dsl-pa is a Domain Specific Language Parsing Assistant library designed to take advantage of the C++ logic shortcut operators such as && and ||. dsl-pa function calls extract sections of language input based on a specified alphabet. Calls to dsl-pa functions are combined using the C++ shortcut operators in order to parse a language in a reasonably compact form. Consequently all dsl-pa functions return either a boolean value or a value, such as an integer, that can be implicitly converted to a bool. The idea is that the set of shortcut operations should mirror the BNF or similar notation (such as ABNF) that is used to describe the langauge being parsed. Various reader classes can be used to read from file, std::string and memory buffer sources.
This project is now ready for beta use by thrid-parties.
dsl_pa is the main class of the library
Possibly the simplest way to use dsl_pa
is to create your own class that inherits dsl_pa
.
This way all the methods in dsl_pa
become first class citizens and the code is more compact.
Inheritance seems justified here on the basis that your class IS-A parser. However, you don't need to use
dsl_pa
this way, and most of the test code uses dsl_pa
by construction.
If you do use inheritance to use dsl_pa
and you use some form of factory for creating
instances of parsers, you can implement the parse()
virtual method in dsl_pa
to invoke your parsing.
dsl_pa
functions are designed so that they can be combined using C++'s shortcut logical
operators, such as && and ||. For example, if the strucure of your input is:
width=10, height = 5
then you might parse it similar to the following:
size_t width, height; if( opt_space() && fixed( "width" ) && opt_space() && is_char( '=' ) && opt_space() && get_uint( &width ) && opt_space() && is_char( ',' ) && opt_space() && fixed( "height" ) && opt_space() && is_char( '=' ) && opt_space() && get_uint( &height ) ) { fout << "Example 1 OK: w=" << width << " & h=" << height << "\n"; } else { fout << "Unable to parse input\n"; }
A common operation when parsing a language is skiiping white space. This can be done using the following dsl_pa methods:
bool space(); bool opt_space(); bool wsp(); // From ABNF (RFC5234) whitespace: non-newline space chars bool opt_wsp();
space() requires there to be white space (space, tab, plus newline characters) present in order to return true and opt_space() allows white space to be optional.
wsp() and opt_wsp() are similar to space() and opt_space(), but only accepts non-newline whitespace characters. They are handy for parsing line based syntaxes.
dsl_pa
has a number of functions for reading items of data into std::strings. These are:
size_t /*num chars read*/ get( std::string * p_output, const alphabet & r_alphabet ); size_t get( std::string * p_output, const alphabet & r_alphabet, size_t max_chars ); size_t get_until( std::string * p_output, const alphabet & r_alphabet ); size_t get_bounded_until( std::string * p_output, const alphabet & r_alphabet, size_t max_chars ); size_t get_escaped_until( std::string * p_output, const alphabet & r_alphabet, char escape_char ); size_t get_until( std::string * p_output, const alphabet & r_alphabet, char escape_char, size_t max_chars );
In the above functions the p_output argument points to the instance of std::string that is to receive the output. Any parsed data is appended to the string. This allows multiple get...() functions to accumulate data into a single string. If you wish to clear a std::string first you can use the dsl_pa::clear() method within your set of shortcut operators.
The r_alphabet parameter takes a reference to an alphabet class. An alphabet specifies the set of characters that you want to either parse into your string (using the get() methods) or not get in your string (using the get...until() methods.)
dsl_pa
has a number of functions for reading items of data such as integers, floats
and booleans.
bool /*is_parsed*/ get_bool( std::string * p_input ); bool /*is_parsed*/ get_bool( bool * p_bool ); size_t /*num chars read*/ get_int( std::string * p_num ); size_t /*num chars read*/ get_int( int * p_int ); size_t /*num chars read*/ get_uint( std::string * p_num ); size_t /*num chars read*/ get_uint( unsigned int * p_int ); bool get_float( std::string * p_num ); bool get_float( double * p_float ); bool get_float( float * p_float ); bool get_sci_float( std::string * p_num ); bool get_sci_float( double * p_float ); bool get_sci_float( float * p_float );
Occasionally when parsing a langauge you need to parse fixed text. The following dsl-pa functions support this:
bool fixed( const char * p_seeking ); bool ifixed( const char * p_seeking ); bool get_fixed( std::string * p_output, const char * p_seeking ); bool get_ifixed( std::string * p_output, const char * p_seeking );
If the specified text is not found in its entirity then the parser's input location will be restored to where it was before the function was called.
The methods without get_ in the name with simply skip over the specified text if it is present. The methods with get_ in the name will collect the parsed text. The methods with _ifixed in the name are case-insensitive for characters in the ASCII range. The other methods are case sensitive.
The language input is assumed to be in UTF-8 encoding and operations are done on C++ char
s. It is assumed that
any parsing decisions of the input language will be based on the ASCII range of characters and any char valued 0x80 and
above is just considered to be part of "the rest" of Unicode. Hence dsl-pa operates on a char
by char
basis and isn't
multi-byte character aware.
A value of 0
is used to indicate the end of input has been reached.


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I have heard tales of his travels across Europe, the United states but most stories come from countries in eastern Asia such as China, the Philippines and Thailand.
Not only did I grow up hearing of these tales from my uncle, I also have an older sister who has gone travelling at every opportunity.
She has gone Interrailing across Europe, been to south America and countries in Africa such as Morocco, Nigeria and South Africa. As a result I have the travel bug.
we saw Billy Elliot in the O2 Arena and also got a tour of London.
The second time I saw an Arsenal match in the Emirates stadium with my father.
We saw the salt mines and also went to Auschwitz/Birkenau Concentration camp
me and my brother saw a Champions League match between Barcelona and Arsenal in the Camp Nou
we went on the amusements for a weekend
We will be starting in Milan then off to Bologna, Venice, Ljubljana, Zagreb and finishing in Budapest where we will be staying for a week.
This will be my first time travelling with just my friends and I as before this I have only travelled with my family or my secondary school.


:code:`PyUniProt` is python software interface developed by the
`Department of Bioinformatics `_
at the Fraunhofer Institute for Algorithms and Scientific Computing
`SCAI `_
to the data provided by the `European Bioinformatics Institute (EMBL-EBI) `_ on their
`UniProt website `_.
The content of UniProt and the use of PyUniProt in combination with `PyBEL `_ supports
successfully scientists in the `IMI `_ funded projects
`AETIONOMY `_ and `PHAGO `_
in the identification of potential drugs in complex disease networks with several thousands of
relationships compiled from `BEL `_ statements.
Aim of this software project is to provide an programmatic access to locally stored UniProt data and
allow a filtered export in several formats used in the scientific community. Many query functions allow search in the
data and use it as `pandas.DataFrame` in Jupyter notebooks.
We will focus our software development on the analysis and extension of biological disease knowledge networks.
PyUniProt is an ongoing project and needs improvement. We are happy if you want support our project or start
a scientific cooperation with us.