Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper.addSection()

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

Class org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper

Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper.addSection()

org.bioinfo.ngs.qc.qualimap.gui.utils.StatsKeeper.addSection()


        StatsKeeper summaryKeeper = reporter.getSummaryStatsKeeper();


        StatsKeeper.Section section = new StatsKeeper.Section("Globals");
        section.addRow("Number of samples", Integer.toString( bamQCResults.size() ));
        summaryKeeper.addSection(section);


        StatsKeeper tableDataKeeper = reporter.getTableDataStatsKeeper();


        StatsKeeper.Section headerSection = new StatsKeeper.Section("header");
        String[] header = {"Sample name", "Coverage mean", "Coverage std",

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        StatsKeeper.Section headerSection = new StatsKeeper.Section("header");
        String[] header = {"Sample name", "Coverage mean", "Coverage std",
                "GC percentage", "Mapping quality mean", "Insert size median" };
        headerSection.addRow( header );
        tableDataKeeper.addSection(headerSection);


        StatsKeeper.Section dataSection = new StatsKeeper.Section("data");


        for (SampleInfo bamQcResult : bamQCResults) {
            String path = bamQcResult.path + File.separator + "genome_results.txt";

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            sample[4] = stats.getMedianInsertSize();
            sampleData.add(sample);




        }
        tableDataKeeper.addSection(dataSection);






    }

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        readsAlignment.addRow("No feature assigned:", sdf.formatLong(computeCountsTask.getNoFeatureNumber()));
        readsAlignment.addRow("Non-unique alignment:", sdf.formatLong(computeCountsTask.getAlignmentNotUniqueNumber()));
        readsAlignment.addRow("Ambiguous alignment:", sdf.formatLong(computeCountsTask.getAmbiguousNumber()));
        readsAlignment.addRow("Not aligned:", sdf.formatLong(computeCountsTask.getNotAlignedNumber()));


        summaryKeeper.addSection(readsAlignment);


        StatsKeeper.Section readsOrigin = new StatsKeeper.Section("Reads genomic origin");
        long totalReadCount = computeCountsTask.getTotalReadCounts() + computeCountsTask.getNoFeatureNumber();
        long exonicReadCount = totalReadCount - computeCountsTask.getNoFeatureNumber();
        long intronicReadCount = th.getNumIntronicReads();

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                sdf.formatPercentage( (100.*exonicReadCount) /  totalReadCount ));
        readsOrigin.addRow("Intronic: ", sdf.formatLong(intronicReadCount) + " / " +
                sdf.formatPercentage( (100.*intronicReadCount) /  totalReadCount ));
        readsOrigin.addRow("Intergenic: ", sdf.formatLong(intergenicReadCount) + " / " +
                sdf.formatPercentage( (100.*intergenicReadCount) /  totalReadCount ));
        summaryKeeper.addSection(readsOrigin);


        //TODO: fix this in case of SE reads
        /*if (computeCountsTask.getLibraryProtocol() != LibraryProtocol.NON_STRAND_SPECIFIC) {
            StatsKeeper.Section libraryProtocol = new StatsKeeper.Section("Library protocol");
            double correctlyMappedPercentage =

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        StatsKeeper.Section transcriptCoverage = new StatsKeeper.Section("Transcript coverage profile");
        transcriptCoverage.addRow("5' bias:", sdf.formatDecimal(transcriptDataHandler.getMedianFivePrimeBias()));
        transcriptCoverage.addRow("3' bias:", sdf.formatDecimal(transcriptDataHandler.getMedianThreePrimeBias()));
        transcriptCoverage.addRow("5'-3' bias:", sdf.formatDecimal(transcriptDataHandler.getMedianFiveToThreeBias()));


        summaryKeeper.addSection(transcriptCoverage);


        StatsKeeper.Section junctionAnalysisSection = new StatsKeeper.Section("Junction analysis");
        long numReadsWithJunctions = th.getNumReadsWithJunctions();
        junctionAnalysisSection.addRow("Reads at junctions:", sdf.formatLong(numReadsWithJunctions));
        if (numReadsWithJunctions > 0) {

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                junctionAnalysisSection.addRow(info.getJunctionString(), sdf.formatPercentage(info.getPercentage()));
                count += 1;
            }


        }
        summaryKeeper.addSection(junctionAnalysisSection);








    }

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