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/**
* @file translateMath.java
* @brief Translates infix formulas into MathML and vice-versa
* @author Nicolas Rodriguez (translated from libSBML C++ examples)
* @author Ben Bornstein
* @author Michael Hucka
*
* <!--------------------------------------------------------------------------
* 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) 2013-2014 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.
* ------------------------------------------------------------------------ -->
*/
import java.io.IOException;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLReader;
import org.sbml.libsbml.libsbml;
public class translateMath
{
public static void main (String[] args)
{
if (args.length != 0)
{
println("Usage: java translateMath\n");
System.exit(1);
}
println("This program translates infix formulas into MathML and" +
" vice-versa. \nCtrl-D or Ctrl-Z quits and triggers" +
" translation.\n");
char c;
int i = 0;
String mathStr = new String();
try
{
// Hit CTRL-Z on PC's to send EOF, CTRL-D on Unix
while (i != -1)
{
// Read a character from keyboard.
i = System.in.read();
// System.in.read() returns everything, including things
// like return, backspace, etc. Filter those out.
if (i < 32 || i > 127)
continue;
// 1 byte character is returned as an int, so cast it to a char.
c = (char) i;
mathStr += c;
}
}
catch (IOException ioe)
{
println( "IO error:" + ioe );
}
// If the input starts with '<', assume it's XML content.
String result = (mathStr.charAt(0) == '<') ?
translateMathML(mathStr) : translateInfix(mathStr);
println("Result:\n");
println(result);
}
/**
* Translates the given infix formula into MathML.
*
* @return the MathML as a string.
*/
static String translateInfix (String formula)
{
return libsbml.writeMathMLToString( libsbml.parseFormula(formula) );
}
/**
* 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.
*/
static String translateMathML (String xml)
{
return libsbml.formulaToString( libsbml.readMathMLFromString(xml) );
}
static void println (String msg)
{
System.out.println(msg);
}
/**
* Loads the SWIG-generated libSBML Java module when this class is
* loaded, or reports a sensible diagnostic message about why it failed.
*/
static
{
String varname;
String shlibname;
if (System.getProperty("os.name").startsWith("Mac OS"))
{
varname = "DYLD_LIBRARY_PATH"; // We're on a Mac.
shlibname = "'libsbmlj.jnilib'";
}
else
{
varname = "LD_LIBRARY_PATH"; // We're not on a Mac.
shlibname = "'libsbmlj.so' and/or 'libsbml.so'";
}
try
{
System.loadLibrary("sbmlj");
// For extra safety, check that the jar file is in the classpath.
Class.forName("org.sbml.libsbml.libsbml");
}
catch (UnsatisfiedLinkError e)
{
System.err.println("Error encountered while attempting to load libSBML:");
e.printStackTrace();
System.err.println("Please check the value of your " + varname +
" environment variable and/or" +
" your 'java.library.path' system property" +
" (depending on which one you are using) to" +
" make sure it list the directories needed to" +
" find the " + shlibname + " library file and the" +
" libraries it depends upon (e.g., the XML parser).");
System.exit(1);
}
catch (ClassNotFoundException e)
{
System.err.println("Error: unable to load the file 'libsbmlj.jar'." +
" It is likely that your -classpath command line " +
" setting or your CLASSPATH environment variable " +
" do not include the file 'libsbmlj.jar'.");
System.exit(1);
}
catch (SecurityException e)
{
System.err.println("Error encountered while attempting to load libSBML:");
e.printStackTrace();
System.err.println("Could not load the libSBML library files due to a"+
" security exception.\n");
System.exit(1);
}
}
}
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