//**********************************************************************************************************************
vector<string> RenameFileCommand::setParameters(){
try {
CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pflow);
CommandParameter pfile("file", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfile);
CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pbiom);
CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pphylip);
CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcolumn);
CommandParameter psummary("summary", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psummary);
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psabund);
CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(porder);
CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptree);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pshared);
CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pcount);
CommandParameter poutputname("new", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poutputname);
CommandParameter pinputname("input", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pinputname);
CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prelabund);
CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psff);
CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pconstaxonomy);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
CommandParameter pmothurgenerated("shorten", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmothurgenerated);
CommandParameter pdeleteold("deleteold", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdeleteold);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter pprefix("prefix", "String", "", "", "", "", "","",false,false); parameters.push_back(pprefix);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "RenameFileCommand", "setParameters");
exit(1);
}
}
/*!
* This is done by running
* each reaction as far forward or backward as possible, subject
* to the constraint that all mole numbers remain
* non-negative. Reactions for which \f$ \Delta \mu^0 \f$ are
* positive are run in reverse, and ones for which it is negative
* are run in the forward direction. The end result is equivalent
* to solving the linear programming problem of minimizing the
* linear Gibbs function subject to the element and
* non-negativity constraints.
*/
int VCS_SOLVE::vcs_setMolesLinProg() {
int ik, irxn;
double test = -1.0E-10;
#ifdef DEBUG_MODE
std::string pprefix(" --- seMolesLinProg ");
if (m_debug_print_lvl >= 2) {
plogf(" --- call setInitialMoles\n");
}
#endif
// m_mu are standard state chemical potentials
// Boolean on the end specifies standard chem potentials
// m_mix->getValidChemPotentials(not_mu, DATA_PTR(m_mu), true);
// -> This is already done coming into the routine.
double dg_rt;
int idir;
double nu;
double delta_xi, dxi_min = 1.0e10;
bool redo = true;
int jcomp;
int retn;
int iter = 0;
bool abundancesOK = true;
int usedZeroedSpecies;
std::vector<double> sm(m_numElemConstraints*m_numElemConstraints, 0.0);
std::vector<double> ss(m_numElemConstraints, 0.0);
std::vector<double> sa(m_numElemConstraints, 0.0);
std::vector<double> wx(m_numElemConstraints, 0.0);
std::vector<double> aw(m_numSpeciesTot, 0.0);
for (ik = 0; ik < m_numSpeciesTot; ik++) {
if (m_speciesUnknownType[ik] != VCS_SPECIES_INTERFACIALVOLTAGE) {
m_molNumSpecies_old[ik] = MAX(0.0, m_molNumSpecies_old[ik]);
}
}
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
}
#endif
while (redo) {
if (!vcs_elabcheck(0)) {
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf("%s Mole numbers failing element abundances\n", pprefix.c_str());
plogf("%sCall vcs_elcorr to attempt fix\n", pprefix.c_str());
}
#endif
retn = vcs_elcorr(VCS_DATA_PTR(sm), VCS_DATA_PTR(wx));
if (retn >= 2) {
abundancesOK = false;
} else {
abundancesOK = true;
}
} else {
abundancesOK = true;
}
/*
* Now find the optimized basis that spans the stoichiometric
* coefficient matrix, based on the current composition, m_molNumSpecies_old[]
* We also calculate sc[][], the reaction matrix.
*/
retn = vcs_basopt(FALSE, VCS_DATA_PTR(aw), VCS_DATA_PTR(sa),
VCS_DATA_PTR(sm), VCS_DATA_PTR(ss),
test, &usedZeroedSpecies);
if (retn != VCS_SUCCESS) return retn;
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf("iteration %d\n", iter);
}
#endif
redo = false;
iter++;
if (iter > 15) break;
// loop over all reactions
for (irxn = 0; irxn < m_numRxnTot; irxn++) {
// dg_rt is the Delta_G / RT value for the reaction
ik = m_numComponents + irxn;
dg_rt = m_SSfeSpecies[ik];
dxi_min = 1.0e10;
const double *sc_irxn = m_stoichCoeffRxnMatrix[irxn];
for (jcomp = 0; jcomp < m_numElemConstraints; jcomp++) {
dg_rt += m_SSfeSpecies[jcomp] * sc_irxn[jcomp];
}
// fwd or rev direction.
// idir > 0 implies increasing the current species
// idir < 0 implies decreasing the current species
idir = (dg_rt < 0.0 ? 1 : -1);
if (idir < 0) {
dxi_min = m_molNumSpecies_old[ik];
}
for (jcomp = 0; jcomp < m_numComponents; jcomp++) {
nu = sc_irxn[jcomp];
// set max change in progress variable by
// non-negativity requirement
if (nu*idir < 0) {
delta_xi = fabs(m_molNumSpecies_old[jcomp]/nu);
// if a component has nearly zero moles, redo
// with a new set of components
if (!redo) {
if (delta_xi < 1.0e-10 && (m_molNumSpecies_old[ik] >= 1.0E-10)) {
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
plogf(" --- Component too small: %s\n", m_speciesName[jcomp].c_str());
}
#endif
redo = true;
}
}
if (delta_xi < dxi_min) dxi_min = delta_xi;
}
}
// step the composition by dxi_min, check against zero, since
// we are zeroing components and species on every step.
// Redo the iteration, if a component went from positive to zero on this step.
double dsLocal = idir*dxi_min;
m_molNumSpecies_old[ik] += dsLocal;
m_molNumSpecies_old[ik] = MAX(0.0, m_molNumSpecies_old[ik]);
for (jcomp = 0; jcomp < m_numComponents; jcomp++) {
bool full = false;
if (m_molNumSpecies_old[jcomp] > 1.0E-15) {
full = true;
}
m_molNumSpecies_old[jcomp] += sc_irxn[jcomp] * dsLocal;
m_molNumSpecies_old[jcomp] = MAX(0.0, m_molNumSpecies_old[jcomp]);
if (full) {
if (m_molNumSpecies_old[jcomp] < 1.0E-60) {
redo = true;
}
}
}
}
// set the moles of the phase objects to match
// updateMixMoles();
// Update the phase objects with the contents of the m_molNumSpecies_old vector
// vcs_updateVP(0);
#ifdef DEBUG_MODE
if (m_debug_print_lvl >= 2) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
}
#endif
}
#ifdef DEBUG_MODE
if (m_debug_print_lvl == 1) {
printProgress(m_speciesName, m_molNumSpecies_old, m_SSfeSpecies);
plogf(" --- setInitialMoles end\n");
}
#endif
retn = 0;
if (!abundancesOK) {
retn = -1;
} else if (iter > 15) {
retn = 1;
}
return retn;
}