}
}
-
/***********************************************************************/
/***********************************************************************/
-
//Child Classes Below
/***********************************************************************/
int ReadNewickTree::read() {
try {
+ holder = "";
int c, error;
int comment = 0;
//if you are not a nexus file
if ((c = filehandle.peek()) != '#') {
while((c = filehandle.peek()) != EOF) {
+ while ((c = filehandle.peek()) != EOF) {
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
//make new tree
T = new Tree();
numNodes = T->getNumNodes();
globaldata->gTree.push_back(T);
}
}
+
+ if (error != 0) { readOk = error; }
return readOk;
}
catch(exception& e) {
n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off
lc = readNewickInt(filehandle, n, T);
- if (lc == -1) { return -1; } //reports an error in reading
+ if (lc == -1) { cout << "error with lc" << endl; return -1; } //reports an error in reading
if(filehandle.peek()==','){
readSpecialChar(filehandle,',',"comma");
}
if(rooted != 1){
rc = readNewickInt(filehandle, n, T);
- if (rc == -1) { return -1; } //reports an error in reading
+ if (rc == -1) { cout << "error with rc" << endl; return -1; } //reports an error in reading
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
}
int blen = 0;
- if(d == ':') { blen = 1; }
+ if(d == ':') { blen = 1; }
f.putback(d);
int n1 = T->getIndex(name);
//adds sequence names that are not in group file to the "xxx" group
- if(n1 == -1) {
- cerr << "Name: " << name << " not found in your groupfile. \n"; readOk = -1; return n1;
+ if(group == "not found") {
+ cout << "Name: " << name << " is not in your groupfile, and will be disregarded. \n"; //readOk = -1; return n1;
- //globaldata->gTreemap->namesOfSeqs.push_back(name);
- //globaldata->gTreemap->treemap[name].groupname = "xxx";
- //globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+ globaldata->gTreemap->namesOfSeqs.push_back(name);
+ globaldata->gTreemap->treemap[name].groupname = "xxx";
- //map<string, int>::iterator it;
- //it = globaldata->gTreemap->seqsPerGroup.find("xxx");
- //if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
- // globaldata->gTreemap->namesOfGroups.push_back("xxx");
- // globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
- //}else {
- // globaldata->gTreemap->seqsPerGroup["xxx"]++;
- //}
+ map<string, int>::iterator it;
+ it = globaldata->gTreemap->seqsPerGroup.find("xxx");
+ if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
+ globaldata->gTreemap->namesOfGroups.push_back("xxx");
+ globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
+ }else {
+ globaldata->gTreemap->seqsPerGroup["xxx"]++;
+ }
- //find index in tree of name
- //n1 = T->getIndex(name);
- //group = "xxx";
- //numLeaves++;
- //numNodes = 2*numLeaves - 1;
+ group = "xxx";
}
T->tree[n1].setGroup(group);