Package org.broad.igv.tdf

Examples of org.broad.igv.tdf.TDFDataSource

682
683
684
685
686
687
688
689
690
691
692
            String trackId = multiTrack ? path + "_" + heading : path;
            String trackName = multiTrack ? heading : name;
            final DataSource dataSource = locator.getPath().endsWith(".counts") ?
                    new GobyCountArchiveDataSource(locator) :
                    new TDFDataSource(reader, trackNumber, heading, genome);
            DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);

            String displayName = (name == null || multiTrack) ? heading : name;
            track.setName(displayName);
            track.setTrackType(type);
View Full Code Here
905
906
907
908
909
910
911
912
913
914
915
                }
                if (covPath != null) {
                    if (FileUtils.resourceExists(covPath)) {
                        log.debug("Loading TDF for coverage: " + covPath);
                        TDFReader reader = TDFReader.getReader(covPath);
                        TDFDataSource ds = new TDFDataSource(reader, 0, alignmentTrack.getName() + " coverage", genome);
                        covTrack.setDataSource(ds);
                    }

                }
            }
View Full Code Here
545
546
547
548
549
550
551
552
553
554
555
        if (timeSignalSources == null) {
            if (timeSignalPaths != null && timeSignalPaths.length > 0) {
                timeSignalSources = new WrappedDataSource[timeSignalPaths.length];
                for (int i = 0; i < timeSignalPaths.length; i++) {
                    try {
                        timeSignalSources[i] = new WrappedDataSource(new TDFDataSource(TDFReader.getReader(timeSignalPaths[i]), 0, "", genome));
                        timeSignalSources[i].setNormalizeCounts(true, 1.0e9f);
                    } catch (Exception e) {
                        timeSignalSources[i] = null;
                        e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                    }
View Full Code Here
580
581
582
583
584
585
586
587
588
589
590
    WrappedDataSource getSignalSource(final String chr, final int contextStart, final int contextEnd, final int zoom) {
        if (signalSource == null && signalPath != null && !signalSourceLoading) {
            signalSourceLoading = true;
            NamedRunnable runnable = new NamedRunnable() {
                public void run() {
                    signalSource = new WrappedDataSource(new TDFDataSource(TDFReader.getReader(signalPath), 0, "", genome));
                    signalSource.setNormalizeCounts(true, 1.0e9f);
                    signalSource.getSummaryScoresForRange(chr, contextStart, contextEnd, zoom);
                }

                public String getName() {
View Full Code Here
800
801
802
803
804
805
806
807
808
809
810
                if (file != null) {
                    prefs.setLastTrackDirectory(file.getParentFile());
                    String path = file.getAbsolutePath();
                    if (path.endsWith(".tdf") || path.endsWith(".tdf")) {
                        TDFReader reader = TDFReader.getReader(file.getAbsolutePath());
                        TDFDataSource ds = new TDFDataSource(reader, 0, getName() + " coverage", genome);
                        setDataSource(ds);
                        IGV.getInstance().repaintDataPanels();
                    } else if (path.endsWith(".counts")) {
                        CoverageDataSource ds = new GobyCountArchiveDataSource(file);
                        setDataSource(ds);
View Full Code Here
393
394
395
396
397
398
399
400
401
    }

    private float getCount(String filename, String chr, int zoom, int pos, Genome genome) {
        TDFReader reader = TDFReader.getReader(filename);
        TDFDataset ds = reader.getDataset(chr, zoom, WindowFunction.mean);
        TDFDataSource dataSource = new TDFDataSource(reader, 0, "test", genome);
        List<LocusScore> scores = dataSource.getSummaryScoresForRange(chr, pos - 1, pos + 1, zoom);
        return scores.get(0).getScore();
    }
View Full Code Here
2018
2019
2020
2021
2022
2023
2024
2025
2026
2027
2028
                            if (file != null) {
                                prefs.setLastTrackDirectory(file.getParentFile());
                                String path = file.getAbsolutePath();
                                if (path.endsWith(".tdf") || path.endsWith(".tdf")) {
                                    TDFReader reader = TDFReader.getReader(file.getAbsolutePath());
                                    TDFDataSource ds = new TDFDataSource(reader, 0, getName() + " coverage", genome);
                                    getCoverageTrack().setDataSource(ds);
                                    refresh();
                                } else if (path.endsWith(".counts")) {
                                    CoverageDataSource ds = new GobyCountArchiveDataSource(file);
                                    getCoverageTrack().setDataSource(ds);
View Full Code Here
151
152
153
154
155
156
157
158
    }

    private void initCoverageSource(String covPath) {
        if (ParsingUtils.pathExists(covPath)) {
            TDFReader reader = TDFReader.getReader(covPath);
            coverageSource = new TDFDataSource(reader, 0, "", genome);
        }
    }
View Full Code Here
48
49
50
51
52
53
54
55
56
57
58
59
60
61
    public EWigTrack(ResourceLocator locator, Genome genome) {
        super(locator);

        TDFReader reader = TDFReader.getReader(locator.getPath());
        scoreSource = new TDFDataSource(reader, 4, "Pi", genome);

        setDataRange(new DataRange(0, 0, 10));
        baseSources = new HashMap();
        for (int i = 0; i < 4; i++) {
            TDFDataSource src = new TDFDataSource(reader, i, Character.toString(nucleotides[i]), genome);
            baseSources.put(nucleotides[i], src);
        }
    }
View Full Code Here
TOP

Related Classes of org.broad.igv.tdf.TDFDataSource

  • org.broad.igv.data.BasicScore
  • org.broad.igv.data.CompositeScore
  • org.broad.igv.data.NamedScore
  • org.broad.igv.feature.Chromosome
  • org.broad.igv.feature.LocusScore
  • org.broad.igv.peaks.PeakTrack
  • org.broad.igv.sam.AlignmentTrack$PopupMenu
  • org.broad.igv.sam.CoverageTrack
  • org.broad.igv.sam.EWigTrack
  • org.broad.igv.tools.IGVToolsCountTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.