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+23,11 @@ package fr.inra.pappso.xtandempipeline.output; -import java.io.IOException; import java.io.OutputStream; -import java.io.PipedInputStream; -import java.io.PipedOutputStream; - -import javax.xml.datatype.DatatypeConfigurationException; -import javax.xml.stream.XMLStreamException; import org.apache.log4j.Logger; import fr.inra.pappso.csv2ods.Ods2Csv; -import fr.inra.pappso.libodsstream.OdsDocWriter; import fr.inra.pappso.xtandempipeline.MsException.MSMSException; public class CsvRedundantPeptideOutput extends OdsRedundantPeptideOutput { @@ -44,29 +37,12 @@ public class CsvRedundantPeptideOutput extends OdsRedundantPeptideOutput { public CsvRedundantPeptideOutput(OutputStream outputStream) throws MSMSException { + ods2csv = new Ods2Csv(); try { - - PipedOutputStream pos = new PipedOutputStream(); - PipedInputStream pis = new PipedInputStream(pos); - - odsTable = new OdsDocWriter(pos); - - ods2csv = new Ods2Csv(); - ods2csv.setSourceInputStream(pis); - ods2csv.setSinkOutputStream(outputStream); - //ods2csv.setSeparator('\t'); - (new Thread(ods2csv)).start(); - //ods2csv.run(); - } catch (IOException e) { - String message = "IOException " + e.getMessage(); - logger.error(message); - throw new MSMSException(message); - } catch (XMLStreamException e) { - String message = "XMLStreamException " + e.getMessage(); - logger.error(message); - throw new MSMSException(message); - } catch (DatatypeConfigurationException e) { - String message = "DatatypeConfigurationException " + e.getMessage(); + odsTable = ods2csv.getOdsDocPipedOutput(outputStream); + } catch (Exception e) { + String message = "error getting OdsDocPipedOutput " + + e.getMessage(); logger.error(message); throw new MSMSException(message); } -- GitLab