BioLegato - PCD: Python-esque Command Definition
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Version #1. Informal Syntax and Semantics of PCD.
GENERAL FORMAT OF THE SYNTAX %<VARIABLE> label <LABEL_STR> type <TYPES> default <VALUE> #FOR slider TYPE min <VALUE> max <VALUE> #FOR file TYPE format <FILE FORMAT TYPES> save <SAVE_VALUE> overwrite <OVERWRITE_VALUE> content <CONTENT_VALUE> #FOR chooser or choice_menu TYPE choices <LABEL_CHOICES> <VALUES> #FOR button TYPE command <COMMAND_STR>
<LABEL_STR> : any string <TYPES>: slider, text, tempfile, chooser, choice_menu, button <VALUE>: For silder type: numerical. For text type: string. For chooser type: depend of the choice <FILE FORMAT TYPES>: FASTA, GDE, GebBank, etc <SAVE_VALUE>: BOOLEAN: true or false <OVERWRITE_VALUE>: BOOLEAN: true or false <CONTENT_VALUE: empty or canvas <COMMAND_STR>: string with the command line
It was obtained to have the same behavior as the GDEMenu syntax.
We have proven this version, developing the Conversion Software Application (from GDE to PCD) and the parsing program ==> it is working OK.
Preliminary file conversion done
From here, we get the strict BNF notation and the general notation
PCD version 1 defined using BNF (Backus-Naur Form) Metalanguage
Version #2
We have to include in the syntax new features:
BioLegato - Internal format discussion
Proposals to choose the version #2
Proposal #1 - From Pythom
Examples:
Object/sequence variables
%START
type
slider
min
0
max
len(@sequence)
Conditional variables
%END
type
slider
min
if len(@sequence) < 50
0
else
50
max
1000
Tabbed Panes
^Group 1
%Data 1
type
slider
min
0
max
100
.....
^Group 2
%Data 2
type
text
label
Number of:
.....
Proposal #2 - Simplification
Examples:
Object/sequence variables
%START
type
slider
min
0
max
@sequence.length
Conditional variables
%END
type
slider
min
!(@sequence.length < 50 ? 0 : 50)
max
@sequence.length
Tabbed Panes
^ Group 1
%Data 1
type
slider
min
0
max
100
.....
^ Group 2
%Data 2
type
text
label
Number of:
.....
Proposal #3 - Verbose
Examples:
all code can be embedded by <{}> and interpreted as such
tab Tab1
var START
min
0
max
<{ $sequence.length }>
default
<{
if sequence.length > 50
write 50
else
write $sequence.length
}>
var END
min
0
,,,,
tab Tab2
var ABC
...
Proposal #4 - Hybrid
Examples:
all code can be embedded by <{}> and interpreted as such
Object/sequence variables
%START
type
slider
min
0
max
@sequence.length
Conditional variables
%END
type
slider
min
<{ if (sequence.length < 50)
then
0
else
50
print "tea time!" }>
max
@sequence.length
Tabbed Panes
^Group 1
%Data 1
type
slider
min
0
max
100
.....
^Group 2
%Data 2
type
text
label
Number of:
.....
Comments:
# abc
##### xyz
### ***
# all comments are defined as a sequence of # followed by a mandatory space (or new line if you only want to use #'s in the comment). Following the mandaory space you may use any combination of
# characters to define your comment, as the parser will ignore any line beginning with one or more #'s followed by a space (or any line containing only #'s).
# as a regular expression /#*(\s[^\n]*)?/
- we use <{ and }> because they are uncommon and do not need to be escaped often
Proposal #5 - Verbose-est
Examples:
#Variables are defined using "var" name
var START
type
slider
min
0
max
@sequence.length #values from the sequence in the canvas are taken as @sequence
error #SANITY CHECKING possible errors are define with "error" word.
higher_than_0 #SANITY CHECKING This is the kind of error associated to this
variable
#Conditional variables
var END
type
slider
min
if (@sequence.length < 50) then min=0 #natural conditional instructions. As other languages
else min=50
max
@sequence.length
#Tabbed Panes. Tabs are defined using "tab" name
tab Group 1
var Data 1
type
slider
min
0
max
100
var Data 2
type
text
default
xxxx
error
blank_string
tab Group 2
var Data 3
type
text
label
Number of:
..................
#to include ICONS in this menu option
icon /image1.png
#to include MOUSE-OVER TOOL TIPS in this menu option
tip "Number a Sequence"
#to define DEPENDENTS/CONDITIONS
var x1
type
slider
min
0
max
1000
var x2
type
slider
min
100
max
500
dependence
if x1 >= 100 then default=100
else default=grayed_out
var x3
type
slider
min
100
max
500
dependence
if x1+x2 >= 100 then default=x1+x2
else default=grayed_out
Comments:
# abc
##### xyz
### ***
# all comments are defined as a sequence of # followed by a mandatory space (or new line if you only want to use #'s in the comment). Following the mandaory space you may use any combination of
# characters to define your comment, as the parser will ignore any line beginning with one or more #'s followed by a space (or any line containing only #'s).
# as a regular expression /#*(\s[^\n]*)?/
Proposal #6 - simplifying things
Examples:
####
# NOTE: All indentation should be 3 spaces; however, because this has been formatted multiple times, this Wiki version may contain uneven spacing
# NOTE: Fields can be defined inline (e.g. type "ABC")
####
# All strings must be put in quotation marks
name "NUMSEQ - ...."
#to include ICONS in this menu option
icon "image1.png"
#to include MOUSE-OVER TOOL TIPS in this menu option
tip "Number a Sequence"
#Variables are defined using "var" name
var START
type "slider"
min 0
max
sequence.length #values from the sequence in the canvas are taken as @sequence
check #SANITY CHECKING possible errors are define with "error" word.
if START < 0 then error_message "value less than 0" #SANITY CHECKING This is the kind of error associated to this variable
#Conditional variables
var END
type
"slider"
min
if (@sequence.length < 50) then min=0 #natural conditional instructions. As other languages
else min=50
max
sequence.length
#Tabbed Panes. Tabs are defined using "tab" name
tab Group 1
var Data 1
type
"slider"
min
0
max
100
var Data 2
type
"text"
default
"xxxx"
check
if text = "" error = "This variable should not be empty" #SANITY CHECKING This is the kind of error associated to this variable
tab Group 2
var Data 3
type
"text"
label
Number of:
..................
#to define DEPENDENTS/CONDITIONS
var x1
type
"slider"
min
0
max
1000
var x2
type
"slider"
min
100
max
500
dependence #Dependent condition
if x1 >= 100
default=100
else
default=grayed_out
var x3
type
"slider"
min
100
max
500
check #Dependent condition
if x1+x2 >= 100 then default=x1+x2
else default=grayed_out
Comments:
# abc
##### xyz
### ***
# all comments are defined as a sequence of # followed by a mandatory space (or new line if you only want to use #'s in the comment). Following the mandaory space you may use any combination of
# characters to define your comment, as the parser will ignore any line beginning with one or more #'s followed by a space (or any line containing only #'s).
# as a regular expression /#*(\s[^\n]*)?/
Proposal 6 EBNF (dynamic indent/dedent version)
<file> ::= <section> <file>
| <section>
<section> ::= <param>
| <tab>
| <ofield>
<ofield> ::= <t_name> <text>
| <t_icon> <text>
| <t_tip> <text>
| <t_system> <indent> <systems> <dedent>
<systems> ::= <systems> <nl> <system>
| <system>
<system> ::= <t_all>
| <t_linux32>
| <t_linux64>
| <t_osx_x86>
| <t_sunsparc>
| <t_sunx64>
| <t_win32>
<tab> ::= <t_tab> <name> <indent> <params> <dedent>
<params> ::= <param> <nl> <params>
| <param>
<param> ::= <t_param> <indent> <pfields> <dedent>
<pfields> ::= <pfield> <nl> <pfields>
| <pfield>
<pfield> ::= <t_name> <ptext>
| <t_type> <ptext>
| <t_default> <ptext>
| <t_default> <pnum>
| <t_default> <pbool>
| <t_min> <pnum>
| <t_max> <pnum>
| <t_format> <file_format>
| <t_save> <pbool>
| <t_overwrite> <boolean_value>
| <t_content> <content_value>
| <t_shell> <ptext>
| <t_close> <pbool>
| <t_choices> <indent> <choice_list> <dedent>
<file_format> ::= <t_fasta>
| <t_gde>
| <t_genbank>
| <t_flat>
| <t_raw>
<choice_list> ::= <identifier> <space> <number>
| <identifier> <space> <text>
| <identifier> <indent> <number <dedent>
| <identifier> <indent> <text> <dedent>
<pnum> ::= <space> <number>
| <indent> <number> <dedent>
<pbool> ::= <space> <bool>
| <indent> <bool> <dedent>
<ptext> ::= <space> <text>
| <indent> <text> <dedent>
<name> ::= <identifier>
<bool> ::= <t_true>
| <t_false>
<var> ::= <identifier>
SPECIAL
*******
<comment> ::= <hash_symbols> <space> <unbound_text>
| <hash_symbols> <space>
| <hash_symbols>
<hash_symbols> ::= '#' <hash_symbols>
| '#'
<nl> ::= new line separator (no indentation change)
<indent> ::= increase indentation by 3 spaces (matches newline)
<dedent> ::= decrease indentation by 3 spaces (matches newline)
KEYWORDS
********
<t_all> ::= 'all'
<t_choices> ::= 'choices'
<t_close> ::= 'close'
<t_content> ::= 'content'
<t_default> ::= 'default'
<t_false> ::= 'false'
<t_fasta> ::= 'fasta'
<t_flat> ::= 'flat'
<t_format> ::= 'format'
<t_gde> ::= 'gde'
<t_genbank> ::= 'genbank'
<t_icon> ::= 'icon'
<t_linux32> ::= 'linux32'
<t_linux64> ::= 'linux64'
<t_max> ::= 'max'
<t_min> ::= 'min'
<t_name> ::= 'name'
<t_osx64> ::= 'osx86_64'
<t_ovwerwrite> ::= 'overwrite'
<t_param> ::= 'var'
<t_raw> ::= 'raw'
<t_tab> ::= 'tab'
<t_tip> ::= 'tip'
<t_true> ::= 'true'
<t_type> ::= 'type'
<t_save> ::= 'save'
<t_shell> ::= 'shell'
<t_sunsparc> ::= 'sunsparc'
<t_sunx64> ::= 'sunx86'
<t_win32> ::= 'win32'
TOKENS
******
<space> ::= ' ' <space>
| '\t' <space>
| ' '
| '\t'
<number> ::= <digits> '.' <digits>
| <digits>
<digits> ::= <digit> <digits>
| <digit>
<digit> ::= 0 - 9
<unbound_text> ::= any character
<text> ::= '"' <quoted_text> '"'
<quoted_text> ::= any non " character
| '"' '"'
Proposal 6 EBNF (limited/static indent version - this is if the above system won't work) - pre-programming code
<file> ::= <section> <nl> <file>
| <section>
<section> ::= <param>
| <tab>
| <ofield>
| <blank_line>
<ofield> ::= <t_name> <text>
| <t_icon> <text>
| <t_tip> <text>
| <t_system> <indent> <systems> <dedent>
<systems> ::= <systems> <nl> <system>
| <system>
<system> ::= <t_all>
| <t_linux32>
| <t_linux64>
| <t_osx_x86>
| <t_sunsparc>
| <t_sunx64>
| <t_win32>
<param> ::= <t_param> <nl> <pfields>
<pfields> ::= <ind> <pfield> <nl> <pfields>
| <ind> <pfield>
<pfield> ::= <text_param> <inda> <text>
| <num_param> <inda> <number>
| <bool_param> <inda> <bool>
| <any_param> <inda> <any_type>
| <t_format> <inda> <file_format>
| <t_content> <inda> <content_value>
| <t_choices> <nl> <choice_list>
<choice_list> ::= <identifier> <indb> <any> <nl> <choice_list>
| <identifier> <indb> <any> <nl>
<tab> ::= <t_tab> <name> <nl> <tparams>
<tparams> ::= <ind> <tparam> <nl> <tparams>
| <ind> <tparam>
<tparam> ::= <ind> <t_param> <nl> <tpfields>
<tpfields> ::= <ind> <ind> <tpfield> <nl> <tpfields>
| <ind> <ind> <tpfield>
<tpfield> ::= <text_param> <indb> <ptext>
| <num_param> <indb> <number>
| <bool_param> <indb> <bool>
| <any_param> <indb> <any_type>
| <t_format> <indb> <file_format>
| <t_content> <indb> <content_value>
| <t_choices> <nl> <tchoice_list>
<choice_list> ::= <identifier> <indc> <any> <nl> <choice_list>
| <identifier> <indc> <any> <nl>
<inda> ::= <space>
| <nl> <ind> <ind>
<indb> ::= <space>
| <nl> <ind> <ind> <ind>
<indc> ::= <space>
| <nl> <ind> <ind> <ind> <ind>
<name> ::= <identifier>
TYPES
*****
<bool> ::= <t_true>
| <t_false>
<text> ::= '"' <quoted_text> '"'
<number> ::= <digits> '.' <digits>
| <digits>
TOKEN CLASSES
*************
<any_type> ::= <bool>
| <text>
| <number>
<any_param> ::= <t_default>
<text_param> ::= <t_name>
| <t_type>
| <t_shell>
<num_param> ::= <t_min>
| <t_max>
<bool_param> ::= <t_close>
| <t_save>
| <t_overwrite>
<file_format> ::= <t_fasta>
| <t_gde>
| <t_genbank>
| <t_flat>
| <t_raw>
SPECIAL
*******
<comment> ::= <hash_symbols> <space> <unbound_text>
| <hash_symbols> <space>
| <hash_symbols>
<hash_symbols> ::= '#' <hash_symbols>
| '#'
<blank_line> ::= <space> <blank_line>
KEYWORDS
********
<t_all> ::= 'all'
<t_choices> ::= 'choices'
<t_close> ::= 'close'
<t_content> ::= 'content'
<t_default> ::= 'default'
<t_false> ::= 'false'
<t_fasta> ::= 'fasta'
<t_flat> ::= 'flat'
<t_format> ::= 'format'
<t_gde> ::= 'gde'
<t_genbank> ::= 'genbank'
<t_icon> ::= 'icon'
<t_linux32> ::= 'linux32'
<t_linux64> ::= 'linux64'
<t_max> ::= 'max'
<t_min> ::= 'min'
<t_name> ::= 'name'
<t_osx64> ::= 'osx86_64'
<t_ovwerwrite> ::= 'overwrite'
<t_param> ::= 'var'
<t_raw> ::= 'raw'
<t_tab> ::= 'tab'
<t_tip> ::= 'tip'
<t_true> ::= 'true'
<t_type> ::= 'type'
<t_save> ::= 'save'
<t_shell> ::= 'shell'
<t_sunsparc> ::= 'sunsparc'
<t_sunx64> ::= 'sunx86'
<t_win32> ::= 'win32'
TOKENS
******
<space> ::= ' ' <space>
| '\t' <space>
| ' '
| '\t'
<nl> ::= '\n'
<ind> ::= ' '
<digits> ::= <digit> <digits>
| <digit>
<digit> ::= 0 - 9
<quoted_text> ::= anything but '"'
| '"' '"'
<unbound_text> ::= any character
Proposal 6 EBNF (limited/static indent version + code) - in-progress
<file> ::= <section> <nl> <file>
| <section>
<section> ::= <param>
| <tab>
| <ofield>
| <blank_line>
<ofield> ::= <t_name> <text>
| <t_icon> <text>
| <t_tip> <text>
| <t_system> <indent> <systems> <dedent>
<systems> ::= <systems> <nl> <system>
| <system>
<system> ::= <t_all>
| <t_linux32>
| <t_linux64>
| <t_osx_x86>
| <t_sunsparc>
| <t_sunx64>
| <t_win32>
<param> ::= <t_param> <nl> <pfields>
<pfields> ::= <ind> <pfield> <nl> <pfields>
| <ind> <pfield>
<pfield> ::= <text_param> <inda> <text>
| <num_param> <inda> <number>
| <bool_param> <inda> <bool>
| <any_param> <inda> <any_type>
| <t_format> <inda> <file_format>
| <t_content> <inda> <content_value>
| <t_choices> <nl> <choice_list>
<choice_list> ::= <identifier> <indb> <any> <nl> <choice_list>
| <identifier> <indb> <any> <nl>
<tab> ::= <t_tab> <name> <nl> <tparams>
<tparams> ::= <ind> <tparam> <nl> <tparams>
| <ind> <tparam>
<tparam> ::= <ind> <t_param> <nl> <tpfields>
<tpfields> ::= <ind> <ind> <tpfield> <nl> <tpfields>
| <ind> <ind> <tpfield>
<tpfield> ::= <text_param> <indb> <ptext>
| <num_param> <indb> <number>
| <bool_param> <indb> <bool>
| <any_param> <indb> <any_type>
| <t_format> <indb> <file_format>
| <t_content> <indb> <content_value>
| <t_choices> <nl> <tchoice_list>
<choice_list> ::= <identifier> <indc> <any> <nl> <choice_list>
| <identifier> <indc> <any> <nl>
<inda> ::= <space>
| <nl> <ind> <ind>
<indb> ::= <space>
| <nl> <ind> <ind> <ind>
<indc> ::= <space>
| <nl> <ind> <ind> <ind> <ind>
<name> ::= <identifier>
CODE
****
<code> ::= <math>
| <if_then>
<if_then> ::= <t_if> <cond> <t_then> <code>
<cond> ::= <math> <comp> <math> <andor> <cond>
| <math> <comp> <math>
<andor> ::= <t_and>
| <t_or>
| <t_xor>
<comp> ::= <t_eq>
| <t_lt>
| <t_gt>
<math> ::= <m_open> <math> <m_close>
| <norv> <op> <norv>
| <norv>
<op> ::= <t_plus>
| <t_minus>
| <t_mul>
| <t_div>
<norv> ::= <number>
| <variable>
<variable> ::= <identifier>
TYPES
*****
<bool> ::= <t_true>
| <t_false>
<text> ::= '"' <quoted_text> '"'
<number> ::= <digits> '.' <digits>
| <digits>
TOKEN CLASSES
*************
<any_type> ::= <bool>
| <text>
| <number>
<any_param> ::= <t_default>
<text_param> ::= <t_name>
| <t_type>
| <t_shell>
<num_param> ::= <t_min>
| <t_max>
<bool_param> ::= <t_close>
| <t_save>
| <t_overwrite>
<file_format> ::= <t_fasta>
| <t_gde>
| <t_genbank>
| <t_flat>
| <t_raw>
SPECIAL
*******
<comment> ::= <hash_symbols> <space> <unbound_text>
| <hash_symbols> <space>
| <hash_symbols>
<hash_symbols> ::= '#' <hash_symbols>
| '#'
<blank_line> ::= <space> <blank_line>
KEYWORDS
********
<t_all> ::= 'all'
<t_and> ::= 'and'
<t_choices> ::= 'choices'
<t_close> ::= 'close'
<t_content> ::= 'content'
<t_default> ::= 'default'
<t_false> ::= 'false'
<t_fasta> ::= 'fasta'
<t_flat> ::= 'flat'
<t_format> ::= 'format'
<t_gde> ::= 'gde'
<t_genbank> ::= 'genbank'
<t_icon> ::= 'icon'
<t_if> ::= 'if'
<t_linux32> ::= 'linux32'
<t_linux64> ::= 'linux64'
<t_max> ::= 'max'
<t_min> ::= 'min'
<t_name> ::= 'name'
<t_or> ::= 'or'
<t_osx64> ::= 'osx86_64'
<t_ovwerwrite> ::= 'overwrite'
<t_param> ::= 'var'
<t_raw> ::= 'raw'
<t_tab> ::= 'tab'
<t_then> ::= 'then'
<t_tip> ::= 'tip'
<t_true> ::= 'true'
<t_type> ::= 'type'
<t_save> ::= 'save'
<t_shell> ::= 'shell'
<t_sunsparc> ::= 'sunsparc'
<t_sunx64> ::= 'sunx86'
<t_win32> ::= 'win32'
<t_xor> ::= 'xor'
SYMBOLIC TOKENS
***************
<m_open> ::= '('
<m_close> ::= ')'
<t_plus> ::= '+'
<t_minus> ::= '-'
<t_mul> ::= '*'
<t_div> ::= '/'
<t_eq> ::= '='
<t_lt> ::= '<'
<t_gt> ::= '>'
TOKENS
******
<space> ::= ' ' <space>
| '\t' <space>
| ' '
| '\t'
<nl> ::= '\n'
<ind> ::= ' '
<digits> ::= <digit> <digits>
| <digit>
<digit> ::= 0 - 9
<quoted_text> ::= anything but '"'
| '"' '"'
<unbound_text> ::= any character
