Package org.broad.igv.cli_plugin

Examples of org.broad.igv.cli_plugin.PluginFeatureSource


            String name = (String) outputComponents.get(outputAttr).getValue();

            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);
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