/***********************************************************************/
//This class reads a file in Newick form and stores it in a tree.
-int ReadNewickTree::read(TreeMap* tmap) {
+int ReadNewickTree::read(CountTable* ct) {
try {
holder = "";
int c, error;
//if you are not a nexus file
if ((c = filehandle.peek()) != '#') {
- while((c = filehandle.peek()) != EOF) {
+ 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;
}
//make new tree
- T = new Tree(tmap);
+ T = new Tree(ct);
numNodes = T->getNumNodes();
numLeaves = T->getNumLeaves();
- error = readTreeString(tmap);
+ error = readTreeString(ct);
//save trees for later commands
Trees.push_back(T);
//if you are a nexus file
}else if ((c = filehandle.peek()) == '#') {
//get right number of seqs from nexus file.
- Tree* temp = new Tree(tmap); delete temp;
+ Tree* temp = new Tree(ct); delete temp;
- nexusTranslation(tmap); //reads file through the translation and updates treemap
- while((c = filehandle.peek()) != EOF) {
+ 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) {
+ while ((c = filehandle.peek()) != EOF) {
+ if (m->control_pressed) { filehandle.close(); return 0; }
if(holder == "[" || holder == "[!"){
comment = 1;
}
filehandle.putback(c); //put back first ( of tree.
//make new tree
- T = new Tree(tmap);
+ T = new Tree(ct);
numNodes = T->getNumNodes();
numLeaves = T->getNumLeaves();
//read tree info
- error = readTreeString(tmap);
+ error = readTreeString(ct);
//save trees for later commands
Trees.push_back(T);
}
/**************************************************************************************************/
//This function read the file through the translation of the sequences names and updates treemap.
-string ReadNewickTree::nexusTranslation(TreeMap* tmap) {
+string ReadNewickTree::nexusTranslation(CountTable* ct) {
try {
holder = "";
filehandle >> holder;
if(holder == "tree" && comment != 1){return holder;}
}
-
- //update treemap
- tmap->namesOfSeqs.clear();
-
- /*char c;
- string number, name;
- while ((c = filehandle.peek()) != EOF) {
-
- filehandle >> number;
-
- if ((number == "tree") || (number == ";") ) { name = number; break; }
-
- filehandle >> name;
-
- char lastChar;
- if (name.length() != 0) { lastChar = name[name.length()-1]; }
-
- if ((name == "tree") || (name == ";") ) { break; }
-
- if (lastChar == ',') { name.erase(name.end()-1); } //erase the comma
- */
-
+
string number, name;
for(int i=0;i<numSeqs;i++){
filehandle >> number;
filehandle >> name;
name.erase(name.end()-1); //erase the comma
-
- //insert new one with new name
- string group = tmap->getGroup(name);
- tmap->treemap[toString(number)].groupname = group;
- tmap->treemap[toString(number)].vectorIndex = tmap->getIndex(name);
- //erase old one. so treemap[sarah].groupnumber is now treemap[1].groupnumber. if number is 1 and name is sarah.
- tmap->treemap.erase(name);
- tmap->namesOfSeqs.push_back(number);
+ ct->renameSeq(name, toString(number));
}
return name;
}
/**************************************************************************************************/
-int ReadNewickTree::readTreeString(TreeMap* tmap) {
+int ReadNewickTree::readTreeString(CountTable* ct) {
try {
int n = 0;
if(ch == '('){
n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off
- lc = readNewickInt(filehandle, n, T, tmap);
- if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
+ lc = readNewickInt(filehandle, n, T, ct);
+ if (lc == -1) { m->mothurOut("error with lc"); m->mothurOutEndLine(); m->control_pressed = true; return -1; } //reports an error in reading
if(filehandle.peek()==','){
readSpecialChar(filehandle,',',"comma");
}
if(rooted != 1){
- rc = readNewickInt(filehandle, n, T, tmap);
- if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); return -1; } //reports an error in reading
+ rc = readNewickInt(filehandle, n, T, ct);
+ if (rc == -1) { m->mothurOut("error with rc"); m->mothurOutEndLine(); m->control_pressed = true; return -1; } //reports an error in reading
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
}
/**************************************************************************************************/
-int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, TreeMap* tmap) {
+int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T, CountTable* ct) {
try {
if (m->control_pressed) { return -1; }
//read all children
vector<int> childrenNodes;
while(f.peek() != ')'){
- int child = readNewickInt(f, n, T, tmap);
+ int child = readNewickInt(f, n, T, ct);
if (child == -1) { return -1; } //reports an error in reading
//cout << "child = " << child << endl;
childrenNodes.push_back(child);
}else{
T->tree[n].setBranchLength(0.0);
}
-
- //T->tree[n].setChildren(lc,rc);
- //T->tree[lc].setParent(n);
- //T->tree[rc].setParent(n);
- //T->printTree(); cout << endl;
-
+
return n++;
}else{
f.putback(d);
//set group info
- string group = tmap->getGroup(name);
-
+ vector<string> group = ct->getGroups(name);
+ //cout << name << endl;
//find index in tree of name
int n1 = T->getIndex(name);
//adds sequence names that are not in group file to the "xxx" group
- if(group == "not found") {
+ if(group.size() == 0) {
m->mothurOut("Name: " + name + " is not in your groupfile, and will be disregarded. \n"); //readOk = -1; return n1;
- tmap->namesOfSeqs.push_back(name);
- tmap->treemap[name].groupname = "xxx";
-
- map<string, int>::iterator it;
- it = tmap->seqsPerGroup.find("xxx");
- if (it == tmap->seqsPerGroup.end()) { //its a new group
- tmap->addGroup("xxx");
- tmap->seqsPerGroup["xxx"] = 1;
- }else {
- tmap->seqsPerGroup["xxx"]++;
- }
-
- group = "xxx";
- }
-
- vector<string> tempGroup; tempGroup.push_back(group);
-
- T->tree[n1].setGroup(tempGroup);
+ vector<string> currentGroups = ct->getNamesOfGroups();
+ if (!m->inUsersGroups("xxx", currentGroups)) { ct->addGroup("xxx"); }
+ currentGroups = ct->getNamesOfGroups();
+ vector<int> thisCounts; thisCounts.resize(currentGroups.size(), 0);
+ for (int h = 0; h < currentGroups.size(); h++) {
+ if (currentGroups[h] == "xxx") { thisCounts[h] = 1; break; }
+ }
+ ct->push_back(name, thisCounts);
+
+ group.push_back("xxx");
+ }
+ T->tree[n1].setGroup(group);
T->tree[n1].setChildren(-1,-1);
if(blen == 1){
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