int ReadNewickTree::read(CountTable* ct) {
try {
holder = "";
int c, error;
int comment = 0;
//if you are not a nexus file
if ((c = filehandle.peek()) != '#') {
while((c = filehandle.peek()) != EOF) {
if (m->control_pressed) { filehandle.close(); return 0; }
while ((c = filehandle.peek()) != EOF) {
if (m->control_pressed) { filehandle.close(); return 0; }
// get past comments
if(c == '[') {
comment = 1;
}
if(c == ']'){
comment = 0;
}
if((c == '(') && (comment != 1)){ break; }
filehandle.get();
}
//make new tree
T = new Tree(ct);
numNodes = T->getNumNodes();
numLeaves = T->getNumLeaves();
error = readTreeString(ct);
//save trees for later commands
Trees.push_back(T);
m->gobble(filehandle);
}
//if you are a nexus file
}else if ((c = filehandle.peek()) == '#') {
//get right number of seqs from nexus file.
Tree* temp = new Tree(ct); delete temp;
nexusTranslation(ct); //reads file through the translation and updates treemap
while((c = filehandle.peek()) != EOF) {
if (m->control_pressed) { filehandle.close(); return 0; }
// get past comments
while ((c = filehandle.peek()) != EOF) {
if (m->control_pressed) { filehandle.close(); return 0; }
if(holder == "[" || holder == "[!"){
comment = 1;
}
if(holder == "]"){
comment = 0;
}
if((holder == "tree" || holder == "end;") && comment != 1){ holder = ""; comment = 0; break;}
filehandle >> holder;
}
//pass over the "tree rep.6878900 = "
while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;}
if (c == EOF ) { break; }
filehandle.putback(c); //put back first ( of tree.
//make new tree
T = new Tree(ct);
numNodes = T->getNumNodes();
numLeaves = T->getNumLeaves();
//read tree info
error = readTreeString(ct);
//save trees for later commands
Trees.push_back(T);
}
}
if (error != 0) { readOk = error; }
filehandle.close();
return readOk;
}
//this code is a mess and should be rethought...-slw
int Tree::parseTreeFile() {
//only takes names from the first tree and assumes that all trees use the same names.
try {
string filename = m->getTreeFile();
ifstream filehandle;
m->openInputFile(filename, filehandle);
int c, comment;
comment = 0;
int done = 1;
//ifyou are not a nexus file
if((c = filehandle.peek()) != '#') {
while((c = filehandle.peek()) != ';') {
if (m->control_pressed) { filehandle.close(); return 0; }
while ((c = filehandle.peek()) != ';') {
if (m->control_pressed) { filehandle.close(); return 0; }
// get past comments
if(c == '[') {
comment = 1;
}
if(c == ']'){
comment = 0;
}
if((c == '(') && (comment != 1)){ break; }
filehandle.get();
}
done = readTreeString(filehandle);
if (done == 0) { break; }
}
//ifyou are a nexus file
}else if((c = filehandle.peek()) == '#') {
string holder = "";
// get past comments
while(holder != "translate" && holder != "Translate"){
if (m->control_pressed) { filehandle.close(); return 0; }
if(holder == "[" || holder == "[!"){
comment = 1;
}
if(holder == "]"){
comment = 0;
}
filehandle >> holder;
//if there is no translate then you must read tree string otherwise use translate to get names
if((holder == "tree") && (comment != 1)){
//pass over the "tree rep.6878900 = "
while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
if(c == EOF) { break; }
filehandle.putback(c); //put back first ( of tree.
done = readTreeString(filehandle);
break;
}
if (done == 0) { break; }
}
//use nexus translation rather than parsing tree to save time
if((holder == "translate") || (holder == "Translate")) {
string number, name, h;
h = ""; // so it enters the loop the first time
while((h != ";") && (number != ";")) {
if (m->control_pressed) { filehandle.close(); return 0; }
filehandle >> number;
filehandle >> name;
//c = , until done with translation then c = ;
h = name.substr(name.length()-1, name.length());
name.erase(name.end()-1); //erase the comma
m->Treenames.push_back(number);
}
if(number == ";") { m->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
}
}
