Package org.broad.igv.cli_plugin

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

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        super.setUp();
        WorkspaceImpl wsp = (WorkspaceImpl) superuser.getWorkspace();
        QueryManagerImpl qm = (QueryManagerImpl) wsp.getQueryManager();
        QueryObjectModelFactoryImpl factory = (QueryObjectModelFactoryImpl) qm
                .getQOMFactory();
        parser = new Parser(factory, superuser.getValueFactory());
    }
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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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  private ManifestParseTree parse(InputStream inputStream) throws IOException, TokenizerException, ParserException {
    Preprocessor preprocessor = new ManifestPreprocessor();
    List<InputLine> contents = preprocessor.process(inputStream);
    Tokenizer tokenizer = new ManifestTokenizer(contents);

    Parser parser = new ManifestParser();
    return parser.parse(tokenizer);
  }
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  private ManifestParseTree parse(InputStream inputStream) throws IOException, TokenizerException, ParserException {
    Preprocessor preprocessor = new ManifestPreprocessor();
    List<InputLine> contents = preprocessor.process(inputStream);
    Tokenizer tokenizer = new ManifestTokenizer(contents);

    Parser parser = new ManifestParser();
    return parser.parse(tokenizer);
  }
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