Package org.broad.igv.cli_plugin

Examples of org.broad.igv.cli_plugin.PluginSpecReader$Tool

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        String userDir = System.getProperty("user.dir");

        String grammarName = userDir + "\\src\\main\\antlr4\\org\\ethereum\\serpent\\Serpent.g4";

        String options[] = {grammarName, "-visitor",  "-package", "org.ethereum.serpent"};
        Tool tool = new Tool(options);
        tool.outputDirectory = userDir + "\\src\\main\\java\\org\\ethereum\\serpent\\";
        tool.processGrammarsOnCommandLine();

//        org.antlr.Tool.main(new String[]{userDir + "\\src\\main\\antlr4\\org\\ethereum\\serpent\\Serpent.g4"});
    }
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        String trackAname = "GSM1004654_100k.bed";
        String trackBname = "GSM1004654_10k.bed";

        //Generate bedtools subtraction track
        PluginSpecReader reader = PluginSpecReader.create(toolPath);
        PluginSpecReader.Tool tool = reader.getTools().get(0);
        PluginSpecReader.Command command = AbstractPluginTest.findCommandElementByName(tool, "Subtract");
    }
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*/
public class RunPluginTest extends AbstractHeadedTest {

    @Test
    public void testCatPlugin() throws Exception {
        PluginSpecReader catReader = AbstractPluginTest.getCatReader();
        AbstractPluginTest.initTool(catReader);

        PluginSpecReader.Tool tool = catReader.getTools().get(0);
        PluginSpecReader.Command command = tool.commandList.get(0);
        RunPlugin rp = new RunPlugin(IGV.getMainFrame(), catReader, tool, command);

        int numTracksBefore = IGV.getInstance().getAllTracks().size();
        rp.okButtonActionPerformed(null);
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