouping/interfaces/GrpProtMatch.java | 0
.../grouping/interfaces/GrpProtein.java | 0
.../output/CsvRedundantPeptideOutput.java | 0
.../output/IndentingXMLStreamWriter.java | 0
.../xtandempipeline/output/MassChroQmlOutput.java | 0
.../xtandempipeline/output/MassChroQmlWriter.java | 0
.../output/OdsRedundantPeptideOutput.java | 0
.../xtandempipeline/output/ProticDbMlOutput.java | 0
.../xtandempipeline/output/ProticDbMlWriter.java | 0
.../pappso/xtandempipeline/sax_parse/Mascot.java | 0
.../xtandempipeline/sax_parse/XtandemPhospho.java | 0
.../xtandempipeline/sax_parse/load_project.java | 0
.../xtandempipeline/sax_parse/msms_output.java | 0
.../sax_parse/new_xtandem_param.java | 0
.../xtandempipeline/sax_parse/parse_file.java | 0
.../xtandempipeline/sax_parse/save_project.java | 0
.../sax_parse/xml_xtandem_param.java | 0
.../pappso/xtandempipeline/sax_parse/xtandem.java | 0
.../sax_parse/xtandem_ms2_spectra.java | 0
.../xtandempipeline/sax_parse/xtandem_params.java | 0
.../xtandempipeline/thread/DataType_Base.java | 0
.../xtandempipeline/thread/DataType_Combine.java | 0
.../xtandempipeline/thread/DataType_individual.java | 0
.../thread/DataType_phosphopeptide.java | 0
.../thread/XtandemCondorAnalysis.java | 0
.../pappso/xtandempipeline/thread/base_shell.java | 0
.../pappso/xtandempipeline/thread/combined.java | 0
.../thread/filtered_and_create_grouping.java | 0
.../pappso/xtandempipeline/thread/individual.java | 0
.../thread/load_result_and_create_grouping.java | 0
.../pappso/xtandempipeline/thread/phosphosite.java | 0
.../xtandempipeline/thread/printing_base.java | 0
.../xtandempipeline/thread/printing_combine.java | 0
.../xtandempipeline/thread/printing_indiv.java | 0
.../thread/printing_phosphopeptide.java | 0
.../inra/pappso/xtandempipeline/thread/process.java | 0
...nitialise_result_filter_and_create_grouping.java | 0
.../thread/save_result_and_filtering.java | 0
.../xtandempipeline/thread/xtandem_analysis.java | 0
.../xtandempipeline/ui/results/Peptide_Details.java | 0
.../ui/results/Peptide_Details_item.java | 0
.../xtandempipeline/ui/results/Peptide_List.java | 0
.../ui/results/Peptide_List_item.java | 0
.../xtandempipeline/ui/results/Protein_Details.java | 0
.../ui/results/Protein_Details_item.java | 0
.../xtandempipeline/ui/results/Protein_List.java | 0
.../ui/results/Protein_List_item.java | 0
.../xtandempipeline/ui/results/window_base.java | 0
.../xtandempipeline/ui/swt/Export_Windows.java | 0
.../xtandempipeline/ui/swt/Filter_Windows.java | 0
.../pappso/xtandempipeline/ui/swt/Main_Windows.java | 0
.../xtandempipeline/ui/swt/Path_configuration.java | 0
.../inra/pappso/xtandempipeline/ui/swt/Running.java | 0
.../ui/swt/Xtandem_Analysis_Param.java | 0
.../xtandempipeline/ui/swt/Xtandem_preset.java | 0
.../src => src}/resources/images/anim.gif | Bin
.../src => src}/resources/images/anim_1.png | Bin
.../src => src}/resources/images/anim_2.png | Bin
.../src => src}/resources/images/anim_3.png | Bin
.../src => src}/resources/images/anim_4.png | Bin
.../src => src}/resources/images/anim_5.png | Bin
.../src => src}/resources/images/anim_6.png | Bin
.../src => src}/resources/images/anim_7.png | Bin
.../src => src}/resources/images/anim_8.png | Bin
.../src => src}/resources/images/icon_16.png | Bin
.../src => src}/resources/images/icon_32.png | Bin
.../src => src}/resources/images/icon_64.png | Bin
{xtandempipeline/src => src}/resources/lpdp.html | 0
{xtandempipeline/src => src}/resources/lpti.html | 0
{xtandempipeline/src => src}/resources/ohcw.html | 0
{xtandempipeline/src => src}/resources/ohist.html | 0
{xtandempipeline/src => src}/resources/olp.html | 0
{xtandempipeline/src => src}/resources/om.html | 0
{xtandempipeline/src => src}/resources/omvev.html | 0
{xtandempipeline/src => src}/resources/oosc.html | 0
{xtandempipeline/src => src}/resources/opara.html | 0
{xtandempipeline/src => src}/resources/opath.html | 0
{xtandempipeline/src => src}/resources/operf.html | 0
{xtandempipeline/src => src}/resources/oph.html | 0
{xtandempipeline/src => src}/resources/oprot.html | 0
{xtandempipeline/src => src}/resources/oresu.html | 0
{xtandempipeline/src => src}/resources/osequ.html | 0
{xtandempipeline/src => src}/resources/osp.html | 0
{xtandempipeline/src => src}/resources/ospec.html | 0
{xtandempipeline/src => src}/resources/osrb.html | 0
{xtandempipeline/src => src}/resources/oxp.html | 0
{xtandempipeline/src => src}/resources/pcctmc.html | 0
{xtandempipeline/src => src}/resources/pcntmc.html | 0
{xtandempipeline/src => src}/resources/pcs.html | 0
{xtandempipeline/src => src}/resources/pcsemi.html | 0
{xtandempipeline/src => src}/resources/pctrmm.html | 0
{xtandempipeline/src => src}/resources/pmrmf.html | 0
{xtandempipeline/src => src}/resources/pntrmm.html | 0
{xtandempipeline/src => src}/resources/pqa.html | 0
{xtandempipeline/src => src}/resources/pqp.html | 0
{xtandempipeline/src => src}/resources/pstpb.html | 0
{xtandempipeline/src => src}/resources/pt.html | 0
{xtandempipeline/src => src}/resources/pua.html | 0
{xtandempipeline/src => src}/resources/rcsemi.html | 0
{xtandempipeline/src => src}/resources/refine.html | 0
{xtandempipeline/src => src}/resources/refmm.html | 0
{xtandempipeline/src => src}/resources/refmvev.html | 0
{xtandempipeline/src => src}/resources/refpctm.html | 0
{xtandempipeline/src => src}/resources/refpmm.html | 0
.../src => src}/resources/refpmmotif.html | 0
{xtandempipeline/src => src}/resources/refpntm.html | 0
{xtandempipeline/src => src}/resources/rmm.html | 0
{xtandempipeline/src => src}/resources/rpm.html | 0
{xtandempipeline/src => src}/resources/rpmm.html | 0
.../src => src}/resources/rpmmotif.html | 0
{xtandempipeline/src => src}/resources/rsaps.html | 0
{xtandempipeline/src => src}/resources/rsp.html | 0
{xtandempipeline/src => src}/resources/rss.html | 0
{xtandempipeline/src => src}/resources/rtp.html | 0
{xtandempipeline/src => src}/resources/rua.html | 0
{xtandempipeline/src => src}/resources/ruc.html | 0
{xtandempipeline/src => src}/resources/rupmffr.html | 0
{xtandempipeline/src => src}/resources/sai.html | 0
{xtandempipeline/src => src}/resources/sbi.html | 0
{xtandempipeline/src => src}/resources/sca.html | 0
{xtandempipeline/src => src}/resources/sci.html | 0
{xtandempipeline/src => src}/resources/scp.html | 0
{xtandempipeline/src => src}/resources/sdr.html | 0
{xtandempipeline/src => src}/resources/sfme.html | 0
{xtandempipeline/src => src}/resources/sfmeu.html | 0
{xtandempipeline/src => src}/resources/sfmme.html | 0
{xtandempipeline/src => src}/resources/sfmmeu.html | 0
{xtandempipeline/src => src}/resources/sfmt.html | 0
{xtandempipeline/src => src}/resources/sir.html | 0
{xtandempipeline/src => src}/resources/smfmz.html | 0
{xtandempipeline/src => src}/resources/smic.html | 0
{xtandempipeline/src => src}/resources/smmcs.html | 0
{xtandempipeline/src => src}/resources/smp.html | 0
{xtandempipeline/src => src}/resources/smpc.html | 0
{xtandempipeline/src => src}/resources/smpmh.html | 0
{xtandempipeline/src => src}/resources/snlm.html | 0
{xtandempipeline/src => src}/resources/snlw.html | 0
{xtandempipeline/src => src}/resources/sp.html | 0
{xtandempipeline/src => src}/resources/spmmem.html | 0
{xtandempipeline/src => src}/resources/spmmep.html | 0
{xtandempipeline/src => src}/resources/spmmeu.html | 0
{xtandempipeline/src => src}/resources/spmmie.html | 0
{xtandempipeline/src => src}/resources/spsbs.html | 0
{xtandempipeline/src => src}/resources/spt.html | 0
{xtandempipeline/src => src}/resources/st.html | 0
{xtandempipeline/src => src}/resources/stp.html | 0
{xtandempipeline/src => src}/resources/suca.html | 0
{xtandempipeline/src => src}/resources/sunlw.html | 0
{xtandempipeline/src => src}/resources/suns.html | 0
{xtandempipeline/src => src}/resources/sxi.html | 0
{xtandempipeline/src => src}/resources/syi.html | 0
{xtandempipeline/src => src}/resources/szi.html | 0
.../src => src}/resources/tandem_api.css | 0
.../src => src}/resources/uml_index.html | 0
.../src => src}/resources/xtandem_model.xml | 0
{xtandempipeline/src => src}/test/MascotTest.java | 0
337 files changed, 0 insertions(+), 0 deletions(-)
rename xtandempipeline/.classpath => .classpath (100%)
rename xtandempipeline/.project => .project (100%)
rename {xtandempipeline/.settings => .settings}/org.eclipse.jdt.core.prefs (100%)
rename xtandempipeline/CMakeLists.txt => CMakeLists.txt (100%)
rename xtandempipeline/COPYING => COPYING (100%)
rename xtandempipeline/README => README (100%)
rename xtandempipeline/build.xml => build.xml (100%)
rename xtandempipeline/build.xml.cmake => build.xml.cmake (100%)
rename xtandempipeline/build_ubuntu.xml.cmake => build_ubuntu.xml.cmake (100%)
rename {xtandempipeline/debian => debian}/changelog (100%)
rename {xtandempipeline/debian => debian}/compat (100%)
rename {xtandempipeline/debian => debian}/control (100%)
rename {xtandempipeline/debian => debian}/copyright (100%)
rename {xtandempipeline/debian => debian}/rules (100%)
rename {xtandempipeline/doc => doc}/Xtandem_batch.pdf (100%)
rename {xtandempipeline/doc => doc}/Xtandem_batch.tex (100%)
rename {xtandempipeline/doc => doc}/Xtandem_parser.pdf (100%)
rename {xtandempipeline/doc => doc}/Xtandem_parser.tex (100%)
rename {xtandempipeline/doc => doc}/animation.svg (100%)
rename {xtandempipeline/doc => doc}/files/dat/FtorfncmO.dat (100%)
rename {xtandempipeline/doc => doc}/files/dat/modificationConversion.txt (100%)
rename {xtandempipeline/doc => doc}/files/xpip/xpip.xsd (100%)
rename {xtandempipeline/doc => doc}/files/xpip/xpip_sample.xml (100%)
rename {xtandempipeline/doc => doc}/images/batch_acceuil.png (100%)
rename {xtandempipeline/doc => doc}/images/batch_process.png (100%)
rename {xtandempipeline/doc => doc}/images/batch_process.xcf (100%)
rename {xtandempipeline/doc => doc}/images/batch_terminal.png (100%)
rename {xtandempipeline/doc => doc}/images/batch_xml_search.png (100%)
rename {xtandempipeline/doc => doc}/images/pappso.pdf (100%)
rename {xtandempipeline/doc => doc}/images/tandem_analysis.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_comparaison.pdf (100%)
rename {xtandempipeline/doc => doc}/images/tandem_comparaison.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_configuration.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_export.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_fdr.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_filter.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_parameter.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_peptide.pdf (100%)
rename {xtandempipeline/doc => doc}/images/tandem_peptide.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_principal.png (100%)
rename {xtandempipeline/doc => doc}/images/tandem_prot.pdf (100%)
rename {xtandempipeline/doc => doc}/images/tandem_prot.png (100%)
rename {xtandempipeline/doc => doc}/images/window_peptide.png (100%)
rename {xtandempipeline/doc => doc}/images/window_peptide_detail.png (100%)
rename {xtandempipeline/doc => doc}/images/window_protein.png (100%)
rename {xtandempipeline/doc => doc}/images/window_protein_detail.png (100%)
rename {xtandempipeline/doc => doc}/logo.svg (100%)
rename {xtandempipeline/doc => doc}/xtandem_pipeline.pdf (100%)
rename {xtandempipeline/doc => doc}/xtandem_pipeline.tex (100%)
rename {xtandempipeline/lib => lib}/PPClient.jar (100%)
rename {xtandempipeline/lib => lib}/batik/batik-anim-1.7.jar (100%)
rename {xtandempipeline/lib => lib}/batik/batik-awt-util-1.7.jar (100%)
rename {xtandempipeline/lib => lib}/batik/batik-bridge-1.7.jar (100%)
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diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java b/src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/filter_unique_peptide_number_to.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/printOdsBase.java b/src/fr/inra/pappso/xtandempipeline/filter_print/printOdsBase.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/printOdsBase.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/printOdsBase.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_base.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_base.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_base.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_base.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_group.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_group.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_group.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_group.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_subgroup.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_subgroup.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_subgroup.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_fasta_to_subgroup.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar_phospho.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar_phospho.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar_phospho.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_compar_phospho.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list_to_phosphopeptide.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list_to_phosphopeptide.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list_to_phosphopeptide.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_peptide_list_to_phosphopeptide.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_combined.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_combined.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_combined.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_combined.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_indiv.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_indiv.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_indiv.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_indiv.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_phosphopeptide.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_phosphopeptide.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_phosphopeptide.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_ods_protein_to_phosphopeptide.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java b/src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/print_pepnovo.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_base.java b/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_base.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_base.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_base.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java b/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_peptide.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java b/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java
rename to src/fr/inra/pappso/xtandempipeline/filter_print/swt_table_protein.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java b/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingBase.java b/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingBase.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingBase.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingBase.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java b/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/Group.java b/src/fr/inra/pappso/xtandempipeline/grouping/Group.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/Group.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/Group.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java b/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashKey4Groups.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashKey4Groups.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashKey4Groups.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashKey4Groups.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashKey4GroupsSet.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashKey4GroupsSet.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashKey4GroupsSet.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashKey4GroupsSet.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptide.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptide.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptide.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashPeptide.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProtein.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashProtein.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProtein.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashProtein.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScan.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScan.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScan.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScan.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetPhospho.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java b/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSetProt.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/SubGroup.java b/src/fr/inra/pappso/xtandempipeline/grouping/SubGroup.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/SubGroup.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/SubGroup.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/SubGroupSet.java b/src/fr/inra/pappso/xtandempipeline/grouping/SubGroupSet.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/SubGroupSet.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/SubGroupSet.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpMsSample.java b/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpMsSample.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpMsSample.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpMsSample.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPeptide.java b/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPeptide.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPeptide.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPeptide.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPhosphoModif.java b/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPhosphoModif.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPhosphoModif.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpPhosphoModif.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java b/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtMatch.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtein.java b/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtein.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtein.java
rename to src/fr/inra/pappso/xtandempipeline/grouping/interfaces/GrpProtein.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java b/src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java
rename to src/fr/inra/pappso/xtandempipeline/output/CsvRedundantPeptideOutput.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/IndentingXMLStreamWriter.java b/src/fr/inra/pappso/xtandempipeline/output/IndentingXMLStreamWriter.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/IndentingXMLStreamWriter.java
rename to src/fr/inra/pappso/xtandempipeline/output/IndentingXMLStreamWriter.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlOutput.java b/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlOutput.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlOutput.java
rename to src/fr/inra/pappso/xtandempipeline/output/MassChroQmlOutput.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlWriter.java b/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlWriter.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/MassChroQmlWriter.java
rename to src/fr/inra/pappso/xtandempipeline/output/MassChroQmlWriter.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java b/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
rename to src/fr/inra/pappso/xtandempipeline/output/OdsRedundantPeptideOutput.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlOutput.java b/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlOutput.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlOutput.java
rename to src/fr/inra/pappso/xtandempipeline/output/ProticDbMlOutput.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlWriter.java b/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlWriter.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/output/ProticDbMlWriter.java
rename to src/fr/inra/pappso/xtandempipeline/output/ProticDbMlWriter.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
rename to src/fr/inra/pappso/xtandempipeline/sax_parse/Mascot.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
rename to src/fr/inra/pappso/xtandempipeline/sax_parse/XtandemPhospho.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java
rename to src/fr/inra/pappso/xtandempipeline/sax_parse/load_project.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/msms_output.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/msms_output.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/msms_output.java
rename to src/fr/inra/pappso/xtandempipeline/sax_parse/msms_output.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/new_xtandem_param.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/new_xtandem_param.java
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rename to src/fr/inra/pappso/xtandempipeline/sax_parse/new_xtandem_param.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
similarity index 100%
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rename to src/fr/inra/pappso/xtandempipeline/sax_parse/parse_file.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/save_project.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/save_project.java
similarity index 100%
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rename to src/fr/inra/pappso/xtandempipeline/sax_parse/save_project.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xml_xtandem_param.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/xml_xtandem_param.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xml_xtandem_param.java
rename to src/fr/inra/pappso/xtandempipeline/sax_parse/xml_xtandem_param.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
similarity index 100%
rename from xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
rename to src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_ms2_spectra.java b/src/fr/inra/pappso/xtandempipeline/sax_parse/xtandem_ms2_spectra.java
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