void MERFTag::buildMatchTree(Agraph_t* G,Agnode_t* node,Agedge_t* edge,QMap<Agnode_t *,Agnode_t *>* parentNodeMap,QTreeWidgetItem* parentItem, int& id) {
QStringList data;
data << "Type" << formula->name;
QTreeWidgetItem* newItem = new QTreeWidgetItem(parentItem,data);
parentItem = newItem;
char * writable = strdup(formula->name.toStdString().c_str());
if(node == NULL) {
stringstream strs;
strs << id;
string temp_str = strs.str();
char* nodeID = strdup(temp_str.c_str());
Agnode_t * newNode = agnode(G,nodeID, 1);
agset(G,const_cast<char *>("root"),nodeID);
id = id+1;
agset(newNode,const_cast<char *>("label"),writable);
parentNodeMap->insert(newNode,NULL);
node = newNode;
}
else {
stringstream strs;
strs << id;
string temp_str = strs.str();
char* nodeID = strdup(temp_str.c_str());
Agnode_t * newNode = agnode(G,nodeID, 1);
id = id+1;
agset(newNode,const_cast<char *>("label"),writable);
edge = agedge(G, node, newNode, 0, 1);
parentNodeMap->insert(newNode, node);
node = newNode;
}
match->buildMatchTree(G,node,edge,parentNodeMap,parentItem,id);
}
/**
* \brief Set a weight to an edge
* \param graph The graph to modify.
* \param edge The edge whose weight must be changed.
* \param weight The new weight of the edge.
*
*/
void graph__setWeight(Agraph_t* graph, Agedge_t* edge, int weight){
char aux[10];
sprintf(aux, "%d", weight);
agset(edge, "label", aux);
edge->head->u.is_up_to_date = 0;
edge->tail->u.is_up_to_date = 0;
}
/*
* Generic object newindex metamethod handler.
* Lua Stack: ud, key, value
*/
int object_newindex_handler(lua_State *L)
{
char sskey[16], *skey;
if ((!lua_isstring(L, 2)) || (!lua_isstring(L, 3))){
gr_object_t *ud = toobject(L, 1, NULL, STRICT);
skey = agget(ud->p.p, ".attrib");
if (!skey || (strlen(skey) == 0)){
/* Let's create an attrib table on the fly if none exists */
sprintf(sskey, "%p", ud->p.p);
skey = agstrdup(sskey);
agset(ud->p.p, ".attrib", skey);
lua_pushstring(L, skey); /* ud, key, value, skey */
lua_newtable(L); /* ud, key, value, skey, stab */
lua_rawset(L, LUA_REGISTRYINDEX); /* ud, key, value, */
}
lua_pushstring(L, skey); /* ud, key, value, skey */
lua_rawget(L, LUA_REGISTRYINDEX); /* ud, key, value, stab */
lua_pushvalue(L, 2); /* ud, key, value, stab, key */
lua_pushvalue(L, 3); /* ud, key, value, stab, key, value */
lua_rawset(L, -3); /* ud, key, value, stab */
lua_pop(L, -1); /* ud, key, value */
return 0;
}
return setval(L);
}
int main(int argc, char* argv[])
{
struct marsopts opts = init(argc, argv);
Agraph_t* g = agread(opts.fin, (Agdisc_t*)NULL);
Agnode_t* n;
mat z;
init_graph(g);
z = mars(g, opts);
mat_scalar_mult(z, opts.scale);
if(opts.viewer) {
viewer(argc, argv);
} else {
for(n = agfstnode(g); n; n = agnxtnode(g,n)) {
int id = getid(n);
char* s = pos_to_str(&z->m[mindex(id, 0, z)], z->c);
agset(n,"pos",s);
free(s);
}
agwrite(g, opts.fout);
}
mat_free(z);
clean_up(g);
agclose(g);
return 0;
}
int main(int argc, char* argv[])
{
if(argc != 3)
usage();
float scale = atof(argv[1]);
FILE* fin = fopen(argv[2],"r");
Agraph_t* g = agread(fin, (Agdisc_t*)NULL);
Agnode_t* n;
for(n = agfstnode(g); n; n = agnxtnode(g,n)) {
char* pos = agget(n,"pos");
double x,y;
sscanf(pos,"%lf,%lf",&x,&y);
x *= scale;
y *= scale;
char* s = pos_to_str(x,y);
agset(n,"pos",s);
free(s);
}
agwrite(g,stdout);
agclose(g);
return 0;
}
void change_selected_graph_attributes(Agraph_t * g, char *attrname,
char *attrvalue)
{
agattr(g, AGRAPH, attrname, "");
agset(view->g[view->activeGraph], attrname, attrvalue);
}
static void rec_attach_bb(graph_t * g)
{
int c;
char buf[BUFSIZ];
point pt;
sprintf(buf, "%d,%d,%d,%d", GD_bb(g).LL.x, GD_bb(g).LL.y,
GD_bb(g).UR.x, GD_bb(g).UR.y);
agset(g, "bb", buf);
if (GD_label(g) && GD_label(g)->text[0]) {
pt = GD_label(g)->p;
sprintf(buf, "%d,%d", pt.x, YDIR(pt.y));
agset(g, "lp", buf);
}
for (c = 1; c <= GD_n_cluster(g); c++)
rec_attach_bb(GD_clust(g)[c]);
}
void rec_attach_bb(graph_t* g)
{
int c;
char buf[32];
sprintf(buf,"%d,%d,%d,%d", g->u.bb.LL.x, g->u.bb.LL.y,
g->u.bb.UR.x, g->u.bb.UR.y);
agset(g,"bb",buf);
for (c = 1; c <= g->u.n_cluster; c++) rec_attach_bb(g->u.clust[c]);
}
void change_selected_node_attributes(Agraph_t * g, char *attrname,
char *attrvalue)
{
int ind = 0;
agattr(g, AGNODE, attrname, "");
for (ind = 0; ind < GD_selectedNodesCount(g); ind++) {
agset(GD_selectedNodes(g)[ind], attrname, attrvalue);
}
}
void change_selected_graph_attributes(Agraph_t * g, char *attrname,
char *attrvalue)
{
int ind = 0;
agattr(g, AGRAPH, attrname, "");
for (ind = 0; ind < GD_selectedGraphsCount(g); ind++) {
agset(GD_selectedGraphs(g)[ind], attrname, attrvalue);
}
}
static void rec_attach_bb(graph_t * g, Agsym_t* bbsym)
{
int c;
char buf[BUFSIZ];
pointf pt;
sprintf(buf, "%.5g,%.5g,%.5g,%.5g", GD_bb(g).LL.x, YDIR(GD_bb(g).LL.y),
GD_bb(g).UR.x, YDIR(GD_bb(g).UR.y));
agxset(g, bbsym, buf);
if (GD_label(g) && GD_label(g)->text[0]) {
pt = GD_label(g)->pos;
sprintf(buf, "%.5g,%.5g", pt.x, YDIR(pt.y));
agset(g, "lp", buf);
pt = GD_label(g)->dimen;
sprintf(buf, "%.2f", PS2INCH(pt.x));
agset (g, "lwidth", buf);
sprintf(buf, "%.2f", PS2INCH(pt.y));
agset (g, "lheight", buf);
}
for (c = 1; c <= GD_n_cluster(g); c++)
rec_attach_bb(GD_clust(g)[c], bbsym);
}
/*
* Delete an object from Lua registry.
*/
int del_object(lua_State *L, void *key)
{
char *skey;
TRACE("del_object(): key=%p\n", key);
lua_pushlightuserdata(L, key); /* ?, key */
lua_pushnil(L); /* ?, key, nil */
lua_rawset(L, LUA_REGISTRYINDEX); /* ? */
skey = agget(key, ".attrib");
if (skey && (strlen(skey) != 0)) {
lua_pushstring(L, skey);
lua_pushnil(L);
lua_rawset(L, LUA_REGISTRYINDEX);
agset(key, ".attrib", NULL);
agstrfree(skey);
}
return 0;
}
void QGVScene::setRootNode(QGVNode *node)
{
Q_ASSERT(_nodes.contains(node));
agset(_graph->graph(), "root", node->label().toLocal8Bit().data());
}
/*-------------------------------------------------------------------------*\
* Method: e, tail, head = n.edge(self, node, label, flag)
* Finds or creates an edge. The given node is the tail of the edge.
* The created node is the the edge.
* Label is optional.
* The optional flag nocreate=true inhibits auto-creation of the edge.
* Any node given by name is implicitly created and it's userdata returned
* as additional results - even if nocreate is not set.
* Example:
* e, tail, head = n.edge(head, "edge-1", true | false)
* e, tail, head = e:node("headname", "edge-1", true | false)
\*-------------------------------------------------------------------------*/
static int gr_edge(lua_State *L)
{
Agedge_t *e;
gr_edge_t *edge;
int rv;
char *label;
char ename[32];
Agraph_t *g;
gr_node_t *head;
gr_node_t *tail = tonode(L, 1, STRICT);
g = agroot(tail->n);
if (lua_isuserdata(L, 2))
head = tonode(L, 2, STRICT);
else {
lua_pushcfunction(L, gr_create_node); /* tail, nhead, (label), (nocreate), func */
get_object(L, agroot(tail->n)); /* tail, nhead, (label), (nocreate), func, graph */
lua_pushvalue(L, 2); /* ... func, graph, nhead */
if (lua_isboolean(L, 4))
lua_pushvalue(L, 4); /* ... func, graph, nhead, (nocreate) */
else
lua_pushboolean(L, 0); /* ... func, graph, nhead, false */
lua_call(L, 3, 1); /* tail, nhead, (label), head */
if (lua_isnil(L, -1))
return 2;
head = tonode(L, -1, STRICT);
lua_pop(L,1); /* tail, nhead, (label) */
}
g = agroot(tail->n);
if (g != agroot(head->n)){
luaL_error(L, "head/tail not in same graph");
}
label = (char *) luaL_optstring(L, 3, NULL); /* ud, peer, name, (flag) */
if ((e = agedge(g, tail->n, head->n, label, 0)) != NULL){
rv = get_object(L, e); /* ud, peer, name, (flag), edge */
if (lua_isnil(L, -rv)){
/* not yet registered */
lua_pop(L, rv); /* ud, peer, name, (flag) */
edge = lua_newuserdata(L, sizeof(gr_edge_t)); /* ud, peer, name, (flag), edge */
edge->e = e;
if (label)
agset(e, "label", label);
edge->name = strdup(agnameof(e));
edge->type = AGEDGE;
edge->status = ALIVE;
new_edge(L);
lua_pushlightuserdata(L, tail);
lua_pushlightuserdata(L, head); /* ud, peer, name, (flag), edge, tail, head */
return 3;
} else {
/* Edge already registered */
lua_pushlightuserdata(L, tail);
lua_pushlightuserdata(L, head);
return rv + 2; /* ud, peer, name, (flag), edge, tail, head */
}
} else {
/* Edge does not exist */
if (lua_toboolean(L, 4)){
lua_pushnil(L);
lua_pushstring(L, "edge not found");
return 2;
}
edge = lua_newuserdata(L, sizeof(gr_edge_t));
sprintf(ename, "edge@%u", newid());
if ((edge->e = agedge(g, tail->n, head->n, ename, 1)) == NULL){
luaL_error(L, "agedge failed");
return 0;
}
if (label)
agset(edge->e, "label", label);
edge->name = strdup(agnameof(edge->e));
edge->type = AGEDGE;
edge->status = ALIVE;
new_edge(L);
lua_pushlightuserdata(L, tail);
lua_pushlightuserdata(L, head);
return 3;
}
}
void attach_attrs_and_arrows(graph_t* g, int* sp, int* ep)
{
int e_arrows; /* graph has edges with end arrows */
int s_arrows; /* graph has edges with start arrows */
int i, j, sides;
char buf[BUFSIZ]; /* Used only for small strings */
unsigned char xbuffer[BUFSIZ]; /* Initial buffer for xb */
agxbuf xb;
node_t *n;
edge_t *e;
pointf ptf;
int dim3 = (GD_odim(g) >= 3);
Agsym_t* bbsym;
gv_fixLocale (1);
e_arrows = s_arrows = 0;
setYInvert(g);
agxbinit(&xb, BUFSIZ, xbuffer);
safe_dcl(g, AGNODE, "pos", "");
safe_dcl(g, AGNODE, "rects", "");
N_width = safe_dcl(g, AGNODE, "width", "");
N_height = safe_dcl(g, AGNODE, "height", "");
safe_dcl(g, AGEDGE, "pos", "");
if (GD_has_labels(g) & NODE_XLABEL)
safe_dcl(g, AGNODE, "xlp", "");
if (GD_has_labels(g) & EDGE_LABEL)
safe_dcl(g, AGEDGE, "lp", "");
if (GD_has_labels(g) & EDGE_XLABEL)
safe_dcl(g, AGEDGE, "xlp", "");
if (GD_has_labels(g) & HEAD_LABEL)
safe_dcl(g, AGEDGE, "head_lp", "");
if (GD_has_labels(g) & TAIL_LABEL)
safe_dcl(g, AGEDGE, "tail_lp", "");
if (GD_label(g)) {
safe_dcl(g, AGRAPH, "lp", "");
safe_dcl(g, AGRAPH, "lwidth", "");
safe_dcl(g, AGRAPH, "lheight", "");
if (GD_label(g)->text[0]) {
ptf = GD_label(g)->pos;
sprintf(buf, "%.5g,%.5g", ptf.x, YDIR(ptf.y));
agset(g, "lp", buf);
ptf = GD_label(g)->dimen;
sprintf(buf, "%.2f", PS2INCH(ptf.x));
agset(g, "lwidth", buf);
sprintf(buf, "%.2f", PS2INCH(ptf.y));
agset(g, "lheight", buf);
}
}
bbsym = safe_dcl(g, AGRAPH, "bb", "");
for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
if (dim3) {
int k;
sprintf(buf, "%.5g,%.5g,%.5g", ND_coord(n).x, YDIR(ND_coord(n).y), POINTS_PER_INCH*(ND_pos(n)[2]));
agxbput (&xb, buf);
for (k = 3; k < GD_odim(g); k++) {
sprintf(buf, ",%.5g", POINTS_PER_INCH*(ND_pos(n)[k]));
agxbput (&xb, buf);
}
agset(n, "pos", agxbuse(&xb));
} else {
sprintf(buf, "%.5g,%.5g", ND_coord(n).x, YDIR(ND_coord(n).y));
agset(n, "pos", buf);
}
sprintf(buf, "%.5g", PS2INCH(ND_ht(n)));
agxset(n, N_height, buf);
sprintf(buf, "%.5g", PS2INCH(ND_lw(n) + ND_rw(n)));
agxset(n, N_width, buf);
if (ND_xlabel(n) && ND_xlabel(n)->set) {
ptf = ND_xlabel(n)->pos;
sprintf(buf, "%.5g,%.5g", ptf.x, YDIR(ptf.y));
agset(n, "xlp", buf);
}
if (strcmp(ND_shape(n)->name, "record") == 0) {
set_record_rects(n, ND_shape_info(n), &xb);
agxbpop(&xb); /* get rid of last space */
agset(n, "rects", agxbuse(&xb));
} else {
polygon_t *poly;
int i;
if (N_vertices && isPolygon(n)) {
poly = (polygon_t *) ND_shape_info(n);
sides = poly->sides;
if (sides < 3) {
char *p = agget(n, "samplepoints");
if (p)
sides = atoi(p);
else
sides = 8;
if (sides < 3)
sides = 8;
}
for (i = 0; i < sides; i++) {
if (i > 0)
agxbputc(&xb, ' ');
if (poly->sides >= 3)
sprintf(buf, "%.5g %.5g",
PS2INCH(poly->vertices[i].x),
YFDIR(PS2INCH(poly->vertices[i].y)));
else
sprintf(buf, "%.5g %.5g",
ND_width(n) / 2.0 * cos(i / (double) sides * M_PI * 2.0),
YFDIR(ND_height(n) / 2.0 * sin(i / (double) sides * M_PI * 2.0)));
agxbput(&xb, buf);
}
agxset(n, N_vertices, agxbuse(&xb));
}
}
if (State >= GVSPLINES) {
for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
if (ED_edge_type(e) == IGNORED)
continue;
if (ED_spl(e) == NULL)
continue; /* reported in postproc */
for (i = 0; i < ED_spl(e)->size; i++) {
if (i > 0)
agxbputc(&xb, ';');
if (ED_spl(e)->list[i].sflag) {
s_arrows = 1;
sprintf(buf, "s,%.5g,%.5g ",
ED_spl(e)->list[i].sp.x,
YDIR(ED_spl(e)->list[i].sp.y));
agxbput(&xb, buf);
}
if (ED_spl(e)->list[i].eflag) {
e_arrows = 1;
sprintf(buf, "e,%.5g,%.5g ",
ED_spl(e)->list[i].ep.x,
YDIR(ED_spl(e)->list[i].ep.y));
agxbput(&xb, buf);
}
for (j = 0; j < ED_spl(e)->list[i].size; j++) {
if (j > 0)
agxbputc(&xb, ' ');
ptf = ED_spl(e)->list[i].list[j];
sprintf(buf, "%.5g,%.5g", ptf.x, YDIR(ptf.y));
agxbput(&xb, buf);
}
}
agset(e, "pos", agxbuse(&xb));
if (ED_label(e)) {
ptf = ED_label(e)->pos;
sprintf(buf, "%.5g,%.5g", ptf.x, YDIR(ptf.y));
agset(e, "lp", buf);
}
if (ED_xlabel(e) && ED_xlabel(e)->set) {
ptf = ED_xlabel(e)->pos;
sprintf(buf, "%.5g,%.5g", ptf.x, YDIR(ptf.y));
agset(e, "xlp", buf);
}
if (ED_head_label(e)) {
ptf = ED_head_label(e)->pos;
sprintf(buf, "%.5g,%.5g", ptf.x, YDIR(ptf.y));
agset(e, "head_lp", buf);
}
if (ED_tail_label(e)) {
ptf = ED_tail_label(e)->pos;
sprintf(buf, "%.5g,%.5g", ptf.x, YDIR(ptf.y));
agset(e, "tail_lp", buf);
}
}
}
}
rec_attach_bb(g, bbsym);
agxbfree(&xb);
if (HAS_CLUST_EDGE(g))
undoClusterEdges(g);
*sp = s_arrows;
*ep = e_arrows;
gv_fixLocale (0);
}
/**
* \brief Add an edge to a graph
* \param graph The graph to modify.
* \param n1 The first node of the new edge.
* \param n2 The second node of the new edge.
* \param weight The weight of the new edge.
*
*/
void graph__addEdge(Agraph_t* graph, Agnode_t* n1, Agnode_t* n2, int weight){
Agedge_t *e = agedge(graph, n1, n2);
char aux[10];
sprintf(aux, "%d", weight);
agset(e, "label", aux);
}
/*-------------------------------------------------------------------------*\
* Method: e, tail, head = n.edge(self, node, label, flag)
* Finds or creates an edge. The given node becomes the tail of the edge.
* Label is optional.
* The optional flag nocreate=true inhibits auto-creation.
* Any node given by name is implicitly created and it's userdata returned
* as additional results - even if nocreate is not set.
* Example:
* e, tail, head = e:node(n2, "edge-1")
* e, err = g:edge(...)
\*-------------------------------------------------------------------------*/
static int gr_edge(lua_State *L)
{
Agedge_t *e;
gr_edge_t *edge;
int rv;
char *label;
char sbuf[32];
Agraph_t *g;
gr_node_t *head;
gr_node_t *tail = tonode(L, 1, STRICT);
if (lua_isuserdata(L, 2))
head = tonode(L, 2, STRICT);
else {
/* Create a node given by name */
lua_pushcfunction(L, gr_create_node); /* tail, nhead, (label), func */
get_object(L, tail->n->graph); /* tail, nhead, (label), func, graph */
lua_pushstring(L, (const char *) luaL_checkstring(L, 2)); /* ... func, graph, nhead */
if (lua_isboolean(L, 4))
lua_pushvalue(L, 4);
else
lua_pushboolean(L, 0);
/* g.node(self, name, flag) */
lua_call(L, 3, 1); /* tail, nhead, (label), head */
head = tonode(L, -1, STRICT);
lua_pop(L,1); /* tail, nhead, (label) */
}
g = tail->n->graph;
if (tail->n->graph != head->n->graph){
luaL_error(L, "head/tail not in same graph");
}
label = (char *) luaL_optstring(L, 3, ""); /* ud, peer, name, (flag) */
if ((e = agfindedge(g, tail->n, head->n)) != NULL){
/* Edge exists */
rv = get_object(L, e); /* ud, peer, name, (flag), edge */
if (lua_isnil(L, -rv)){
lua_pop(L, rv); /* ud, peer, name, (flag) */
/* Edge not yet registered */
edge = lua_newuserdata(L, sizeof(gr_edge_t)); /* ud, peer, name, (flag), edge */
edge->e = e;
if (strlen(label) > 0)
agset(e, "label", label);
sprintf(sbuf, "edge@%d", AGID(e));
edge->name = strdup(sbuf);
edge->type = AGEDGE;
set_object(L, e); /* ud, peer, name, (flag), edge */
new_edge(L);
lua_pushlightuserdata(L, tail);
lua_pushlightuserdata(L, head); /* ud, peer, name, (flag), edge, tail, head */
return 3;
} else {
/* Edge already registered */
lua_pushlightuserdata(L, tail);
lua_pushlightuserdata(L, head);
return rv + 2; /* ud, peer, name, (flag), edge, tail, head */
}
} else {
/* Edge does not exist */
if (lua_toboolean(L, 4)){
lua_pushnil(L);
lua_pushstring(L, "edge not found");
return 2;
}
edge = lua_newuserdata(L, sizeof(gr_edge_t));
if (!(edge->e = agedge(g, tail->n, head->n))){
luaL_error(L, "agedge failed");
return 0;
}
if (strlen(label) > 0)
agset(edge->e, "label", label);
sprintf(sbuf, "edge@%d", AGID(edge->e));
edge->name = strdup(sbuf);
edge->type = AGEDGE;
set_object(L, edge->e);
new_edge(L);
lua_pushlightuserdata(L, tail);
lua_pushlightuserdata(L, head);
return 3;
}
}
mat mars(Agraph_t* g, struct marsopts opts)
{
int i, j, n = agnnodes(g), k = MIN(n, MAX(opts.k, 2)), iter = 0;
mat dij, u, u_trans, q, r, q_t, tmp, tmp2, z;
double* s = (double*) malloc(sizeof(double)*k);
double* ones = (double*) malloc(sizeof(double)*n);
double* d;
int* anchors = (int*) malloc(sizeof(int)*k);
int* clusters = NULL;
double change = 1, old_stress = -1;
dij = mat_new(k, n);
u = mat_new(n,k);
tmp = mat_new(n,k);
darrset(ones,n,-1);
select_anchors(g, dij, anchors, k);
if(opts.color) {
for(i = 0; i < k; i++) {
Agnode_t* anchor = get_node(anchors[i]);
agset(anchor, "color", "red");
}
}
if(opts.power != 1) {
clusters = graph_cluster(g,dij,anchors);
}
singular_vectors(g, dij, opts.power, u, s);
vec_scalar_mult(s, k, -1);
u_trans = mat_trans(u);
d = mat_mult_for_d(u, s, u_trans, ones);
for(i = 0; i < u->c; i++) {
double* col = mat_col(u,i);
double* b = inv_mul_ax(d,col,u->r);
for(j = 0; j < u->r; j++) {
tmp->m[mindex(j,i,tmp)] = b[j];
}
free(b);
free(col);
}
tmp2 = mat_mult(u_trans,tmp);
for(i = 0; i < k; i++) {
tmp2->m[mindex(i,i,tmp2)] += (1.0/s[i]);
}
q = mat_new(tmp2->r, tmp2->c);
r = mat_new(tmp2->c, tmp2->c);
qr_factorize(tmp2,q,r);
q_t = mat_trans(q);
if(opts.given) {
z = get_positions(g, opts.dim);
} else {
z = mat_rand(n, opts.dim);
}
translate_by_centroid(z);
if(opts.viewer) {
init_viewer(g, opts.max_iter);
append_layout(z);
}
old_stress = stress(z, dij, anchors, opts.power);
while(change > EPSILON && iter < opts.max_iter) {
mat right_side;
double new_stress;
if(opts.power == 1) {
right_side = barnes_hut(z);
} else {
right_side = barnes_hut_cluster(z, dij, clusters, opts.power);
}
for(i = 0; i < opts.dim; i++) {
double sum = 0;
double* x;
double* b = mat_col(right_side,i);
for(j = 0; j < right_side->r; j++) {
sum += b[j];
}
x = inv_mul_full(d, b, right_side->r, u, u_trans, q_t, r);
for(j = 0; j < z->r; j++) {
z->m[mindex(j,i,z)] = x[j] - sum/right_side->r;
}
free(x);
free(b);
}
adjust_anchors(g, anchors, k, z);
update_anchors(z, dij, anchors, opts.power);
translate_by_centroid(z);
if(opts.viewer) {
append_layout(z);
}
new_stress = stress(z, dij, anchors, opts.power);
change = fabs(new_stress-old_stress)/old_stress;
old_stress = new_stress;
mat_free(right_side);
iter++;
}
mat_free(dij);
mat_free(u);
mat_free(u_trans);
mat_free(q);
mat_free(r);
mat_free(q_t);
mat_free(tmp);
mat_free(tmp2);
free(s);
free(ones);
free(d);
free(anchors);
free(clusters);
return z;
}
SBML_ODESOLVER_API int drawModel(Model_t *m, 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.");
drawModelTxt(m, file);
#else
GVC_t *gvc;
Agraph_t *g;
Agnode_t *r;
Agnode_t *s;
Agedge_t *e;
Agsym_t *a;
Species_t *sp;
Reaction_t *re;
const ASTNode_t *math;
SpeciesReference_t *sref;
ModifierSpeciesReference_t *mref;
char *output[4];
char *command = "dot";
char *formatopt;
char *outfile;
int i,j;
int reversible;
char name[WORDSIZE];
char label[WORDSIZE];
/* setting name of outfile */
ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
sprintf(outfile, "-o%s_rn.%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");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
re = Model_getReaction(m,i);
reversible = Reaction_getReversible(re);
sprintf(name, "%s", Reaction_getId(re));
r = agnode(g,name);
a = agnodeattr(g, "shape", "ellipse");
agxset(r, a->index, "box");
sprintf(label, "%s", Reaction_isSetName(re) ?
Reaction_getName(re) : Reaction_getId(re));
agset(r, "label", label);
sprintf(label, "%s.htm", Reaction_getId(re));
a = agnodeattr(g, "URL", "");
agxset(r, a->index, label);
for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {
mref = Reaction_getModifier(re,j);
sp = Model_getSpeciesById(m, ModifierSpeciesReference_getSpecies(mref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g,name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,s,r);
a = agedgeattr(g, "style", "");
agxset(e, a->index, "dashed");
a = agedgeattr(g, "arrowhead", "");
agxset(e, a->index, "odot");
}
for ( j=0; j<Reaction_getNumReactants(re); j++ ) {
sref = Reaction_getReactant(re,j);
sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g, name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,s,r);
a = agedgeattr(g, "label", "");
if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
agxset (e, a->index, SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
sprintf(name, "%g", SpeciesReference_getStoichiometry(sref));
agxset (e, a->index, name);
}
}
if ( reversible == 1 ) {
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "onormal");
}
}
for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
sref = Reaction_getProduct(re,j);
sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
sprintf(name,"%s", Species_getId(sp));
s = agnode(g,name);
sprintf(label, "%s", Species_isSetName(sp) ?
Species_getName(sp) : Species_getId(sp));
agset(s, "label", label);
if ( Species_getBoundaryCondition(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "blue");
}
if ( Species_getConstant(sp) ) {
a = agnodeattr(g, "color", "");
agxset(s, a->index, "green4");
}
sprintf(label, "%s.htm", Species_getId(sp));
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,r,s);
a = agedgeattr(g, "label", "");
if ( SpeciesReference_isSetStoichiometryMath(sref) ) {
math = SpeciesReference_getStoichiometryMath(sref);
if ( (strcmp(SBML_formulaToString(math),"1") !=
0) ) {
agxset (e, a->index, SBML_formulaToString(math));
}
}
else {
if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
sprintf(name, "%g",SpeciesReference_getStoichiometry(sref));
agxset (e, a->index,name);
}
}
if ( reversible == 1 ) {
a = agedgeattr(g, "arrowtail", "");
agxset(e, a->index, "onormal");
}
}
}
/* 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);
#else
agclose(g);
#endif
/* 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;
}
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;
}
void attach_attrs_and_arrows(graph_t* g, int* sp, int* ep)
{
int e_arrows; /* graph has edges with end arrows */
int s_arrows; /* graph has edges with start arrows */
int i, j, sides;
char buf[BUFSIZ]; /* Used only for small strings */
unsigned char xbuffer[BUFSIZ]; /* Initial buffer for xb */
agxbuf xb;
node_t *n;
edge_t *e;
point pt;
e_arrows = s_arrows = 0;
setYInvert(g);
agxbinit(&xb, BUFSIZ, xbuffer);
safe_dcl(g, g->proto->n, "pos", "", agnodeattr);
safe_dcl(g, g->proto->n, "rects", "", agnodeattr);
N_width = safe_dcl(g, g->proto->n, "width", "", agnodeattr);
N_height = safe_dcl(g, g->proto->n, "height", "", agnodeattr);
safe_dcl(g, g->proto->e, "pos", "", agedgeattr);
if (GD_has_labels(g) & EDGE_LABEL)
safe_dcl(g, g->proto->e, "lp", "", agedgeattr);
if (GD_has_labels(g) & HEAD_LABEL)
safe_dcl(g, g->proto->e, "head_lp", "", agedgeattr);
if (GD_has_labels(g) & TAIL_LABEL)
safe_dcl(g, g->proto->e, "tail_lp", "", agedgeattr);
if (GD_label(g)) {
safe_dcl(g, g, "lp", "", agraphattr);
if (GD_label(g)->text[0]) {
pt = GD_label(g)->p;
sprintf(buf, "%d,%d", pt.x, YDIR(pt.y));
agset(g, "lp", buf);
}
}
safe_dcl(g, g, "bb", "", agraphattr);
for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
sprintf(buf, "%d,%d", ND_coord_i(n).x, YDIR(ND_coord_i(n).y));
agset(n, "pos", buf);
sprintf(buf, "%.2f", PS2INCH(ND_ht_i(n)));
agxset(n, N_height->index, buf);
sprintf(buf, "%.2f", PS2INCH(ND_lw_i(n) + ND_rw_i(n)));
agxset(n, N_width->index, buf);
if (strcmp(ND_shape(n)->name, "record") == 0) {
set_record_rects(n, ND_shape_info(n), &xb);
agxbpop(&xb); /* get rid of last space */
agset(n, "rects", agxbuse(&xb));
} else {
polygon_t *poly;
int i;
if (N_vertices && isPolygon(n)) {
poly = (polygon_t *) ND_shape_info(n);
sides = poly->sides;
if (sides < 3) {
char *p = agget(n, "samplepoints");
if (p)
sides = atoi(p);
else
sides = 8;
if (sides < 3)
sides = 8;
}
for (i = 0; i < sides; i++) {
if (i > 0)
agxbputc(&xb, ' ');
if (poly->sides >= 3)
sprintf(buf, "%.3f %.3f",
PS2INCH(poly->vertices[i].x),
YFDIR(PS2INCH(poly->vertices[i].y)));
else
sprintf(buf, "%.3f %.3f",
ND_width(n) / 2.0 * cos(i /
(double) sides *
PI * 2.0),
YFDIR(ND_height(n) / 2.0 *
sin(i / (double) sides * PI * 2.0)));
agxbput(&xb, buf);
}
agxset(n, N_vertices->index, agxbuse(&xb));
}
}
if (State >= GVSPLINES) {
for (e = agfstout(g, n); e; e = agnxtout(g, e)) {
if (ED_edge_type(e) == IGNORED)
continue;
if (ED_spl(e) == NULL)
continue; /* reported in postproc */
for (i = 0; i < ED_spl(e)->size; i++) {
if (i > 0)
agxbputc(&xb, ';');
if (ED_spl(e)->list[i].sflag) {
s_arrows = 1;
sprintf(buf, "s,%d,%d ",
ED_spl(e)->list[i].sp.x,
YDIR(ED_spl(e)->list[i].sp.y));
agxbput(&xb, buf);
}
if (ED_spl(e)->list[i].eflag) {
e_arrows = 1;
sprintf(buf, "e,%d,%d ",
ED_spl(e)->list[i].ep.x,
YDIR(ED_spl(e)->list[i].ep.y));
agxbput(&xb, buf);
}
for (j = 0; j < ED_spl(e)->list[i].size; j++) {
if (j > 0)
agxbputc(&xb, ' ');
pt = ED_spl(e)->list[i].list[j];
sprintf(buf, "%d,%d", pt.x, YDIR(pt.y));
agxbput(&xb, buf);
}
}
agset(e, "pos", agxbuse(&xb));
if (ED_label(e)) {
pt = ED_label(e)->p;
sprintf(buf, "%d,%d", pt.x, YDIR(pt.y));
agset(e, "lp", buf);
}
if (ED_head_label(e)) {
pt = ED_head_label(e)->p;
sprintf(buf, "%d,%d", pt.x, YDIR(pt.y));
agset(e, "head_lp", buf);
}
if (ED_tail_label(e)) {
pt = ED_tail_label(e)->p;
sprintf(buf, "%d,%d", pt.x, YDIR(pt.y));
agset(e, "tail_lp", buf);
}
}
}
}
rec_attach_bb(g);
agxbfree(&xb);
if (HAS_CLUST_EDGE(g))
undoClusterEdges(g);
*sp = s_arrows;
*ep = e_arrows;
}
/* twopi_layout:
*/
void twopi_layout(Agraph_t * g)
{
Agnode_t *ctr = 0;
char *s;
int setRoot = 0;
pointf sc;
int doScale = 0;
int r;
if (agnnodes(g) == 0) return;
twopi_init_graph(g);
s = agget(g, "root");
if ((s = agget(g, "root"))) {
if (*s) {
ctr = agfindnode(g, s);
if (!ctr) {
agerr(AGWARN, "specified root node \"%s\" was not found.", s);
agerr(AGPREV, "Using default calculation for root node\n");
setRoot = 1;
}
}
else {
setRoot = 1;
}
}
if ((s = agget(g, "scale")) && *s) {
if ((r = sscanf (s, "%lf,%lf",&sc.x,&sc.y))) {
if (r == 1) sc.y = sc.x;
doScale = 1;
if (Verbose)
fprintf (stderr, "scale = (%f,%f)\n", sc.x, sc.y);
}
}
if (agnnodes(g)) {
Agraph_t **ccs;
Agraph_t *sg;
Agnode_t *c = NULL;
Agnode_t *n;
int ncc;
int i;
ccs = ccomps(g, &ncc, 0);
if (ncc == 1) {
c = circleLayout(g, ctr);
if (setRoot && !ctr)
ctr = c;
n = agfstnode(g);
free(ND_alg(n));
ND_alg(n) = NULL;
if (doScale)
scaleGraph (g, c, sc);
adjustNodes(g);
spline_edges(g);
} else {
pack_info pinfo;
getPackInfo (g, l_node, CL_OFFSET, &pinfo);
pinfo.doSplines = 0;
for (i = 0; i < ncc; i++) {
sg = ccs[i];
if (ctr && agcontains(sg, ctr))
c = ctr;
else
c = 0;
nodeInduce(sg);
c = circleLayout(sg, c);
if (setRoot && !ctr)
ctr = c;
if (doScale)
scaleGraph (sg, c, sc);
adjustNodes(sg);
}
n = agfstnode(g);
free(ND_alg(n));
ND_alg(n) = NULL;
packSubgraphs(ncc, ccs, g, &pinfo);
spline_edges(g);
}
for (i = 0; i < ncc; i++) {
agdelete(g, ccs[i]);
}
free(ccs);
}
if (setRoot)
agset (g, "root", agnameof (ctr));
dotneato_postprocess(g);
}
static void color(Agraph_t * g)
{
int nn, i, j, cnt;
Agnode_t *n, *v, **nlist;
Agedge_t *e;
char *p;
double x, y, maxrank = 0.0;
double sum[NC], d, lowsat, highsat;
if (agfindattr(g->proto->n, "pos") == NULL) {
fprintf(stderr,
"graph must be run through 'dot' before 'gvcolor'\n");
exit(1);
}
if (agfindattr(g->proto->n, "style") == NULL)
agnodeattr(g, "style", "filled");
if ((p = agget(g, "Defcolor")))
setcolor(p, Defcolor);
if ((p = agget(g, "rankdir")) && (p[0] == 'L'))
LR = 1;
if ((p = agget(g, "flow")) && (p[0] == 'b'))
Forward = 0;
if ((p = agget(g, "saturation"))) {
if (sscanf(p, "%lf,%lf", &lowsat, &highsat) == 2) {
MinRankSaturation = lowsat;
MaxRankSaturation = highsat;
AdjustSaturation = 1;
}
}
/* assemble the sorted list of nodes and store the initial colors */
nn = agnnodes(g);
nlist = (Agnode_t **) malloc(nn * sizeof(Agnode_t *));
i = 0;
for (n = agfstnode(g); n; n = agnxtnode(g, n)) {
nlist[i++] = n;
if ((p = agget(n, "color")))
setcolor(p, ND_x(n));
p = agget(n, "pos");
sscanf(p, "%lf,%lf", &x, &y);
ND_relrank(n) = (LR ? x : y);
if (maxrank < ND_relrank(n))
maxrank = ND_relrank(n);
}
if (LR != Forward)
for (i = 0; i < nn; i++) {
n = nlist[i];
ND_relrank(n) = maxrank - ND_relrank(n);
}
qsort((void *) nlist, (size_t) nn, sizeof(Agnode_t *),
(int (*)(const void *, const void *)) cmpf);
/* this is the pass that pushes the colors through the edges */
for (i = 0; i < nn; i++) {
n = nlist[i];
/* skip nodes that were manually colored */
cnt = 0;
for (j = 0; j < NC; j++)
if (ND_x(n)[j] != 0.0)
cnt++;
if (cnt > 0)
continue;
for (j = 0; j < NC; j++)
sum[j] = 0.0;
cnt = 0;
for (e = agfstedge(g, n); e; e = agnxtedge(g, e, n)) {
v = e->head;
if (v == n)
v = e->tail;
d = ND_relrank(v) - ND_relrank(n) - 0.01;
if (d < 0) {
double t = 0.0;
for (j = 0; j < NC; j++) {
t += ND_x(v)[j];
sum[j] += ND_x(v)[j];
}
if (t > 0.0)
cnt++;
}
}
if (cnt)
for (j = 0; j < NC; j++)
ND_x(n)[j] = sum[j] / cnt;
}
/* apply saturation adjustment and convert color to string */
for (i = 0; i < nn; i++) {
double h, s, b, t;
char buf[64];
n = nlist[i];
t = 0.0;
for (j = 0; j < NC; j++)
t += ND_x(n)[j];
if (t > 0.0) {
h = ND_x(n)[0];
if (AdjustSaturation) {
s = ND_relrank(n) / maxrank;
if (!Forward)
s = 1.0 - s;
s = MinRankSaturation
+ s * (MaxRankSaturation - MinRankSaturation);
} else
s = 1.0;
s = s * ND_x(n)[1];
b = ND_x(n)[2];
} else {
h = Defcolor[0];
s = Defcolor[1];
b = Defcolor[2];
}
sprintf(buf, "%f %f %f", h, s, b);
agset(n, "color", buf);
}
}
void attach_attrs(graph_t* g)
{
int i,j,sides;
char buf[BUFSIZ],*p;
node_t *n;
edge_t *e;
point pt;
safe_dcl(g,g->proto->n,"pos","",agnodeattr);
safe_dcl(g,g->proto->n,"rects","",agnodeattr);
N_width = safe_dcl(g,g->proto->n,"width","",agnodeattr);
N_height = safe_dcl(g,g->proto->n,"height","",agnodeattr);
safe_dcl(g,g->proto->e,"pos","",agedgeattr);
if (g->u.has_edge_labels) safe_dcl(g,g->proto->e,"lp","",agedgeattr);
if (g->u.label) {
safe_dcl(g,g,"lp","",agraphattr);
pt = g->u.label->p;
sprintf(buf,"%d,%d",pt.x,pt.y);
agset(g,"lp",buf);
}
safe_dcl(g,g,"bb","",agraphattr);
for (n = agfstnode(g); n; n = agnxtnode(g,n)) {
sprintf(buf,"%d,%d",n->u.coord.x,n->u.coord.y);
agset(n,"pos",buf);
sprintf(buf,"%.2f",PS2INCH(n->u.ht));
agxset(n,N_height->index,buf);
sprintf(buf,"%.2f",PS2INCH(n->u.lw + n->u.rw));
agxset(n,N_width->index,buf);
if (strcmp (n->u.shape->name, "record") == 0) {
buf[0] = '\000', rectbufp = &buf[0];
set_record_rects (n, (field_t *)(n->u.shape_info));
if (rectbufp > &buf[0]) /* get rid of last space */
*(--rectbufp) = '\000';
agset(n,"rects",buf);
}
else {
extern void poly_init(node_t *);
polygon_t *poly;
int i;
if (N_vertices && (n->u.shape->initfn == poly_init)) {
poly = (polygon_t*) n->u.shape_info;
p = buf;
sides = poly->sides;
if (sides < 3) {
char *p = agget(n,"samplepoints");
if (p) sides = atoi(p);
else sides = 8;
if (sides < 3) sides = 8;
}
for (i = 0; i < sides; i++) {
if (i > 0) {*p++ = ' ';}
if (poly->sides >= 3)
sprintf(p,"%.3lf %.3lf",
poly->vertices[i].x,poly->vertices[i].y);
else
sprintf(p,"%.3lf %.3lf",
n->u.width/2.0 * cos(i/(double)sides * PI * 2.0),
n->u.height/2.0 * sin(i/(double)sides * PI * 2.0));
while (*p) p++;
}
agxset(n,N_vertices->index,buf);
}
}
for (e = agfstout(g,n); e; e = agnxtout(g,e)) {
p = buf;
if (e->u.spl == NULL)
{fprintf(stderr,"lost spline of %s %s\n",e->tail->name,e->head->name); continue;}
for (i = 0; i < e->u.spl->size; i++) {
if (i > 0) *p++ = ';';
if (e->u.spl->list[i].sflag) {
sprintf (p, "s,%d,%d ",e->u.spl->list[i].sp.x,e->u.spl->list[i].sp.y);
while (*p) p++;
}
if (e->u.spl->list[i].eflag) {
sprintf (p, "e,%d,%d ",e->u.spl->list[i].ep.x,e->u.spl->list[i].ep.y);
while (*p) p++;
}
for (j = 0; j < e->u.spl->list[i].size; j++) {
if (j > 0) *p++ = ' ';
pt = e->u.spl->list[i].list[j];
sprintf(p,"%d,%d",pt.x,pt.y);
while (*p) p++;
}
*p = '\0';
}
agset(e,"pos",buf);
if (e->u.label) {
pt = e->u.label->p;
sprintf(buf,"%d,%d",pt.x,pt.y);
agset(e,"lp",buf);
}
}
}
rec_attach_bb(g);
}
