diff --git a/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java b/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java index dcec61e9f8049bfdaebe62e333f48fdea1815915..f01d96196ea816366b2c9febccd212eb1434831a 100644 --- a/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java +++ b/src/fr/inra/pappso/xtandempipeline/thread/printing_base.java @@ -190,6 +190,8 @@ public class printing_base extends process { this.printComparSpectra(odsDoc); logger.debug("Print new spectra specific"); this.printComparSpecificSpectra(odsDoc); + logger.debug("Print new compar pai"); + this.printComparPai(odsDoc); logger.debug("Print new spectra (expert)"); this.printSpectraList(odsDoc); @@ -209,6 +211,10 @@ public class printing_base extends process { this.add_current_progress(); } + protected void printComparPai(OdsDocWriter odsDoc) throws Exception { + + } + protected void printComparSpecificSpectra(OdsDocWriter odsDoc) throws Exception { } diff --git a/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java b/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java index c9ed21cda05bc61e8f2cd356ff5c37dcb5b229e9..65c37c584b4b545612ab3168aaea102f70017882 100644 --- a/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java +++ b/src/fr/inra/pappso/xtandempipeline/thread/printing_combine.java @@ -5,6 +5,7 @@ import fr.inra.pappso.libodsstream.OdsDocWriter; import fr.inra.pappso.xtandempipeline.MsException.StopException; import fr.inra.pappso.xtandempipeline.class_msms.config; import fr.inra.pappso.xtandempipeline.class_msms.Identification; +import fr.inra.pappso.xtandempipeline.output.SpreadSheets.OdsComparPaiOutput; import fr.inra.pappso.xtandempipeline.output.SpreadSheets.OdsComparSpecificSpectraOutput; import fr.inra.pappso.xtandempipeline.output.SpreadSheets.OdsComparSpectraOutput; @@ -14,6 +15,40 @@ public class printing_combine extends printing_base { super(conf); } + @Override + protected void printComparPai(OdsDocWriter odsDoc) throws Exception { + logger.debug("printComparPai begin"); + + // Verification pas arrete + if (this.isStop()) + throw new StopException(""); + this.add_current_progress(); + + this.set_view("Printing compar PAI results"); + if (this.isCsv) { + Ods2Csv ods2csv = new Ods2Csv(); + ods2csv.setSinkFilename(this.getfileout().getAbsolutePath() + + "_compar_pai.txt"); + + odsDoc = ods2csv.getOdsDocPipedOutput(); + } else { + } + + OdsComparPaiOutput writer = new OdsComparPaiOutput(odsDoc); + // output.open(this.getfileout().getAbsolutePath() + "_compar.txt"); + for (Identification ident : this.identifications) { + this.writeMsSampleName(ident, odsDoc); + writer.write(ident); + } + logger.debug("printComparPai end"); + + if (this.isCsv) { + odsDoc.close(); + logger.debug("csv file closed " + + this.getfileout().getAbsolutePath() + "_compar_pai.txt"); + } + } + @Override protected void printComparSpectra(OdsDocWriter odsDoc) throws Exception { logger.debug("printComparSpectra begin");