readFluxMLModel.cpp

#include <iostream>

#include <fluxml/FluxML.h>
#include <fluxml/MGroup.h>
#include <fluxml/MMDocument.h>
#include <fluxml/XMLFramework.h>

using namespace std;
using namespace flux;

std::string make_section_head(const std::string& section_name)
{
    std::string line(80, '=');
    std::string fill((line.length() - section_name.length()) / 2, ' ');
    std::string header = line + "\n" + fill + section_name + "\n" + line;
    return header;
}

int main(int argc, char* argv[])
{

    /** check number of specified arguments **/
    if (argc != 2)
    {
        cout << endl << "Usage: readFluxML filename" << endl << endl;
        return 1;
    }

    /** make sure error Messages go somewhere **/
    PUBLISHLOG(stderr_log);

    const char* filename = argv[1];
    xml::FluxMLDocument * fml = 0;
    try
    {
        fml = new xml::FluxMLDocument(filename);
    }
    catch (xml::XMLException& e)
    {
        cerr << "Problem with opening File " << filename << ":" << endl << e.toString() << endl;
        exit(1);
    }
    cout << make_section_head("metabolites") << endl;
    /** print network metabolites **/
    charptr_map<data::Pool*> * poolMap = fml->getPoolMap();
    charptr_map<data::Pool*>::const_iterator pi;
    for (pi = poolMap->begin(); pi != poolMap->end(); ++pi)
    {
        data::Pool* pool = pi->value;
        cout << "pool: " << pool->getName() << "\t atoms: "
             << pool->getNumAtoms() << endl;
    }

    /** print network reactions **/
    cout << endl << make_section_head("reactions") << endl;
    const std::list<data::IsoReaction*>* reactionList = fml->getReactions();
    std::list<data::IsoReaction*>::const_iterator ri;
    for (ri = reactionList->begin(); ri != reactionList->end(); ++ri)
    {
        data::IsoReaction* reaction = *ri;
        cout << "reaction: " << reaction->getName() << "\t atoms: "
             << reaction->getNumAtoms() << endl;

        /** print reaction educts **/
        const std::list<data::IsoReaction::Isotopomer*> educts =
            reaction->getEducts();
        std::list<data::IsoReaction::Isotopomer*>::const_iterator ei;
        for (ei = educts.begin(); ei != educts.end(); ++ei)
            cout << "educt-name: " << (*ei)->name << "\t educt-cfg: "
                 << (*ei)->atom_cfg << endl;

        /** print reaction products **/
        const std::list<data::IsoReaction::Isotopomer*> products =
            reaction->getProducts();
        for (ei = products.begin(); ei != products.end(); ++ei)
            cout << "educt-name: " << (*ei)->name << "\t educt-cfg: "
                 << (*ei)->atom_cfg << endl;
    }

    cout << endl << make_section_head("configuration default") << endl;
    /** select "default" configuration**/
    data::Configuration * cfg = fml->getConfiguration("default");
    if (cfg == 0)
    {
        fWARNING("aborting: \"default\" configuration not found.");
        delete fml;
        xml::framework::terminate();
        return EXIT_FAILURE;
    }

    cout << endl << make_section_head("constraints") << endl;
    /** print model constraints **/
    charptr_array cons;
    charptr_array::const_iterator consi;

    /** netflux constraints **/
    cons = cfg->getConstraintFluxesNet();
    for (consi = cons.begin(); consi != cons.end(); ++consi)
        cout << "net: " << *consi << endl;

    /** xchflux constraints **/
    cons = cfg->getConstraintFluxesXch();
    for (consi = cons.begin(); consi != cons.end(); ++consi)
        cout << "xch: " << *consi << endl;

    /** poolsize constraints **/
    cons = cfg->getConstraintPools();
    for (consi = cons.begin(); consi != cons.end(); ++consi)
        cout << "pool: " << *consi << endl;

    cout << endl << make_section_head("input tracers") << endl;
    /** print tracer specification **/
    list<data::InputPool*> const & IPL = cfg->getInputPools();
    list<data::InputPool*>::const_iterator ip;
    cout << "tracers: " << endl;
    for (ip = IPL.begin(); ip != IPL.end(); ++ip)
    {
        data::InputPool & I = *(*ip);
        cout << "pool: " << I.getName() << "\t cost: " << I.getCost() << endl;
    }

    cout << endl << make_section_head("measurement data") << endl;
    /** print experimental data **/
    xml::MMDocument * mmdoc = 0;
    mmdoc = cfg->getMMDocument();

    charptr_array mgroup_names = mmdoc->getGroupNames();
    charptr_array::const_iterator mgi;

    for (mgi = mgroup_names.begin(); mgi != mgroup_names.end(); mgi++)
    {
        xml::MGroup * mgroups = mmdoc->getGroupByName(*mgi);
        cout << "group-id: " << mgroups->getGroupId() << "\t group-spec: "
             << mgroups->getSpec() << endl;
    }

    /** free allocated memory **/
    delete fml;
    xml::framework::terminate();
    return EXIT_SUCCESS;
}