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

Package org.bioinfo.ngs.qc.qualimap.beans

Class org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter

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

org.bioinfo.ngs.qc.qualimap.beans.BamQCRegionReporter.computeChartsBuffers()
Create all the charts from the input file/s and save each of them into a bufferedImage @param bamStats BamStats class that contains the information of the graphics titles @param locator Genomic locator @param isPairedData Paired data identifier @throws IOException Error during computation




            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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        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){


            BamQCRegionReporter outsideReporter = new BamQCRegionReporter(selectedRegionsAvailable, false);

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            }
            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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      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");




      // Set the reporter into the created tab
      resultManager.addReporter(reporter);

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        outsideReporter.loadReportData(bamQC.getOutsideBamStats());
        bamDialog.getProgressStream().setText("OK");


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


        // Set the reporters into the created tab
        resultManager.addReporter(outsideReporter);
            }

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