List of loadReportData() Examples

Examples of loadReportData()

org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.loadReportData()
Function to load the data variables obtained from the input file/s @param bamStats data read in the input file

Examples of org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.loadReportData()

            BamQCRegionReporter bamQcReporter = new BamQCRegionReporter(false, true);




            try {
                bamQc.run();
                bamQcReporter.loadReportData(bamQc.getBamStats());
                bamQcReporter.computeChartsBuffers(bamQc.getBamStats(), bamQc.getLocator(), bamQc.isPairedData());
            } catch (Exception e) {
                assertTrue("Error calculating stats. " + e.getMessage(), false);
                e.printStackTrace();
                return;

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Examples of org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.loadReportData()


            compareProperties(calculatedProps, test.getResultsPath());


            if (test.getComputeOutsideStats() && test.getOutsideResultsPath() != null) {
                BamQCRegionReporter outsideReporter = new BamQCRegionReporter(true, false);
                outsideReporter.loadReportData(bamQc.getOutsideBamStats());
                /*outsideReporter.computeChartsBuffers(bamQc.getOutsideBamStats(),
                        bamQc.getLocator(), bamQc.isPairedData());*/
                Properties outsideProps = outsideReporter.generateBamQcProperties();


                /*try {

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Examples of org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.loadReportData()


        reporter.writeReport(bamQC.getBamStats(),outdir);


        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.BAM_QC);


        reporter.loadReportData(bamQC.getBamStats());
        reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        resultManager.addReporter(reporter);


        if(selectedRegionsAvailable && computeOutsideStats){

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Examples of org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.loadReportData()

                outsideReporter.setGenomeGCContentName(genomeToCompare);
            }
            bamQC.prepareInputDescription(outsideReporter, paintChromosomeLimits);
            outsideReporter.writeReport(bamQC.getOutsideBamStats(),outdir);


            outsideReporter.loadReportData(bamQC.getOutsideBamStats());
            outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());


            resultManager.addReporter(outsideReporter);
        }

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Examples of org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.loadReportData()

                String genomeName = bamDialog.getGenomeName();
                reporter.setGenomeGCContentName(genomeName);
            }


      bamDialog.getProgressStream().setText("   text report...");
      reporter.loadReportData(bamQC.getBamStats());
      bamDialog.getProgressStream().setText("OK");


      bamDialog.getProgressStream().setText("   charts...");
      reporter.computeChartsBuffers(bamQC.getBamStats(), bamQC.getLocator(), bamQC.isPairedData());
        bamDialog.getProgressStream().setText("OK");

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Examples of org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.loadReportData()

                    outsideReporter.setGenomeGCContentName(genomeName);
                }


        // save stats
        bamDialog.getProgressStream().setText("   outside text report...");
        outsideReporter.loadReportData(bamQC.getOutsideBamStats());
        bamDialog.getProgressStream().setText("OK");


        // save charts
        bamDialog.getProgressStream().setText("   outside charts...");
        outsideReporter.computeChartsBuffers(bamQC.getOutsideBamStats(), bamQC.getLocator(), bamQC.isPairedData());

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