void NodeSig(phylo P, sample S, int outmethod, int abundWeighted) {
// Currently need to use taxon name of interior as a marker,
// because Mesquite will not show all labels, but if it will soon,
// best to use notes, and not muck around with taxon name
//TODO modifying to use abundances, need longs instead of ints for counters
int plot, node, taxon, i, ordHI, ordLO, run;
int tipsReal_n[P.nnodes];
float test_r[RUNS];
char mark[2];
char tmp[15];
int **tips_rn;
// was: int tips_rn[RUNS][MaxNode+1];
phylo Out[S.nsamples];
int *attach;
attach = ivector(0, S.ntaxa-1);
tips_rn = imatrix(0, RUNS-1, 0, P.nnodes-1);
for (i = 0; i < S.nsamples; i++) {
Out[i] = P; // all the pointers in Out are the same as those in Intree
// careful not to change any preexisting arrays in Out, or they will
// also be changed in Intree!
if (TreeView == 0)
Out[i].arenotes = 1;
if (TreeView == 1)
Out[i].arenotes = 0;
// dimension a new array for Out names:
if (TreeView == 0)
Out[i].notes = cmatrix(0, P.nnodes-1, 0, MAXNOTELENGTH+10);
if (TreeView == 1)
Out[i].taxon = cmatrix(0, P.nnodes-1, 0, MAXTAXONLENGTH+10);
}
// for each plot
if (outmethod == 1)
printf("plot\tnode\tnode_name \tntaxa\tmedian\trank\tsig\n");
for (plot = 0; plot < S.nsamples; plot++) {
if (S.srec[plot] > 2) {
for (node = 0; node < P.nnodes; node++) {
tipsReal_n[node] = 0;
for (run = 0; run < RUNS; run++)
tips_rn[run][node] = 0;
}
// need to reset it
AttachSampleToPhylo(S, P, attach);
// follow up from tips, adding 1 to each node passed through
for (taxon = 0; taxon < S.srec[plot]; taxon++) {
i = P.t2n[ attach[ S.id[plot][taxon] ] ];
while (i != -1) {
if (abundWeighted)
tipsReal_n[i] += S.abund[plot][taxon];
else
tipsReal_n[i]++;
i = P.up[i];
}
}
// ooo this is slow, putting rnd inside the plot loop!
for (run = 0; run < RUNS; run++) {
// now randomize the plot
// RandomizeB(plot);
PhylogenyAttachShuffle(P, S, attach);
for (taxon = 0; taxon < S.srec[plot]; taxon++) {
i = P.t2n[ attach[ S.id[plot][taxon] ] ];
while (i != -1) {
if (abundWeighted)
tips_rn[run][i] += S.abund[plot][taxon];
else
tips_rn[run][i]++;
i = P.up[i];
}
}
}
// now unpeel the nodes
for (node = 0; node < P.nnodes; node++) {
if (TreeView == 0)
strcpy(Out[plot].notes[node], "");
if (TreeView == 1)
strcpy(Out[plot].taxon[node], "");
// interior nodes only
if (P.noat[node] != 0) {
ordHI = 0;
ordLO = 0;
for (run = 0; run < RUNS; run++) {
if (tips_rn[run][node] < tipsReal_n[node])
ordHI++;
if (tips_rn[run][node] > tipsReal_n[node])
ordLO++;
}
strcpy(mark, " ");
if (ordLO >= (int) ((float) RUNS * 0.975)) {
strcpy(mark, "-");
if (TreeView == 0)
strcat(Out[plot].notes[node], "SIGLESS");
if (TreeView == 1) {
sprintf(tmp, "LESS_%d_", node);
strcpy(Out[plot].taxon[node], tmp);
}
if (outmethod == 1)
printf("%d\t%d\t%-10s\t%d\t%d\t%d\t%d\t%s\n", plot
+1, node, P.taxon[node], tipsReal_n[node],
(int) test_r[(int) ((float) RUNS * 0.5)], ordHI,
ordLO, mark);
} else if (ordHI >= (int) ((float) RUNS * 0.975)) {
strcpy(mark, "+");
if (TreeView == 0)
strcat(Out[plot].notes[node], "SIGMORE");
if (TreeView == 1) {
sprintf(tmp, "MORE_%d_", node);
strcpy(Out[plot].taxon[node], tmp);
}
if (outmethod == 1)
printf("%d\t%d\t%-20s\t%d\t%d\t%d\t%d\t%s\n", plot
+1, node, P.taxon[node], tipsReal_n[node],
(int) test_r[(int) ((float) RUNS * 0.5)], ordHI,
ordLO, mark);
}
// printf("%s\t%s\n", Out.taxon[node], Intree.taxon[node]);
else if (outmethod == 1)
printf("%d\t%d\t%-20s\t%d\t%d\t%d\t%d\t%s\n", plot+1,
node, P.taxon[node], tipsReal_n[node],
(int) test_r[(int) ((float) RUNS * 0.5)], ordHI,
ordLO, mark);
}
if ((TreeView == 1) && (strcmp(P.taxon[node], ".") != 0)) {
strcat(Out[plot].taxon[node], P.taxon[node]);
}
}
}
// Name tree
strcpy(Out[plot].phyname, "NodeSig_");
strcat(Out[plot].phyname, S.pname[plot]);
}
if (outmethod ==0)
WriteNexus(Out, S.nsamples, ReadSample(SampleFile), 1,
ReadTraits(TraitFile), 1);
}
//-----------------------------------------------------------------------------
bool psNPCLoader::LoadFromFile(csString &filename)
{
area.Clear();
CPrintf(CON_DEBUG, "Importing NPC from file: %s\n",filename.GetData());
// try to read data from the file
csRef<iVFS> vfs = csQueryRegistry<iVFS> (psserver->GetObjectReg());
csRef<iDataBuffer> data(vfs->ReadFile(filename.GetData()));
if(!data || !data->GetSize())
{
CPrintf(CON_ERROR, "Error: Couldn't load file '%s'.\n", filename.GetData());
return false;
}
csRef<iDocumentSystem> xml;
xml.AttachNew(new csTinyDocumentSystem);
csRef<iDocument> doc = xml->CreateDocument();
const char* error = doc->Parse(data);
if(error)
{
Error2("Error in XML: %s", error);
return false;
}
npcRoot = doc->GetRoot()->GetNode("npc");
if(!npcRoot)
{
CPrintf(CON_ERROR, "Error: no <npc> tag found\n");
return false;
}
dialogManager = new psDialogManager;
npc = new psCharacter;
npc->SetCharType(PSCHARACTER_TYPE_NPC);
// process xml data
if(!ReadBasicInfo() || !ReadLocation())
{
CPrintf(CON_ERROR, "Error: Failed to load NPC data\n");
return false;
}
ReadDescription();
ReadTraits();
ReadStats();
ReadMoney();
ReadSkills();
ReadTrainerInfo();
ReadMerchantInfo();
ReadFactions();
ReadKnowledgeAreas();
ReadSpecificKnowledge();
ReadSpecialResponses();
// insert processed data into the database
if(!WriteToDatabase())
{
CPrintf(CON_ERROR, "Error: Failed to insert data into the database\n");
return false;
}
return true;
}