Package org.bioinfo.ngs.qc.qualimap.gui.utils

Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.AnalysisDialogLoggerThread

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        String homePath = settingsDlg.getHomeFrame().getQualimapFolder() + File.separator;

        MultisampleBamQcAnalysis multiBamQcAnalysis = new MultisampleBamQcAnalysis(tabProperties, homePath,
                settingsDlg.getDataItems());
        AnalysisDialogLoggerThread outputParsingThread= new AnalysisDialogLoggerThread( settingsDlg ) ;
        multiBamQcAnalysis.setOutputParsingThread(outputParsingThread);

        if (settingsDlg.runBamQcFirst()) {
            multiBamQcAnalysis.setRunBamQcFirst( settingsDlg.getBamQcConfig() );
        }
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                infoFilePath =  homePath + "species" + File.separator + settingsDlg.getSelectedSpecies();
            }
            countsAnalysis.setInfoFilePath(infoFilePath);
        }

        AnalysisDialogLoggerThread outputParsingThread= new AnalysisDialogLoggerThread( settingsDlg ) ;
        countsAnalysis.setOutputParsingThread(outputParsingThread);

        try {
            countsAnalysis.run();
        } catch (Exception e) {
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    // reporting
    bamQC.activeReporting(outputDirPath.toString());

    // setup logging
        AnalysisDialogLoggerThread loggerThread = new AnalysisDialogLoggerThread(bamDialog);
        bamQC.setLoggerThread(loggerThread);

        bamDialog.setUiEnabled(false);
        bamDialog.getProgressStream().setText("Running BAM file analysis...");
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Related Classes of org.bioinfo.ngs.qc.qualimap.gui.utils.AnalysisDialogLoggerThread

  • org.bioinfo.ngs.qc.qualimap.gui.threads.BamAnalysisThread
  • org.bioinfo.ngs.qc.qualimap.gui.threads.CountsQCAnalysisThread
  • org.bioinfo.ngs.qc.qualimap.gui.threads.MultisampleBamQcThread
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