List of formatPercentage() Examples

Examples of formatPercentage()

org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

        acgtContent.addRow("Number/percentage of A's", sdf.formatLong(getaNumber()) +
                " / " + sdf.formatPercentage(getaPercent()));
    acgtContent.addRow("Number/percentage of C's",sdf.formatLong(getcNumber()) +
                " / " + sdf.formatPercentage(getcPercent()));
    acgtContent.addRow("Number/percentage of T's", sdf.formatLong(gettNumber()) +
                " / " + sdf.formatPercentage(gettPercent()));
    acgtContent.addRow("Number/percentage of G's",sdf.formatLong(getgNumber()) +
                " / " + sdf.formatPercentage(getgPercent()));
    acgtContent.addRow("Number/percentage of N's",sdf.formatLong(getnNumber()) +
                " / " + sdf.formatPercentage(getnPercent()));
    acgtContent.addRow("GC Percentage", sdf.formatPercentage(getGcPercent()));

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

    acgtContent.addRow("Number/percentage of C's",sdf.formatLong(getcNumber()) +
                " / " + sdf.formatPercentage(getcPercent()));
    acgtContent.addRow("Number/percentage of T's", sdf.formatLong(gettNumber()) +
                " / " + sdf.formatPercentage(gettPercent()));
    acgtContent.addRow("Number/percentage of G's",sdf.formatLong(getgNumber()) +
                " / " + sdf.formatPercentage(getgPercent()));
    acgtContent.addRow("Number/percentage of N's",sdf.formatLong(getnNumber()) +
                " / " + sdf.formatPercentage(getnPercent()));
    acgtContent.addRow("GC Percentage", sdf.formatPercentage(getGcPercent()));


        summaryStatsKeeper.addSection(acgtContent);

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

    acgtContent.addRow("Number/percentage of T's", sdf.formatLong(gettNumber()) +
                " / " + sdf.formatPercentage(gettPercent()));
    acgtContent.addRow("Number/percentage of G's",sdf.formatLong(getgNumber()) +
                " / " + sdf.formatPercentage(getgPercent()));
    acgtContent.addRow("Number/percentage of N's",sdf.formatLong(getnNumber()) +
                " / " + sdf.formatPercentage(getnPercent()));
    acgtContent.addRow("GC Percentage", sdf.formatPercentage(getGcPercent()));


        summaryStatsKeeper.addSection(acgtContent);

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

                " / " + sdf.formatPercentage(gettPercent()));
    acgtContent.addRow("Number/percentage of G's",sdf.formatLong(getgNumber()) +
                " / " + sdf.formatPercentage(getgPercent()));
    acgtContent.addRow("Number/percentage of N's",sdf.formatLong(getnNumber()) +
                " / " + sdf.formatPercentage(getnPercent()));
    acgtContent.addRow("GC Percentage", sdf.formatPercentage(getGcPercent()));


        summaryStatsKeeper.addSection(acgtContent);

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()


        int numIndels = numInsertions + numDeletions;
        if ( numIndels > 0 || numMismatches > 0 || alignmentErrorRate > 0) {
            StatsKeeper.Section indelsSection = new StatsKeeper.Section("Mismatches and indels" + postfix);
            if (alignmentErrorRate > 0) {
                indelsSection.addRow("General error rate", sdf.formatPercentage(alignmentErrorRate * 100.0));
            }
            if (numMismatches > 0) {
                indelsSection.addRow("Mismatches",sdf.formatDecimal(numMismatches));
            }
            //indelsSection.addRow("Total reads with indels", sdf.formatInteger(numIndels));

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

            }
            //indelsSection.addRow("Total reads with indels", sdf.formatInteger(numIndels));
            if (numIndels > 0) {
                indelsSection.addRow("Insertions",sdf.formatDecimal(numInsertions) );
                indelsSection.addRow("Deletions",sdf.formatDecimal(numDeletions) );
                indelsSection.addRow("Homopolymer indels",sdf.formatPercentage(homopolymerIndelFraction * 100.0) );
            }


            summaryStatsKeeper.addSection(indelsSection);


        }

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

        long totalReadCount = computeCountsTask.getTotalReadCounts() + computeCountsTask.getNoFeatureNumber();
        long exonicReadCount = totalReadCount - computeCountsTask.getNoFeatureNumber();
        long intronicReadCount = th.getNumIntronicReads();
        long intergenicReadCount = th.getNumIntergenicReads();
        readsOrigin.addRow("Exonic: ", sdf.formatLong(exonicReadCount) + " / " +
                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);

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

        long intronicReadCount = th.getNumIntronicReads();
        long intergenicReadCount = th.getNumIntergenicReads();
        readsOrigin.addRow("Exonic: ", sdf.formatLong(exonicReadCount) + " / " +
                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

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

        readsOrigin.addRow("Exonic: ", sdf.formatLong(exonicReadCount) + " / " +
                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");

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Examples of org.bioinfo.ngs.qc.qualimap.gui.utils.StringUtilsSwing.formatPercentage()

            List<JunctionInfo> junctionList = th.computeSortedJunctionsMap();


            int count = 0;
            for(int i = junctionList.size() -1; i >= 0 && count <= 10; i--){
                JunctionInfo info = junctionList.get(i);
                junctionAnalysisSection.addRow(info.getJunctionString(), sdf.formatPercentage(info.getPercentage()));
                count += 1;
            }


        }
        summaryKeeper.addSection(junctionAnalysisSection);

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