libSBML C++ API  5.18.0
translateL3Math.cpp

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

/**
* @file translateL3Math.cpp
* @brief Translates infix formulas into MathML and vice-versa, using the L3 parser instead of the old L1 parser.
* @author Lucian Smith
* @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 <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sbml/SBMLTypes.h>
#define BUFFER_SIZE 1024
using namespace std;
char *translateInfix (const char *formula, const L3ParserSettings& settings);
char *translateMathML (const char *xml);
int
main (int argc, char* argv[])
{
char line[BUFFER_SIZE];
char* trimmed;
char* result;
char* str;
size_t len;
SBMLDocument* doc = NULL;
StringBuffer_t* sb = StringBuffer_create(1024);
cout << endl
<< "This program translates L3 infix formulas into MathML and" << endl
<< "vice-versa. Enter or return on an empty line triggers" << endl
<< "translation. Ctrl-C quits" << endl
<< endl;
L3ParserSettings settings;
while (1)
{
cout << "Enter infix formula, MathML expression, or change parsing rules with the keywords:\nLOG_AS_LOG10, LOG_AS_LN, LOG_AS_ERROR, EXPAND_UMINUS, COLLAPSE_UMINUS, TARGETL2, TARGETL3, NO_UNITS, UNITS, or FILE:<filename>\n(Ctrl-C to quit):"
<< endl << endl;
cout << "> " ;
cin.getline(line, BUFFER_SIZE, '\n');
while (line != 0)
{
trimmed = util_trim(line);
len = strlen(trimmed);
if (len > 0)
{
if (strcmp(line, "LOG_AS_LOG10")==0) {
cout << "Now parsing 'log(x)' as 'log10(x)'" << endl << endl << "> ";
}
else if (strcmp(line, "LOG_AS_LN")==0) {
cout << "Now parsing 'log(x)' as 'ln(x)'" << endl << endl << "> ";
}
else if (strcmp(line, "LOG_AS_ERROR")==0) {
cout << "Now parsing 'log(x)' as an error" << endl << endl << "> ";
}
else if (strcmp(line, "EXPAND_UMINUS")==0) {
cout << "Will now leave multiple unary minuses expanded, and all negative numbers will be translated using the <minus> construct." << endl << endl << "> ";
}
else if (strcmp(line, "COLLAPSE_UMINUS")==0) {
cout << "Will now collapse multiple unary minuses, and incorporate a negative sign into digits." << endl << endl << "> ";
}
else if (strcmp(line, "TARGETL2")==0) {
settings.setParseUnits(false);
settings.setParseAvogadroCsymbol(false);
cout << "Will now target SBML Level 2 MathML, with no units on numbers, and no csymbol 'avogadro'." << endl << endl << "> ";
}
else if (strcmp(line, "NO_UNITS")==0) {
settings.setParseUnits(false);
cout << "Will now target MathML but with no units on numbers." << endl << endl << "> ";
}
else if (strcmp(line, "UNITS")==0) {
settings.setParseUnits(true);
cout << "Will now target MathML but with units on numbers." << endl << endl << "> ";
}
else if (strcmp(line, "TARGETL3")==0) {
settings.setParseUnits(true);
settings.setParseAvogadroCsymbol(true);
cout << "Will now target SBML Level 3 MathML, including having units on numbers, and the csymbol 'avogadro'." << endl << endl << "> ";
}
else if (line[0] == 'F' && line[1] == 'I' && line[2]=='L' && line[3]=='E' && line[4]==':') {
string filename(line);
filename = filename.substr(5, filename.size());
delete doc;
doc = readSBMLFromFile(filename.c_str());
if (doc->getModel()==NULL) {
cout << "File '" << filename << "' not found or no model present. Clearing the Model parsing object." << endl << endl << "> ";
}
else {
cout << "Using model from file " << filename << " to parse infix: all symbols present in that model will not be translated as native MathML or SBML-defined elements." << endl << endl << "> ";
}
settings.setModel(doc->getModel());
}
else {
StringBuffer_append (sb, trimmed);
StringBuffer_appendChar(sb, ' ');
}
}
else
{
str = StringBuffer_getBuffer(sb);
result = (str[0] == '<') ? translateMathML(str) : translateInfix(str, settings);
cout << "Result:" << endl << endl << result << endl << endl << endl;
StringBuffer_reset(sb);
break;
}
cin.getline(line, BUFFER_SIZE, '\n');
}
}
StringBuffer_free(sb);
return 0;
}
/**
* Translates the given infix formula into MathML.
*
* @return the MathML as a string. The caller owns the memory and is
* responsible for freeing it.
*/
char *
translateInfix (const char* formula, const L3ParserSettings& settings)
{
char* result;
ASTNode* math = SBML_parseL3FormulaWithSettings(formula, &settings);
if (math==NULL) {
}
else {
result = writeMathMLToString(math);
ASTNode_free(math);
}
return result;
}
/**
* Translates the given MathML into an infix formula. The MathML must
* contain no leading whitespace, but an XML header is optional.
*
* @return the infix formula as a string. The caller owns the memory and
* is responsible for freeing it.
*/
char *
translateMathML (const char* xml)
{
char* result;
ASTNode_t* math;
math = readMathMLFromString(xml);
result = SBML_formulaToString(math);
ASTNode_free(math);
return result;
}