                                  acdpretty



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Function

   Correctly reformat an application ACD file

Description

   acdpretty will generate a correctly, fully formatted ACD file from one
   which is parsable but which is partly or incorrectly formatted.

   acdpretty reads the ACD file and rewrites it with clean formatting to
   the file (ApplicationName).acdpretty which can be used to overwrite the
   original ACD file. The new file might contain many differences. For
   example, abbreviations will be expanded, all sections and attributes
   will be indented, all values will be quoted and lines will be wrapped
   at a reasonable width.

Usage

   Here is a sample session with acdpretty


% acdpretty qatest

Created qatest.acdpretty


   Go to the output files for this example

Command line arguments

   The first parameter is the name of the program to pretty print.

   All other command line parameters and qualifiers are essentially
   ignored as processing stops once the ACD file is printed. A few of the
   general qualifiers have the potential to conflict with the function of
   acdpretty.

Correctly reformat an application ACD file
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   The input file is the ACD file for the specified program

Output file format

   The output file is a pretty printed copy of the original ACD file.

   All sections and attributed will be indented. All values will be
   quoted. Lines will be wrapped at a reasonable width.

   The output file is intended as a standard format for parsers used by
   GUI and other interface wrappers, rather than using the original ACD
   file directly.

  Output files for usage example

  File: qatest.acdpretty

# Example ACD file for QA testing
#

application: qatest [
  groups: "test"
  documentation: "ACD file for QA testing"
]

sequence: asequence [
  parameter: "Y"
  features: "Y"
]

sequence: bsequence [
  parameter: "Y"
]

outfile: outfile [
  parameter: "Y"
]

integer: aint [
  prompt: "first integer"
]

integer: bint [
  prompt: "second integer, first was $(aint)"
  default: "57"
]

string: testalen [
  standard: "Y"
  information: "asequence length $(asequence.length)"
]

string: testblen [
  standard: "Y"
  information: "bsequence length $(bsequence.length)"
]

string: outdir [
  information: "output directory"
]

boolean: logic [
  information: "boolean value"
]

outfile: outtest [
  parameter: "Y"
  odirectory: "$(outdir)"
]

seqout: outseq [
  parameter: "Y"
  features: "Y"
  osdirectory: "$(outdir)"
  ofdirectory: "$(outdir)"
]

Data files

   None

Notes

   acdpretty does not have its own options, but takes a single parameter
   which is the name of the ACD file that is being processed. It is
   invoked by specifying the name of the ACD file after the name of the
   utility application itself:

   acdpretty ApplicationName

   Any command line parameters that would normally be specified for the
   application are essentially ignored as processing stops once the
   reformatted ACD file is printed.

   The format generated by acdpretty is intended as a standard for parsers
   used by GUI and other interface developers. It is far easier writing a
   parser to cope with acdpretty output than one which can cope with the
   ACD sytax in general.

References

Warnings

   A few of the global qualifiers have the potential to conflict with the
   function of acdpretty.

Diagnostic Error Messages

Exit status

   It exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   acdc             Test an application ACD file
   acdtable         Generate an HTML table of parameters from an application ACD
                    file
   acdtrace         Trace processing of an application ACD file (for testing)
   acdvalid         Validate an application ACD file

Author(s)

   Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Completed 9th March 1999

Target users

   This program is intended to be used by developers of applications and
   interfaces.

Comments

   None
