libSBML C API  libSBML 5.20.4 C API
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translateL3Math.c

Translates infix formulas into MathML and vice-versa, using the SBML Level 3 parser instead of the old Level 1 parser.

Translates infix formulas into MathML and vice-versa, using the SBML Level 3 parser instead of the old Level 1 parser.

/**
* @file translateL3Math.c
* @brief Translates infix formulas into MathML and vice-versa, using the L3 parser instead of the old L1 parser.
* @author Sarah Keating
* @author Ben Bornstein
*
* <!--------------------------------------------------------------------------
* This sample program is distributed under a different license than the rest
* of libSBML. This program uses the open-source MIT license, as follows:
*
* Copyright (c) 2013-2018 by the California Institute of Technology
* (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
* and the University of Heidelberg (Germany), with support from the National
* Institutes of Health (USA) under grant R01GM070923. All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the "Software"),
* to deal in the Software without restriction, including without limitation
* the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
* THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS IN THE SOFTWARE.
*
* Neither the name of the California Institute of Technology (Caltech), nor
* of the European Bioinformatics Institute (EMBL-EBI), nor of the University
* of Heidelberg, nor the names of any contributors, may be used to endorse
* or promote products derived from this software without specific prior
* written permission.
* ------------------------------------------------------------------------ -->
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sbml/SBMLTypes.h>
#include "util.h"
#define BUFFER_SIZE 1024
char *translateInfix (const char *formula, L3ParserSettings_t* settings);
char *translateMathML (const char *xml);
int
main (int argc, char* argv[])
{
char *line;
char *result;
char *buffer = (char*)calloc( 1, sizeof(char) );
unsigned long len;
L3ParserSettings_t* settings;
int reading = 1;
SBMLDocument_t* doc = NULL;
printf( "\n" );
printf( "This program translates infix formulas into MathML and\n" );
printf( "vice-versa. An 'enter' or a 'return' on an empty line\n" );
printf( "triggers translation.\n" );
printf( "\n" );
while (reading)
{
printf( "Enter infix formula, MathML expression, \n");
printf( "or change parsing rules with the keywords:\n");
printf( "LOG_AS_LOG10, LOG_AS_LN, LOG_AS_ERROR, EXPAND_UMINUS, ");
printf( "COLLAPSE_UMINUS, TARGETL2, TARGETL3, NO_UNITS, UNITS, ");
printf( "or FILE:<filename>\n\n\n" );
printf( "> " );
do
{
line = trim_whitespace(get_line(stdin));
len = (unsigned int)strlen(line);
if (len > 0)
{
buffer = (char *) realloc( buffer, 1 + strlen(buffer) + len );
if (strcmp(line, "LOG_AS_LOG10")==0) {
printf( "Now parsing 'log(x)' as 'log10(x)'\n\n> ");
}
else if (strcmp(line, "LOG_AS_LN")==0) {
printf( "Now parsing 'log(x)' as 'ln(x)'\n\n> ");
}
else if (strcmp(line, "LOG_AS_ERROR")==0) {
printf( "Now parsing 'log(x)' as an error\n\n> ");
}
else if (strcmp(line, "EXPAND_UMINUS")==0) {
printf( "Will now leave multiple unary minuses expanded, ");
printf("and all negative numbers will be translated using the ");
printf("<minus> construct.\n\n> ");
}
else if (strcmp(line, "COLLAPSE_UMINUS")==0) {
printf( "Will now collapse multiple unary minuses, and incorporate ");
printf("a negative sign into digits.\n\n> ");
}
else if (strcmp(line, "NO_UNITS")==0) {
printf( "Will now target MathML but with no units on numbers.\n\n> ");
}
else if (strcmp(line, "UNITS")==0) {
printf( "Will now target MathML but with units on numbers.\n\n> ");
}
else if (line[0] == 'F' && line[1] == 'I' && line[2]=='L'
&& line[3]=='E' && line[4]==':')
{
size_t len = strlen(line);
char *filename = (char*) malloc(len-5+1);
strncpy(filename, line+5, len-5);
doc = readSBMLFromFile(filename);
if (SBMLDocument_getModel(doc)==NULL) {
printf( "File '%s' not found or no model present.", filename);
printf( "Clearing the Model parsing object.\n\n> ");
}
else {
printf( "Using model from file %s to parse infix:", filename);
printf( "all symbols present in that model will not be translated ");
printf( "as native MathML or SBML-defined elements.\n\n> ");;
}
free(filename);
}
else
{
strncat(buffer, line, len);
strncat(buffer, "\n", 1);
}
}
else
{
result = (buffer[0] == '<') ?
translateMathML(buffer) : translateInfix(buffer, settings);
printf("Result:\n\n%s\n\n\n", result);
free(result);
reading = 0;
}
}
while (len > 0);
}
free(buffer);
free(line);
return 0;
}
/**
* _tTranslates_t _tthe_t _tgiven_t _tinfix_t _tformula_t _tinto_t _tMathML_t.
*
* @_treturn_t _tthe_t _tMathML_t _tas_t _ta_t _tstring_t. _tThe_t _tcaller_t _towns_t _tthe_t _tmemory_t _tand_t _tis_t
* _tresponsible_t _tfor_t _tfreeing_t _tit_t.
*/
char *
translateInfix (const char* formula, L3ParserSettings_t* settings)
{
char* result;
ASTNode_t* math = SBML_parseL3FormulaWithSettings(formula, settings);
if (math==NULL) {
}
else {
result = writeMathMLToString(math);
ASTNode_free(math);
}
return result;
}
/**
* _tTranslates_t _tthe_t _tgiven_t _tMathML_t _tinto_t _tan_t _tinfix_t _tformula_t. _tThe_t _tMathML_t _tmust_t
* _tcontain_t _tno_t _tleading_t _twhitespace_t, _tbut_t _tan_t _tXML_t _theader_t _tis_t _toptional_t.
*
* @_treturn_t _tthe_t _tinfix_t _tformula_t _tas_t _ta_t _tstring_t. _tThe_t _tcaller_t _towns_t _tthe_t _tmemory_t _tand_t
* _tis_t _tresponsible_t _tfor_t _tfreeing_t _tit_t.
*/
char *
translateMathML (const char* xml)
{
char* result;
ASTNode_t* math;
math = readMathMLFromString(xml);
result = SBML_formulaToString(math);
ASTNode_free(math);
return result;
}
void ASTNode_free(ASTNode_t *node)
_tFrees_t _tthe_t _tgiven_t _tASTNode_t_t _tstructure_t, _tincluding_t _tany_t _tchild_t _tnodes_t.
Definition ASTNode.cpp:4644
char * SBML_formulaToString(const ASTNode_t *tree)
@_tif_t _tconly_t @_tmemberof_t _tASTNode_t_t @_tendif_t
Definition FormulaFormatter.cpp:56
ASTNode_t * SBML_parseL3FormulaWithSettings(const char *formula, const L3ParserSettings_t *settings)
_tParses_t _ta_t _ttext_t _tstring_t _tas_t _ta_t _tmathematical_t _tformula_t _tusing_t _tspecific_t...
char * SBML_getLastParseL3Error()
_tReturns_t _tthe_t _tlast_t _terror_t _treported_t _tby_t _tthe_t "_tL3_t" _tmathematical_t _tformul...
L3ParserSettings_t * L3ParserSettings_create()
@_tendcond_t
Definition L3ParserSettings.cpp:358
void L3ParserSettings_setParseUnits(L3ParserSettings_t *settings, int flag)
_tSets_t _tthe_t _tunits_t _toption_t _tassociated_t _twith_t _tthis_t _tL3ParserSettings_t_t _tstruc...
Definition L3ParserSettings.cpp:451
void L3ParserSettings_setParseLog(L3ParserSettings_t *settings, ParseLogType_t type)
_tSets_t _tthe_t _tlog_t _tparsing_t _toption_t _tassociated_t _twith_t _tthis_t _tL3ParserSettings_t...
Definition L3ParserSettings.cpp:407
void L3ParserSettings_setModel(L3ParserSettings_t *settings, const Model_t *model)
_tSets_t _tthe_t _tmodel_t _tassociated_t _twith_t _tthis_t _tL3ParserSettings_t_t _tstructure_t _tto...
Definition L3ParserSettings.cpp:374
void L3ParserSettings_setParseCollapseMinus(L3ParserSettings_t *settings, int flag)
_tSets_t _tthe_t _tcollapse_t _tminus_t _toption_t _tassociated_t _twith_t _tthis_t _tL3ParserSetting...
Definition L3ParserSettings.cpp:429
@ L3P_PARSE_LOG_AS_ERROR
Definition L3ParserSettings.h:305
@ L3P_PARSE_LOG_AS_LN
Definition L3ParserSettings.h:302
@ L3P_PARSE_LOG_AS_LOG10
Definition L3ParserSettings.h:299
ASTNode_t * readMathMLFromString(const char *xml)
@_tendcond_t
Definition MathML.cpp:2273
char * writeMathMLToString(const ASTNode *node)
@_tif_t _tconly_t @_tmemberof_t _tASTNode_t_t @_tendif_t
Definition MathML.cpp:2428
void SBMLDocument_free(SBMLDocument_t *d)
_tFrees_t _tthe_t _tgiven_t _tSBMLDocument_t_t _tstructure_t.
Definition SBMLDocument.cpp:2248
Model_t * SBMLDocument_getModel(SBMLDocument_t *d)
_tReturns_t _tthe_t _tModel_t_t _tstructure_t _tstored_t _tin_t _tthis_t _tSBMLDocument_t_t _tstructu...
Definition SBMLDocument.cpp:2290
SBMLDocument_t * readSBMLFromFile(const char *filename)
@_tcopydoc_t _tdoc_readsbmlfromfile_t
Definition SBMLReader.cpp:455
Include all SBML types in a single header file.
Utility functions.