Examples of org.broad.igv.feature.CachingFeatureSource

org.broad.igv.feature.CachingFeatureSource
A FeatureSource wrapper which provides caching. The cache is only cleared when the source is closed. @author jacob @date 2012/05/15

        DBProfile dbProfile = DBProfile.parseProfile(profileLocator.getPath());


        for (DBProfile.DBTable table : dbProfile.getTableList()) {
            SQLCodecSource source = SQLCodecSource.getFromTable(table);
            if (source != null) {
                CachingFeatureSource cachingReader = new CachingFeatureSource(source);
                FeatureTrack track = new FeatureTrack(profileLocator, cachingReader);
                track.setName(source.getTableName());
                newTracks.add(track);
            } else if (table.getFormat().equals("seg")) {
                Genome genome = GenomeManager.getInstance().getCurrentGenome();

View Full Code Here

            Track newTrack = null;
            switch (outputAttr.type) {
                case FEATURE_TRACK:
                    PluginFeatureSource featSource1 = new PluginFeatureSource(cmdList, argumentValues, outputAttr, specPath, this.forbidEmptyOutput);
                    //featSource1.setQueryTracker(queryTracker);
                    FeatureSource featSource = new CachingFeatureSource(featSource1);
                    newTrack = new FeatureTrack(UUID.randomUUID().toString(), name, featSource);
                    break;
                case DATA_SOURCE_TRACK:
                    PluginDataSource dataSource = new PluginDataSource(GenomeManager.getInstance().getCurrentGenome(), cmdList, argumentValues, outputAttr, specPath);
                    //dataSource.setQueryTracker(queryTracker);
                    newTrack = new DataSourceTrack(null, UUID.randomUUID().toString(), name, dataSource);
                    break;
                case VARIANT_TRACK:
                    PluginFeatureSource VfeatSource1 = new PluginFeatureSource(cmdList, argumentValues, outputAttr, specPath, this.forbidEmptyOutput);
                    FeatureSource VfeatSource = new CachingFeatureSource(VfeatSource1);
                    newTrack = new VariantTrack(name, VfeatSource);
                    break;
            }
            newTracks.add(newTrack);
        }

View Full Code Here

                for(int ci=0; ci < curTrackNames.length; ci++){
                    String tName = curTrackNames[ci];
                    if(tName == null) continue;


                    MotifFinderSource src = new MotifFinderSource(pattern, strands[ci], GenomeManager.getInstance().getCurrentGenome());
                    CachingFeatureSource cachingSrc= new CachingFeatureSource(src);


                    FeatureTrack track = new FeatureTrack(tName, tName, cachingSrc);
                    if(colors[ci] != null) track.setColor(colors[ci]);


                    track.setDisplayMode(Track.DisplayMode.SQUISHED);

View Full Code Here

TOP

Related Classes of org.broad.igv.feature.CachingFeatureSource

org.broad.igv.cli_plugin.ui.RunPlugin

org.broad.igv.tools.motiffinder.MotifFinderPlugin

org.broad.igv.track.TrackLoader

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.