}
}
-
/***********************************************************************/
/***********************************************************************/
-
//Child Classes Below
/***********************************************************************/
/***********************************************************************/
//This class reads a file in Newick form and stores it in a tree.
-void ReadNewickTree::read() {
+int ReadNewickTree::read() {
try {
- int c;
+ 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();
numLeaves = T->getNumLeaves();
- readTreeString();
+ error = readTreeString();
+
//save trees for later commands
globaldata->gTree.push_back(T);
gobble(filehandle);
numLeaves = T->getNumLeaves();
//read tree info
- readTreeString();
+ error = readTreeString();
+
//save trees for later commands
globaldata->gTree.push_back(T);
}
}
+ if (error != 0) { readOk = error; }
+ return readOk;
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
/**************************************************************************************************/
-void ReadNewickTree::readTreeString() {
+int ReadNewickTree::readTreeString() {
try {
int n = 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) { 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) { cout << "error with rc" << endl; return -1; } //reports an error in reading
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
if(n!=0){
cerr << "Internal error: The only taxon is not taxon 0.\n";
- exit(1);
+ //exit(1);
+ readOk = -1; return -1;
}
lc = rc = -1;
}
if(lc!=-1){ T->tree[lc].setParent(n); }
if(rc!=-1){ T->tree[rc].setParent(n); }
}
+ return 0;
}
catch(exception& e) {
if(c == '('){
int lc = readNewickInt(f, n, T);
+ if (lc == -1) { return -1; } //reports an error in reading
readSpecialChar(f,',',"comma");
- int rc = readNewickInt(f, n, T);
+ int rc = readNewickInt(f, n, T);
+ if (rc == -1) { return -1; } //reports an error in reading
if(f.peek()==')'){
- readSpecialChar(f,')',"right parenthesis");
+ readSpecialChar(f,')',"right parenthesis");
}
if(f.peek() == ':'){
- readSpecialChar(f,':',"colon");
- if(n >= numNodes){ cerr << "Error: Too many nodes in input tree\n"; exit(1); }
+ readSpecialChar(f,':',"colon");
+
+ if(n >= numNodes){ cerr << "Error: Too many nodes in input tree\n"; readOk = -1; return -1; }
+
T->tree[n].setBranchLength(readBranchLength(f));
}else{T->tree[n].setBranchLength(0.0); }
}
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 and it will be ignored. \n";
+ 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);
map<string, int>::iterator it;
it = globaldata->gTreemap->seqsPerGroup.find("xxx");
globaldata->gTreemap->seqsPerGroup["xxx"]++;
}
- //find index in tree of name
- n1 = T->getIndex(name);
group = "xxx";
}
T->tree[n1].setGroup(group);
-
T->tree[n1].setChildren(-1,-1);
if(blen == 1){
- f.get();
+ f.get();
T->tree[n1].setBranchLength(readBranchLength(f));
}else{
T->tree[n1].setBranchLength(0.0);