Package org.anchoranalysis.launcher.options

Class CommandLineOptions

Object
CommandLineOptions
public class CommandLineOptions extends Object
All command-line options used by the launcher.
Author:
Owen Feehan
See Also:

  • Field Details

    • SHORT_OPTION_INPUT

      public static final String SHORT_OPTION_INPUT
      Changes inputs.
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    • SHORT_OPTION_INPUT_COPY_NON_INPUTS

      public static final String SHORT_OPTION_INPUT_COPY_NON_INPUTS
      Additionally copies any files in the input directory, unused as inputs.
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    • SHORT_OPTION_INPUT_SUBSET_IDENTIFIER

      public static final String SHORT_OPTION_INPUT_SUBSET_IDENTIFIER
      Subsets the identifier.
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    • SHORT_OPTION_INPUT_RELATIVE_PATH

      public static final String SHORT_OPTION_INPUT_RELATIVE_PATH
      Derives the unique identifier from the **entire relative filename or path** (excluding file extension).
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    • SHORT_OPTION_INPUT_SHUFFLE

      public static final String SHORT_OPTION_INPUT_SHUFFLE
      Shuffles the order of the inputs.
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    • SHORT_OPTION_INPUT_LIMIT

      public static final String SHORT_OPTION_INPUT_LIMIT
      Imposes an upper limit on the number of inputs.
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    • SHORT_OPTION_INPUT_RANDOM_SAMPLE

      public static final String SHORT_OPTION_INPUT_RANDOM_SAMPLE
      Randomly samples a number of inputs.
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    • SHORT_OPTION_TASK

      public static final String SHORT_OPTION_TASK
      Changes task.
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    • SHORT_OPTION_TASK_NUMBER_PROCESSORS

      public static final String SHORT_OPTION_TASK_NUMBER_PROCESSORS
      Suggests a maximum number of processors to use for the task.
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    • SHORT_OPTION_TASK_SIZE

      public static final String SHORT_OPTION_TASK_SIZE
      Suggests dimensions or a scaling factor for certain tasks.
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    • SHORT_OPTION_GROUP

      public static final String SHORT_OPTION_GROUP
      Activates grouping from a subset of the identifier's elements.
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    • SHORT_OPTION_OUTPUT

      public static final String SHORT_OPTION_OUTPUT
      Changes output manager.
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    • SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL

      public static final String SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL
      Enables specific output(s). Multiple outputs are comma-separated.
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    • SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL

      public static final String SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL
      Disables specific output(s). Multiple outputs are comma-separated.
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    • SHORT_OPTION_OUTPUT_ENABLE_ALL

      public static final String SHORT_OPTION_OUTPUT_ENABLE_ALL
      Enables all outputs.
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    • SHORT_OPTION_OUTPUT_CONSOLE_ONLY

      public static final String SHORT_OPTION_OUTPUT_CONSOLE_ONLY
      Output console only. By default, the output directory is opened in the desktop after completion. This disables that behaviour.
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    • SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT

      public static final String SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT
      Suggests an output image file format: e.g -of jpg or -of ome.xml.
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    • SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER

      public static final String SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER
      Outputs with an incrementing number instead of the input identifier.

      (useful for creating sequences of images)

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    • SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES

      public static final String SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES
      Suppressed the subdirectory structure when outputting file identifiers.

      This replaces subdirectories in the outputted filenames with an underscore.

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    • SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER

      public static final String SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER
      Ignores the experiment identifier, when forming an output-path.

      This writes directorly to the output-directory, but not if it already exists.

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    • SHORT_OPTION_DEBUG

      public static final String SHORT_OPTION_DEBUG
      Enables debug-mode: runs only the first available input [whose name contains string].
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    • SHORT_OPTION_LOG_ERROR

      public static final String SHORT_OPTION_LOG_ERROR
      Logs initial BeanXML errors in greater detail to a file-path.
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    • SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS

      public static final String SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS
      Shows additional argument information, otherwise executes as normal.
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    • SHORT_OPTION_SHOW_TASKS

      public static final String SHORT_OPTION_SHOW_TASKS
      Prints the names of predefined tasks that can be easily used with -t.
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    • SHORT_OPTION_HELP

      public static final String SHORT_OPTION_HELP
      Displays help message with all command-line options.
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    • SHORT_OPTION_VERSION

      public static final String SHORT_OPTION_VERSION
      Displays version and authorship information.
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    • LONG_OPTION_INPUT_RANDOM_SAMPLE

      public static final String LONG_OPTION_INPUT_RANDOM_SAMPLE
      Randomly samples a number of inputs.
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    • LONG_OPTION_OUTPUT

      public static final String LONG_OPTION_OUTPUT
      Changes output manager.
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    • LONG_OPTION_OUTPUT_CONSOLE_ONLY

      public static final String LONG_OPTION_OUTPUT_CONSOLE_ONLY
      Output console only. By default, the output directory is opened in the desktop after completion. This disables that behavior.
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    • LONG_OPTION_GROUP

      public static final String LONG_OPTION_GROUP
      Activates grouping from a subset of the identifier's elements.
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  • Method Details

    • addBasicOptions

      public static void addBasicOptions(org.apache.commons.cli.Options options)
      Adds basic options to the Options object.
      Parameters:
      options - the Options object to add the basic options to

    • addAdditionalOptions

      public static void addAdditionalOptions(org.apache.commons.cli.Options options)
      Adds additional options to the Options object.
      Parameters:
      options - the Options object to add the additional options to

    • addInputOptions

      public static void addInputOptions(org.apache.commons.cli.Options options)
      Adds input-related options to the Options object.
      Parameters:
      options - the Options object to add the input options to