END_TEST
START_TEST (test_L3_Model_name)
{
const char *name = "My_Favorite_Factory";
fail_unless( !Model_isSetName(M) );
Model_setName(M, name);
fail_unless( !strcmp(Model_getName(M), name) );
fail_unless( Model_isSetName(M) );
if (Model_getName(M) == name)
{
fail("Model_setName(...) did not make a copy of string.");
}
Model_unsetName(M);
fail_unless( !Model_isSetName(M) );
if (Model_getName(M) != NULL)
{
fail("Model_unsetName(M) did not clear string.");
}
}
END_TEST
START_TEST (test_comp_modelDefinition_name)
{
const char *name = "My_Favorite_Factory";
fail_unless( !Model_isSetName(P) );
Model_setName(P, name);
const char* getchar = Model_getName(P);
fail_unless( !strcmp(getchar, name) );
fail_unless( Model_isSetName(P) );
if (getchar == name)
{
fail("Model_setName(...) did not make a copy of string.");
}
Model_unsetName(P);
fail_unless( !Model_isSetName(P) );
if (Model_getName(P) != NULL)
{
fail("Model_unsetName(P) did not clear string.");
}
}
static int drawJacobyTxt(cvodeData_t *data, char *file)
{
int i, j;
char filename[WORDSIZE];
FILE *f;
sprintf(filename, "%s.dot", file);
f = fopen(filename, "w");
fprintf(f ,"digraph jacoby {\n");
fprintf(f ,"overlap=scale;\n");
if ( Model_isSetName(data->model->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getName(data->model->m),
data->currenttime);
else if ( Model_isSetId(data->model->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getId(data->model->m),
data->currenttime);
else
fprintf(f ,"label=\"at time %g\";\n", data->currenttime);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
for ( i=0; i<data->model->neq; i++ )
{
for ( j=0; j<data->model->neq; j++ )
{
if ( evaluateAST(data->model->jacob[i][j], data) != 0 )
{
fprintf(f ,"%s->%s [label=\"%g\" ",
data->model->names[j],
data->model->names[i],
evaluateAST(data->model->jacob[i][j],
data));
if ( evaluateAST(data->model->jacob[i][j], data) < 0 )
fprintf(f ,"arrowhead=tee color=red];\n");
else
fprintf(f ,"];\n");
}
}
}
for ( i=0; i<data->model->neq; i++ )
{
fprintf(f ,"%s [label=\"%s\"];", data->model->names[i],
data->model->names[i]);
}
fprintf(f, "}\n");
return 1;
}
END_TEST
START_TEST (test_L3_Model_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Model_t *m =
Model_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) m) == SBML_MODEL );
fail_unless( SBase_getMetaId ((SBase_t *) m) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) m) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) m) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) m) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) m) == 1 );
fail_unless( Model_getNamespaces (m) != NULL );
fail_unless( XMLNamespaces_getLength(Model_getNamespaces(m)) == 2 );
fail_unless( Model_getId (m) == NULL );
fail_unless( Model_getName (m) == NULL );
fail_unless( Model_getSubstanceUnits(m) == NULL );
fail_unless( Model_getTimeUnits(m) == NULL );
fail_unless( Model_getVolumeUnits(m) == NULL );
fail_unless( Model_getAreaUnits(m) == NULL );
fail_unless( Model_getLengthUnits(m) == NULL );
fail_unless( Model_getConversionFactor(m) == NULL );
fail_unless( !Model_isSetId (m) );
fail_unless( !Model_isSetName (m) );
fail_unless( !Model_isSetSubstanceUnits(m) );
fail_unless( !Model_isSetTimeUnits(m) );
fail_unless( !Model_isSetVolumeUnits(m) );
fail_unless( !Model_isSetAreaUnits(m) );
fail_unless( !Model_isSetLengthUnits(m) );
fail_unless( !Model_isSetConversionFactor(m) );
Model_free(m);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
static int openXMGrace(cvodeData_t *data)
{
double maxY;
/* Open XMGrace */
if ( !GraceIsOpen() ) {
GraceRegisterErrorFunction(grace_error);
/* Start Grace with a buffer size of 2048 and open the pipe */
if ( GraceOpen(2048) == -1 ) {
fprintf(stderr, "Can't run Grace. \n");
return 1;
}
else if ( GraceIsOpen() ) {
maxY = 1.0;
/*
"with g%d" might become useful, when printing multiple
graphs into one XMGrace subprocess.
*/
/* GracePrintf("with g%d", data->results->xmgrace); */
GracePrintf("world xmax %g", data->currenttime);
GracePrintf("world ymax %g", 1.25*maxY);
GracePrintf("xaxis tick major %g", data->currenttime/10);
/* GracePrintf("xaxis tick minor %d", (int) data->currenttime/100); */
GracePrintf("yaxis tick major %g", (1.25*maxY)/12.5 );
GracePrintf("xaxis label font 4");
GracePrintf("xaxis label \"time\"");
GracePrintf("xaxis ticklabel font 4");
GracePrintf("xaxis ticklabel char size 0.7");
GracePrintf("yaxis label font 4");
GracePrintf("yaxis label \"concentration\"");
GracePrintf("yaxis ticklabel font 4");
GracePrintf("yaxis ticklabel char size 0.7");
if ( Model_isSetName(data->model->simple) )
GracePrintf("subtitle \"%s\"", Model_getName(data->model->simple));
else if ( Model_isSetId(data->model->simple) )
GracePrintf("subtitle \"%s\"", Model_getId(data->model->simple));
else
GracePrintf("subtitle \"model has no name/id\"");
GracePrintf("subtitle font 8");
}
}
else {
fprintf(stderr, "Please close XMGrace first.\n");
return 1;
}
return 0;
}
void printModel(Model_t *m, FILE *f)
{
fprintf(f, "\n");
fprintf(f, "Model Statistics:\n");
fprintf(f, " Model id: %s\n",
Model_isSetId(m) ? Model_getId(m) : "(not set)");
fprintf(f, " Model name: %s\n",
Model_isSetName(m) ? Model_getName(m) : "(not set)");
fprintf(f, "\n");
fprintf(f, " Compartments: %d\n", Model_getNumCompartments(m));
fprintf(f, " Species: %d\n", Model_getNumSpecies(m));
fprintf(f, " Reactions: %d\n", Model_getNumReactions(m));
fprintf(f, " Rules: %d\n", Model_getNumRules(m));
fprintf(f, " Events: %d\n", Model_getNumEvents(m));
fprintf(f, " Functions: %d\n", Model_getNumFunctionDefinitions(m) );
fprintf(f, "\n");
}
static int
drawModelTxt(Model_t *m, char *file) {
Species_t *s;
Reaction_t *re;
const ASTNode_t *math;
SpeciesReference_t *sref;
ModifierSpeciesReference_t *mref;
int i,j;
int reversible;
char filename[WORDSIZE];
FILE *f;
sprintf(filename, "%s.dot", file);
f = fopen(filename, "w");
fprintf(f ,"digraph reactionnetwork {\n");
fprintf(f ,"label=\"%s\";\n",
Model_isSetName(m) ?
Model_getName(m) : (Model_isSetId(m) ? Model_getId(m) : "noId") );
fprintf(f ,"overlap=scale;\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
reversible = Reaction_getReversible(re);
for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {
mref = Reaction_getModifier(re,j);
fprintf(f ,"%s->%s [style=dashed arrowhead=odot];\n",
ModifierSpeciesReference_getSpecies(mref), Reaction_getId(re));
}
for ( j=0; j<Reaction_getNumReactants(re); j++ ) {
sref = Reaction_getReactant(re,j);
fprintf(f ,"%s->%s [label=\"",
SpeciesReference_getSpecies(sref), Reaction_getId(re));
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
fprintf(f ,"%s", SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1) {
fprintf(f ,"%g",SpeciesReference_getStoichiometry(sref));
}
}
if ( reversible == 1 ) {
fprintf(f ,"\" arrowtail=onormal];\n");
}
else {
fprintf(f ,"\" ];\n");
}
}
for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
sref = Reaction_getProduct(re,j);
fprintf(f ,"%s->%s [label=\"",
Reaction_getId(re), SpeciesReference_getSpecies(sref));
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
fprintf(f ,"%s ", SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1) {
fprintf(f ,"%g ",SpeciesReference_getStoichiometry(sref));
}
}
if ( reversible == 1 ) {
fprintf(f ,"\" arrowtail=onormal];\n");
}
else {
fprintf(f ,"\" ];\n");
}
}
}
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
fprintf(f ,"%s [label=\"%s\" shape=box];\n",
Reaction_getId(re),
Reaction_isSetName(re) ?
Reaction_getName(re) : Reaction_getId(re));
}
for ( i=0; i<Model_getNumSpecies(m); i++) {
s = Model_getSpecies(m, i);
fprintf(f ,"%s [label=\"%s\"];",
Species_getId(s),
Species_isSetName(s) ? Species_getName(s) : Species_getId(s));
}
fprintf(f ,"}\n");
return 1;
}
SBML_ODESOLVER_API int drawJacoby(cvodeData_t *data, char *file, char *format) {
#if !USE_GRAPHVIZ
SolverError_error(
WARNING_ERROR_TYPE,
SOLVER_ERROR_NO_GRAPHVIZ,
"odeSolver has been compiled without GRAPHIZ functionality. ",
"Graphs are printed to stdout in the graphviz' .dot format.");
drawJacobyTxt(data, file);
#else
int i, j;
GVC_t *gvc;
Agraph_t *g;
Agnode_t *r;
Agnode_t *s;
Agedge_t *e;
Agsym_t *a;
char name[WORDSIZE];
char label[WORDSIZE];
char *output[3];
char *command = "dot";
char *formatopt;
char *outfile;
/* setting name of outfile */
ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
sprintf(outfile, "-o%s_jm.%s", file, format);
/* setting output format */
ASSIGN_NEW_MEMORY_BLOCK(formatopt, strlen(format)+3, char, 0);
sprintf(formatopt, "-T%s", format);
/* construct command-line */
output[0] = command;
output[1] = formatopt;
output[2] = outfile;
output[3] = NULL;
/* set up renderer context */
gvc = (GVC_t *) gvContext();
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION < 4
dotneato_initialize(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
parse_args(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvParseArgs(gvc, 3, output);
#endif
g = agopen("G", AGDIGRAPH);
/* avoid overlapping nodes, for graph embedding by neato */
a = agraphattr(g, "overlap", "");
agxset(g, a->index, "scale");
/* set graph label */
if ( Model_isSetName(data->model->m) )
sprintf(label, "%s at time %g", Model_getName(data->model->m),
data->currenttime);
else if ( Model_isSetId(data->model->m) )
sprintf(label, "%s at time %g", Model_getId(data->model->m),
data->currenttime);
else
sprintf(label, "label=\"at time %g\";\n", data->currenttime);
a = agraphattr(g, "label", "");
agxset(g, a->index, label);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
for ( i=0; i<data->model->neq; i++ ) {
for ( j=0; j<data->model->neq; j++ ) {
if ( evaluateAST(data->model->jacob[i][j], data) != 0 ) {
sprintf(name, "%s", data->model->names[j]);
r = agnode(g,name);
agset(r, "label", data->model->names[j]);
sprintf(label, "%s.htm", data->model->names[j]);
a = agnodeattr(g, "URL", "");
agxset(r, a->index, label);
sprintf(name,"%s", data->model->names[i]);
s = agnode(g,name);
agset(s, "label", data->model->names[i]);
sprintf(label, "%s.htm", data->model->names[i]);
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,r,s);
a = agedgeattr(g, "label", "");
sprintf(name, "%g", evaluateAST(data->model->jacob[i][j], data));
agxset (e, a->index, name);
if ( evaluateAST(data->model->jacob[i][j], data) < 0 ) {
a = agedgeattr(g, "arrowhead", "");
agxset(e, a->index, "tee");
a = agedgeattr(g, "color", "");
agxset(e, a->index, "red");
}
}
}
}
/* Compute a layout */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvBindContext(gvc, g);
dot_layout(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_layout(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvLayoutJobs(gvc, g);
#endif
/* Write the graph according to -T and -o options */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dotneato_write(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
emit_jobs(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvRenderJobs(gvc, g);
#endif
/* Clean out layout data */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_cleanup(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeLayout(gvc, g);
#endif
/* Free graph structures */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#endif
agclose(g);
/* Clean up output file and errors */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvFREEcontext(gvc);
dotneato_eof(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
dotneato_terminate(gvc);
#elif (GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6) || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeContext(gvc);
#endif
xfree(formatopt);
xfree(outfile);
#endif
return 1;
}
static int
drawSensitivityTxt(cvodeData_t *data, char *file, double threshold) {
int i, j;
char filename[WORDSIZE];
FILE *f;
odeModel_t *om;
double *highest;
double *lowest;
om = data->model;
sprintf(filename, "%s.dot", file);
f = fopen(filename, "w");
fprintf(f ,"digraph jacoby {\n");
fprintf(f ,"overlap=scale;\n");
if ( Model_isSetName(om->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getName(om->m),
data->currenttime);
else if ( Model_isSetId(om->m) )
fprintf(f ,"label=\"%s at time %g\";\n", Model_getId(om->m),
data->currenttime);
else
fprintf(f ,"label=\"at time %g\";\n", data->currenttime);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
ASSIGN_NEW_MEMORY_BLOCK(highest, data->nsens, double, 0);
ASSIGN_NEW_MEMORY_BLOCK(lowest, data->nsens, double, 0);
for ( j=0; j<data->nsens; j++ ) {
highest[j] = 0;
lowest[j] = 0;
for ( i=0; i<om->neq; i++ ) {
if ( data->sensitivity[i][j] > highest[j] )
highest[j] = data->sensitivity[i][j];
if ( data->sensitivity[i][j] < lowest[j] )
lowest[j] = data->sensitivity[i][j];
}
}
for ( i=0; i<om->neq; i++ ) {
for ( j=0; j<data->nsens; j++ ) {
if ( (data->sensitivity[i][j] > threshold*highest[j]) ||
(data->sensitivity[i][j] < threshold*lowest[j]) ) {
fprintf(f ,"%s->%s [label=\"%g\" ",
om->names[om->index_sens[j]],
om->names[i],
data->sensitivity[i][j]);
if ( data->sensitivity[i][j] < 0 ) {
fprintf(f ,"arrowhead=tee color=red];\n");
}
else {
fprintf(f ,"];\n");
}
}
}
}
for ( i=0; i<om->neq; i++ ) {
fprintf(f ,"%s [label=\"%s\"];", om->names[i],
om->names[i]);
}
for ( i=0; i<data->nsens; i++ ) {
fprintf(f ,"%s [label=\"%s\"];", om->names[om->index_sens[i]],
om->names[om->index_sens[i]]);
}
fprintf(f, "}\n");
return 1;
}
static int printXMGReactionTimeCourse ( cvodeData_t *data )
{
int i, j, k, n;
double maxY, minY, result;
Model_t *m;
Reaction_t *r;
KineticLaw_t *kl;
ASTNode_t **kls;
odeModel_t *om = data->model;
cvodeResults_t *results = data->results;
maxY = 0.0;
minY = 0.0;
fprintf(stderr,
"Printing time development of reaction fluxes to XMGrace!\n");
if ( om->m == NULL ) {
fprintf(stderr, "Error: No reaction model availabe\n");
return 1;
}
else m = om->m;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr, "Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "flux [substance/time]");
if ( Model_isSetName(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(m),
"reaction flux time courses");
else if ( Model_isSetId(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(m),
"reaction flux time courses");
else
GracePrintf("subtitle \"model has no name, %s/id\"",
"reaction flux time courses");
/* print legend */
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
if ( Reaction_isSetName(r) )
GracePrintf("g0.s%d legend \"%s: %s \"\n", i+1,
Reaction_getId(r), Reaction_getName(r));
else
GracePrintf("g0.s%d legend \"%s \"\n", i+1, Reaction_getId(r));
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
if(!(kls = (ASTNode_t **)calloc(Model_getNumReactions(m),
sizeof(ASTNode_t *))))
fprintf(stderr, "failed!\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
kl = Reaction_getKineticLaw(r);
kls[i] = copyAST(KineticLaw_getMath(kl));
AST_replaceNameByParameters(kls[i], KineticLaw_getListOfParameters(kl));
AST_replaceConstants(m, kls[i]);
}
/* evaluate flux for each time point and print to XMGrace */
for ( i=0; i<=results->nout; i++ ) {
n = 1;
/* set time and variable values to values at time[k] */
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ )
data->value[j] = results->value[j][i];
/* evaluate kinetic law expressions */
for ( j=0; j<Model_getNumReactions(m); j++ ) {
result = evaluateAST(kls[j], data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[i], result);
n++;
}
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "flux");
/* free temporary ASTNodes */
for ( i=0; i<Model_getNumReactions(m); i++ )
ASTNode_free(kls[i]);
free(kls);
return 0;
}
void printPhase(cvodeData_t *data)
{
#if !USE_GRACE
fprintf(stderr,
"odeSolver has been compiled without XMGRACE functionality.\n");
fprintf(stderr,
"Phase diagrams can only be printed to XMGrace at the moment.\n");
#else
int i,j;
double maxY;
double minY;
double maxX;
char *x;
double xvalue;
char *y;
double yvalue;
cvodeResults_t *results;
maxY = 1.0;
maxX = 1.0;
minY = 0.0;
if ( data==NULL || data->results==NULL ) {
Warn(stderr,
"No data available to print! Please integrate model first!\n");
return;
}
results = data->results;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr,
"Error: Couldn't open XMGrace\n");
return;
}
GracePrintf("world xmax %g", 1.25*maxX);
GracePrintf("world ymax %g", 1.25*maxY);
GracePrintf("xaxis tick major %g", (1.25*maxX)/12.5);
/* GracePrintf("xaxis tick minor %d", (int) data->currenttime/100); */
GracePrintf("yaxis tick major %g", (1.25*maxY)/12.5 );
if ( Model_isSetName(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(data->model->m),
"phase diagram");
else if ( Model_isSetId(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(data->model->m),
"phase diagram");
else
GracePrintf("subtitle \"model has no name, %s/id\"", "phase diagram");
GracePrintf("xaxis label \"species 1\"");
GracePrintf("yaxis label \"species 2\"");
printf("Please enter the IDs and NOT the NAMES of species!\n");
printf("In interactive mode press 'c' to see ID/NAME pairs.\n\n");
printf("Please enter the ID of the species for the x axis: ");
x = get_line(stdin);
x = util_trim(x);
GracePrintf("xaxis label \"%s\"", x);
GracePrintf("redraw");
printf("Please enter the ID of the species for the y axis: ");
y = get_line(stdin);
y = util_trim(y);
GracePrintf("yaxis label \"%s\"", y);
GracePrintf("redraw");
/* check if species exist */
xvalue = 1;
yvalue = 1;
for ( j=0; j<data->model->neq; j++ ) {
if ( !strcmp(x, data->model->names[j]) ) {
xvalue = 0;
GracePrintf("xaxis label \"%s\"", data->model->names[j]);
}
if ( !strcmp(y, data->model->names[j]) ) {
yvalue = 0;
GracePrintf("yaxis label \"%s\"", data->model->names[j]);
}
}
if ( xvalue || yvalue ) {
fprintf(stderr, "One of the entered species does not exist.\n");
GraceClose();
fprintf(stderr, "XMGrace subprocess closed. Please try again");
free(x);
free(y);
return;
}
fprintf(stderr, "Printing phase diagram to XMGrace!\n");
for ( i=0; i<=results->nout; ++i ) {
for ( j=0; j<data->model->neq; j++ ){
if ( !strcmp(x, data->model->names[j]) ) {
xvalue = results->value[j][i];
}
if ( !strcmp(y, data->model->names[j]) ) {
yvalue = results->value[j][i];
}
}
GracePrintf("g0.s1 point %g, %g", xvalue, yvalue);
if ( yvalue > maxY ) {
maxY = 1.25*yvalue;
GracePrintf("world ymax %g", maxY);
GracePrintf("yaxis tick major %g", maxY/10);
}
if ( xvalue > maxX ) {
maxX = 1.25*xvalue;
GracePrintf("world xmax %g", maxX);
GracePrintf("xaxis tick major %g", maxX/10);
}
/*
redrawing on each 10th step gives an impression,
how fast the two values change within the phase
diagram.
*/
if ( i%10 == 0 ) {
GracePrintf("redraw");
}
}
GracePrintf("redraw");
closeXMGrace(data, "phase");
free(x);
free(y);
#endif
return;
}
static int printXMGOdeTimeCourse(cvodeData_t *data)
{
int i, j, n;
double maxY;
double minY;
double result;
cvodeResults_t *results;
maxY = 0.01;
minY = 0.0;
fprintf(stderr,
"Printing time development of the ODEs (rates) to XMGrace!\n");
results = data->results;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr,
"Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "ODE values");
if ( Model_isSetName(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(data->model->m),
"ODEs time course");
else if ( Model_isSetId(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(data->model->m),
"ODEs time course");
else
GracePrintf("subtitle \"model has no name/id, %s\"",
"ODEs time course");
/* print legend */
if ( printXMGLegend(data, data->model->neq) > 0 ){
fprintf(stderr,
"Warning: Couldn't print legend\n");
return 1;
}
/* evaluate ODE at each time point and print to XMGrace */
for ( i=0; i<=results->nout; ++i ) {
n = 1;
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ ) {
data->value[j] = results->value[j][i];
}
for ( j=0; j<data->model->neq; j++ ) {
result = evaluateAST(data->model->ode[j],data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[i], result);
n++;
}
/*
if ( i%10 == 0 ) {
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
}
*/
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "rates");
return 0;
}
static int printXMGJacobianTimeCourse ( cvodeData_t *data )
{
int i, j, k, n;
double maxY;
double minY;
double result;
cvodeResults_t *results;
maxY = 0.0;
minY = 0.0;
fprintf(stderr,
"Printing time development of the jacobian matrix to XMGrace!\n");
results = data->results;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr,
"Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "jacobian matrix value");
if ( Model_isSetName(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(data->model->m),
"jacobian matrix time course");
else if ( Model_isSetId(data->model->m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(data->model->m),
"jacobian matrix time course");
else
GracePrintf("subtitle \"model has no name, %s/id\"",
"jacobian matrix time course");
/* print legend */
n = 1;
for ( i=0; i<data->model->neq; i++ ) {
for ( j=0; j<data->model->neq; j++ ) {
GracePrintf("g0.s%d legend \"%s / %s\"\n",
n, data->model->names[i], data->model->names[j]);
n++;
}
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
/* evaluate jacobian matrix for each time point and print to XMGrace */
for ( k = 0; k<=results->nout; k++ ) {
n = 1;
data->currenttime = results->time[i];
for ( i=0; i<data->model->neq; i++ ) {
/* set specie values to values at time[k] */
data->value[i] = results->value[i][k];
for ( j=0; j<data->model->neq; j++ ) {
result = evaluateAST(data->model->jacob[i][j], data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[k], result);
n++;
}
}
/*
if ( k%10 == 0 ) {
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
}
*/
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "jac");
return 0;
}