istringstream iss (tempBuf,istringstream::in);
delete buffer;
- iss >> numNodes; gobble(iss);
+ //read version
+ m->getline(iss); m->gobble(iss);
+
+ iss >> numNodes; m->gobble(iss);
tree.resize(numNodes);
for (int i = 0; i < tree.size(); i++) {
- iss >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(iss);
+ iss >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(iss);
}
//read genus nodes
int numGenus = 0;
- iss >> numGenus; gobble(iss);
+ iss >> numGenus; m->gobble(iss);
int gnode, gsize;
totals.clear();
for (int i = 0; i < numGenus; i++) {
- iss >> gnode >> gsize; gobble(iss);
+ iss >> gnode >> gsize; m->gobble(iss);
uniqueTaxonomies[gnode] = gnode;
totals.push_back(gsize);
MPI_File_close(&inMPI);
#else
- in >> numNodes; gobble(in);
+ //read version
+ string line = m->getline(in); m->gobble(in);
+
+ in >> numNodes; m->gobble(in);
tree.resize(numNodes);
for (int i = 0; i < tree.size(); i++) {
- in >> tree[i].name >> tree[i].level >> tree[i].parent; gobble(in);
+ in >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(in);
}
//read genus nodes
int numGenus = 0;
- in >> numGenus; gobble(in);
+ in >> numGenus; m->gobble(in);
int gnode, gsize;
totals.clear();
for (int i = 0; i < numGenus; i++) {
- in >> gnode >> gsize; gobble(in);
+ in >> gnode >> gsize; m->gobble(in);
uniqueTaxonomies[gnode] = gnode;
totals.push_back(gsize);
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
if (pid == 0) {
- positions = setFilePosEachLine(tfile, num);
+ positions = m->setFilePosEachLine(tfile, num);
//send file positions to all processes
for(int i = 1; i < processors; i++) {
#else
ifstream in;
- openInputFile(tfile, in);
+ m->openInputFile(tfile, in);
//read in users taxonomy file and add sequences to tree
while(!in.eof()){
- in >> name >> tax; gobble(in);
-
+ in >> name >> tax; m->gobble(in);
+
addSeqToTree(name, tax);
}
in.close();
#endif
-
+
assignHeirarchyIDs(0);
-
+
//create file for summary if needed
setUp(tfile);
}
if (pid == 0) { binUnclassified(taxFileNameTest); }
#else
- //create file needed for summary if it doesn't exist
- ifstream FileTest(taxFileNameTest.c_str());
-
- if (!FileTest) {
- binUnclassified(taxFileNameTest);
- }
+ binUnclassified(taxFileNameTest);
#endif
}
catch(exception& e) {
try {
ofstream out;
- openOutputFile(file, out);
+ m->openOutputFile(file, out);
map<string, int>::iterator itBin;
map<string, int>::iterator childPointer;
vector<TaxNode> copy = tree;
-
+
//fill out tree
fillOutTree(0, copy);
-
- //get leaf nodes that may need externsion
+
+ //get leaf nodes that may need extension
for (int i = 0; i < copy.size(); i++) {
if (copy[i].children.size() == 0) {
}
int copyNodes = copy.size();
-
+
//go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
map<int, int>::iterator itLeaf;
for (itLeaf = leafNodes.begin(); itLeaf != leafNodes.end(); itLeaf++) {
int currentNode = itLeaf->second;
//this sequence is unclassified at some levels
- while(level <= maxLevel){
+ while(level < maxLevel){
level++;
/**************************************************************************************************/
void PhyloTree::fillOutTree(int index, vector<TaxNode>& copy) {
try {
+
map<string,int>::iterator it;
it = copy[index].children.find("unclassified");
copy[copy.size()-1].level = copy[index].level + 1;
}
- if (tree[index].level <= maxLevel) {
+ if (tree[index].level < maxLevel) {
for(it=tree[index].children.begin();it!=tree[index].children.end();it++){ //check your children
fillOutTree(it->second, copy);
}
}
-
+
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "fillOutTree");
void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
try {
+
+ //output mothur version
+ out << "#" << m->getVersion() << endl;
+
out << copy.size() << endl;
+ out << maxLevel << endl;
+
for (int i = 0; i < copy.size(); i++) {
out << copy[i].level << '\t'<< copy[i].name << '\t' << copy[i].children.size() << '\t';
#endif
ofstream outTree;
- openOutputFile(treefilename, outTree);
+ m->openOutputFile(treefilename, outTree);
+
+ //output mothur version
+ outTree << "#" << m->getVersion() << endl;
//print treenodes
outTree << tree.size() << endl;