Field Detail

• NUMBER_TO_OUTPUT

  public static final int NUMBER_TO_OUTPUT

  See Also:

  Constant Field Values

Constructor Detail

• CheckDB

  public CheckDB()

  Constructor for HelloWorld.

Method Detail

• init

  public final ReturnValue init()

  Plugin initialization code goes here. This is the first phase of the plugin lifecycle run. Might do things here like set up database access, create temp files, define defaults, etc. Preprocessing can be done here, although normally processing should be done by/during do_run(). The SEQWARE_SETTINGS file contents is passed in here.

  Returns:

• do_test

  public ReturnValue do_test()

  Perform any active system testing here. Use to make sure a DB is available, that a command line tools can be run, etc. You can even write functional tests that run the program you're wrapping on a small known good and then verify the output.

  Returns:

• do_run

  public final ReturnValue do_run()

  Performs the main tasks for the plugin. This is where you actually execute your task and where the bulk of your implementation will go.

  Returns:

• get_description

  public final String get_description()

  get_description.

  Specified by:

  get_description in interface PluginInterface

  Overrides:

  get_description in class Plugin

  Returns:

  a String object.

• main

  public static void main(String[] args)
                   throws IOException,
                          URISyntaxException

  Throws:

  IOException

  URISyntaxException

• clean_up

  public final ReturnValue clean_up()

  Description copied from interface: PluginInterface
  Perform post-task clean-up here. Use to remove temporary files and directories, flush buffers and close db connections, etc.

  Returns:

  Success or failure info from this phase, along with any console output.

• processOutput

  public static void processOutput(SortedMap<CheckDBPluginInterface.Level,Set<String>> result,
                   CheckDBPluginInterface.Level level,
                   String description,
                   List<Integer> list)

  Convenience method for processing output and appending it to the warning map

  Parameters:

  result - a sorted map where results can be appended

  level - Level of message to create

  description - A description of the sw_accessions to be reported from list

  list - a list of sw_accessions to report