char d = f.get();
if(d == EOF){
- cerr << "Error: Input file ends prematurely, expecting a " << name << "\n"; return -1;
- //exit(1);
+ cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";
+ exit(1);
}
if(d != c){
- cerr << "Error: Expected " << name << " in input file. Found " << d << ".\n"; return -1;
- //exit(1);
+ cerr << "Error: Expected " << name << " in input file. Found " << d << ".\n";
+ exit(1);
}
if(d == ')' && f.peek() == '\n'){
gobble(f);
char d = f.get();
if(d == EOF){
- cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n"; return -1;
- //exit(1);
+ cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
+ exit(1);
}
return d;
}
float b;
if(!(f >> b)){
- cerr << "Error: Missing branch length in input tree.\n"; return -1;
- //exit(1);
+ cerr << "Error: Missing branch length in input tree.\n";
+ exit(1);
}
gobble(f);
return b;
}
}
-
/***********************************************************************/
/***********************************************************************/
-
//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) {
try {
int n = 0;
- int lc, rc, error;
+ int lc, rc;
int rooted = 0;
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()==','){
- error = readSpecialChar(filehandle,',',"comma");
- if (error == -1) { readOk = -1; return -1; }
+ readSpecialChar(filehandle,',',"comma");
}
// ';' means end of tree.
else if((ch=filehandle.peek())==';' || ch=='['){
}
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() == ')'){
- error = readSpecialChar(filehandle,')',"right parenthesis");
- if (error == -1) { readOk = -1; return -1; }
+ readSpecialChar(filehandle,')',"right parenthesis");
}
}
}
int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
try {
- int error;
-
int c = readNodeChar(f);
- if (c == -1) { readOk = -1; return -1; }
if(c == '('){
int lc = readNewickInt(f, n, T);
if (lc == -1) { return -1; } //reports an error in reading
- error = readSpecialChar(f,',',"comma");
- if (error == -1) { readOk = -1; return -1; }
+ readSpecialChar(f,',',"comma");
int rc = readNewickInt(f, n, T);
if (rc == -1) { return -1; } //reports an error in reading
if(f.peek()==')'){
- error = readSpecialChar(f,')',"right parenthesis");
- if (error == -1) { readOk = -1; return -1; }
+ readSpecialChar(f,')',"right parenthesis");
}
if(f.peek() == ':'){
- error = readSpecialChar(f,':',"colon");
- if (error == -1) { readOk = -1; return -1; }
+ readSpecialChar(f,':',"colon");
+
if(n >= numNodes){ cerr << "Error: Too many nodes in input tree\n"; readOk = -1; return -1; }
- error = readBranchLength(f);
- if (error == -1) { readOk = -1; return -1; }
- T->tree[n].setBranchLength(error);
+
+ T->tree[n].setBranchLength(readBranchLength(f));
}else{T->tree[n].setBranchLength(0.0); }
T->tree[n].setChildren(lc,rc);
}
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);
if(blen == 1){
f.get();
- error = readBranchLength(f);
- if (error == -1) { readOk = -1; return -1; }
- T->tree[n1].setBranchLength(error);
+ T->tree[n1].setBranchLength(readBranchLength(f));
}else{
T->tree[n1].setBranchLength(0.0);
}