Examples of background_parameter()

Examples of ru.autosome.commons.cli.OutputInformation.background_parameter()

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    OutputInformation infos = new OutputInformation();

    infos.add_parameter("V", "discretization value", discretizer);
    infos.add_parameter("PB", "P-value boundary", pvalue_boundary);

    infos.background_parameter("B", "background", background);

    infos.add_table_parameter("P", "requested P-value", "expected_pvalue");
    infos.add_table_parameter("AP", "actual P-value", "real_pvalue");

    if (background.is_wordwise()) {
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Examples of ru.autosome.commons.cli.OutputInformation.background_parameter()

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      infos.add_parameter("VP", "discretization value, precise", preciseDiscretizer);
      infos.add_parameter("MP", "minimal similarity for the 2nd pass in \'precise\' mode", preciseRecalculationCutoff);
    } else {
      infos.add_parameter("V", "discretization value", roughDiscretizer);
    }
    infos.background_parameter("BQ", "background for query matrix", queryBackground);
    infos.background_parameter("BC", "background for collection", collectionBackground);

    infos.add_table_parameter_without_description("motif", "name");
    infos.add_table_parameter_without_description("similarity", "similarity");
    infos.add_table_parameter_without_description("shift", "shift");
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Examples of ru.autosome.commons.cli.OutputInformation.background_parameter()

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      infos.add_parameter("MP", "minimal similarity for the 2nd pass in \'precise\' mode", preciseRecalculationCutoff);
    } else {
      infos.add_parameter("V", "discretization value", roughDiscretizer);
    }
    infos.background_parameter("BQ", "background for query matrix", queryBackground);
    infos.background_parameter("BC", "background for collection", collectionBackground);

    infos.add_table_parameter_without_description("motif", "name");
    infos.add_table_parameter_without_description("similarity", "similarity");
    infos.add_table_parameter_without_description("shift", "shift");
    infos.add_table_parameter_without_description("overlap", "overlap");
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Examples of ru.autosome.commons.cli.OutputInformation.background_parameter()

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  @Override
  public OutputInformation report_table_layout() {
    OutputInformation infos = new OutputInformation();
    infos.add_parameter("V", "discretization value", discretizer);
    infos.background_parameter("B", "background", background);

    infos.add_table_parameter("T", "threshold", "threshold");
    if (background.is_wordwise()) {
      infos.add_table_parameter("W", "number of recognized words", "numberOfRecognizedWords",new OutputInformation.Callback<PvalueInfo>() {
        @Override
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Examples of ru.autosome.commons.cli.OutputInformation.background_parameter()

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    if (predefinedSecondThreshold != null) {
      infos.add_parameter("T2", "threshold for the 2nd matrix", predefinedSecondThreshold);
    }
    infos.add_parameter("PB", "P-value boundary", pvalueBoundary);
    if (firstBackground.equals(secondBackground)) {
      infos.background_parameter("B", "background", firstBackground);
    } else {
      infos.background_parameter("B1", "background for the 1st model", firstBackground);
      infos.background_parameter("B2", "background for the 2nd model", secondBackground);
    }
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Examples of ru.autosome.commons.cli.OutputInformation.background_parameter()

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    }
    infos.add_parameter("PB", "P-value boundary", pvalueBoundary);
    if (firstBackground.equals(secondBackground)) {
      infos.background_parameter("B", "background", firstBackground);
    } else {
      infos.background_parameter("B1", "background for the 1st model", firstBackground);
      infos.background_parameter("B2", "background for the 2nd model", secondBackground);
    }

    return infos;
  }
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Examples of ru.autosome.commons.cli.OutputInformation.background_parameter()

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    infos.add_parameter("PB", "P-value boundary", pvalueBoundary);
    if (firstBackground.equals(secondBackground)) {
      infos.background_parameter("B", "background", firstBackground);
    } else {
      infos.background_parameter("B1", "background for the 1st model", firstBackground);
      infos.background_parameter("B2", "background for the 2nd model", secondBackground);
    }

    return infos;
  }
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