Examples of org.broad.igv.goby.GobyCountArchiveDataSource

org.broad.igv.goby.GobyCountArchiveDataSource
campagnelab.org">Goby compressed base-level histograms (.counts files). @author Fabien CampagneDate: 6/10/11 Time: 3:18 PM

        for (String heading : reader.getTrackNames()) {


            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);

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        }




        String trackId = locator.getSampleId() + " coverage";
        String trackName = locator.getFileName();
        final DataSource dataSource = new GobyCountArchiveDataSource(locator);


        DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);


        newTracks.add(track);

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                        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);
                        IGV.getInstance().repaintDataPanels();
                    } else {
                        MessageUtils.showMessage("Coverage data must be in .tdf format");
                    }

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                                    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);
                                    refresh();
                                } else {
                                    MessageUtils.showMessage("Coverage data must be in .tdf format");
                                }

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