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

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

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

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

  public List<StatsKeeper.Section> getInputDataSections() {
        return inputDataKeeper.getSections();
    }


    private void prepareSummaryStatsKeeper() {
        StringUtilsSwing sdf = new StringUtilsSwing();
        String postfix = getNamePostfix();


        if (warnings != null && !warnings.isEmpty()) {
            StatsKeeper.Section warningsSection = new StatsKeeper.Section("Warnings");
            for (Map.Entry<String,String> entry : warnings.entrySet()) {
                warningsSection.addRow(entry.getKey(), entry.getValue());
            }
            summaryStatsKeeper.addSection(warningsSection);
        }


        StatsKeeper.Section globals = new StatsKeeper.Section("Globals");


        globals.addRow("Reference size", sdf.formatLong(referenceSize));


        globals.addRow("Number of reads", sdf.formatLong(numReads));


        globals.addRow("Mapped reads", sdf.formatLong(numMappedReads)
                + " / " + sdf.formatPercentage(getPercentMappedReads()));


        globals.addRow("Unmapped reads",
                sdf.formatLong(numReads - numMappedReads) + " / "
                        + sdf.formatPercentage(100.0 - getPercentMappedReads()));


        globals.addRow("Paired reads",
                sdf.formatLong(numPairedReads) + " / "
                        + sdf.formatPercentage(percantagePairedReads) );
        if (numPairedReads > 0) {


            globals.addRow("Mapped reads, only first in pair",
                    sdf.formatLong(numberOfMappedFirstOfPair) + " / " +
                    sdf.formatPercentage(percentageOfMappedFirstOfPair));


            globals.addRow("Mapped reads, only second in pair",
                    sdf.formatLong(numberOfMappedSecondOfPair) + " / " +
                    sdf.formatPercentage(percentageOfMappedSecondOfPair));


            globals.addRow("Mapped reads, both in pair",
                                       sdf.formatLong(numPairedReads - numSingletons) + " / "
                                               + sdf.formatPercentage((getPercentageBothMatesPaired())));


              globals.addRow("Mapped reads, singletons",
                    sdf.formatLong(numSingletons) + " / "
                            + sdf.formatPercentage(getPercentSingletons()));
             }


        globals.addRow("Read min/max/mean length",
                sdf.formatLong(readMinSize) + " / "
                        + sdf.formatLong(readMaxSize) + " / "
                        + sdf.formatDecimal(readMeanSize));


        if (numSelectedRegions == 0) {


            globals.addRow("Clipped reads",
                        sdf.formatInteger(numClippedReads) + " / " +
                        sdf.formatPercentage(getPercentageClippedReads()));
            globals.addRow("Duplication rate", sdf.formatPercentage(duplicationRate));
        }




        summaryStatsKeeper.addSection(globals);


        if (numSelectedRegions > 0) {
            StatsKeeper.Section globalsInRegions = new StatsKeeper.Section("Globals" + postfix);
            globalsInRegions.addRow("Regions size/percentage of reference",
                    sdf.formatLong((numBasesInsideRegions))
                            + " / " + sdf.formatPercentage(getSelectedRegionsPercentage()));




            globalsInRegions.addRow("Mapped reads",
                    sdf.formatLong(numMappedReadsInRegions)
                            + "  /  " + sdf.formatPercentage(percentageMappedReadsInRegions));
            if (numPairedReads > 0) {
                globalsInRegions.addRow("Mapped reads, only first in pair",
                        sdf.formatLong(numMappedFirstOfPairInRegions) + " / " +
                                sdf.formatPercentage(percentageOfMappedFirstOfPairInRegions));


                globalsInRegions.addRow("Mapped reads, only second in pair",
                        sdf.formatLong(numMappedSecondOfPairInRegions) + " / " +
                                sdf.formatPercentage(percentageOfMappedSecondOfPairInRegions));
                globalsInRegions.addRow("Mapped reads, both in pair",
                                   sdf.formatLong(numPairedReadsInRegions - numSingletonsInRegions) + " / "
                                        + sdf.formatPercentage((getPercentageBothMatesPairedInRegions())));
                globalsInRegions.addRow("Mapped reads, singletons",
                        sdf.formatLong(numSingletonsInRegions) + " / "
                                + sdf.formatPercentage(percentageSingletonsInRegions));




                globalsInRegions.addRow("Correct strand reads",
                        sdf.formatLong(numCorrectStrandReads) + " / " +
                        sdf.formatPercentage(percentageCorrectStrandReads) );




                globalsInRegions.addRow("Clipped reads",
                                    sdf.formatInteger(numClippedReads) + " / " +
                                    sdf.formatPercentage(getPercentageClippedReads()));
                globalsInRegions.addRow("Duplication rate", sdf.formatPercentage(duplicationRate));


            }


            summaryStatsKeeper.addSection(globalsInRegions);


        }


        StatsKeeper.Section acgtContent = new StatsKeeper.Section("ACGT Content" + postfix);


        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()));


        summaryStatsKeeper.addSection(acgtContent);






    StatsKeeper.Section coverageSection = new StatsKeeper.Section("Coverage" + postfix);
    coverageSection.addRow("Mean", sdf.formatDecimal(meanCoverage));
    coverageSection.addRow("Standard Deviation",sdf.formatDecimal(stdCoverage) );
    summaryStatsKeeper.addSection(coverageSection);


    StatsKeeper.Section mappingQualitySection = new StatsKeeper.Section("Mapping Quality" + postfix);
    mappingQualitySection.addRow("Mean Mapping Quality", sdf.formatDecimal(meanMappingQuality));
    summaryStatsKeeper.addSection(mappingQualitySection);


        if (meanInsertSize != 0)
        {
            StatsKeeper.Section insertSizeSection = new StatsKeeper.Section("Insert size" + postfix);
            insertSizeSection.addRow("Mean", sdf.formatDecimal(meanInsertSize));
            insertSizeSection.addRow("Standard Deviation", sdf.formatDecimal(stdInsertSize));
            insertSizeSection.addRow("P25/Median/P75", sdf.formatDecimal(p25InsertSize) + " / " +
                    sdf.formatDecimal(medianInsertSize) + " / " + sdf.formatDecimal(p75InsertSize));
            summaryStatsKeeper.addSection(insertSizeSection);
        }


        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));
            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);


        }

View Full Code Here


    private void prepareHtmlSummary(StatsReporter reporter) {




        StatsKeeper summaryKeeper = reporter.getSummaryStatsKeeper();
        StringUtilsSwing sdf = new StringUtilsSwing();
        TranscriptDataHandler th = computeCountsTask.getTranscriptDataHandler();


        StatsKeeper.Section readsAlignment = new StatsKeeper.Section("Reads alignment");


        readsAlignment.addRow("Aligned to genes:", sdf.formatLong(computeCountsTask.getTotalReadCounts()));
        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();
        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
        /*if (computeCountsTask.getLibraryProtocol() != LibraryProtocol.NON_STRAND_SPECIFIC) {
            StatsKeeper.Section libraryProtocol = new StatsKeeper.Section("Library protocol");
            double correctlyMappedPercentage =
                    (100.*computeCountsTask.getProtocolCorrectlyMapped()) / computeCountsTask.getTotalFragmentCount() ;
            libraryProtocol.addRow("Concordant fragments: ",
                    sdf.formatLong(computeCountsTask.getProtocolCorrectlyMapped()) + " / " +
                    sdf.formatPercentage(correctlyMappedPercentage));
        }*/




        TranscriptDataHandler transcriptDataHandler = computeCountsTask.getTranscriptDataHandler();
        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) {
            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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