if (i <= (numLeaves-1)) {
tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
- //the node knows its index
- tree[i].setIndex(i);
//set pcount and pGroup for groupname to 1.
tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
}else if (i > (numLeaves-1)) {
tree[i].setName("");
tree[i].setGroup("");
- //the node knows its index
- tree[i].setIndex(i);
}
}
}
}
/*****************************************************************/
-
+Tree::~Tree() {}
+/*****************************************************************/
int Tree::getIndex(string searchName) {
try {
//Treemap knows name, group and index to speed up search
map<string, int> Tree::mergeGroups(int i) {
try {
-
int lc = tree[i].getLChild();
int rc = tree[i].getRChild();
-
+
//set parsimony groups to left child
map<string,int> parsimony = tree[lc].pGroups;
//look at right child groups and update maxPars if right child has something higher for that group.
for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
- parsimony[it->first]++;
+ it2 = parsimony.find(it->first);
+ if (it2 != parsimony.end()) {
+ parsimony[it->first]++;
+ }else {
+ parsimony[it->first] = 1;
+ }
if(parsimony[it->first] > maxPars){
maxPars = parsimony[it->first];
for(it=parsimony.begin();it!=parsimony.end();it++){
if(it->second == 1){
parsimony.erase(it->first);
- it--;
+// it--;
}
}
//set one remaining groups to 1
exit(1);
}
}
+/*****************************************************************/
+//returns a map with a groupname and the number of times that group was seen in the children
+//for instance if your children are white and black then it would return a map with 2 entries
+// p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
+//and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
+
+map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
+ try {
+
+ int lc = tree[i].getLChild();
+ int rc = tree[i].getRChild();
+
+ //loop through nodes groups removing the ones the user doesn't want
+ for (it = tree[lc].pGroups.begin(); it != tree[lc].pGroups.end(); it++) {
+ if (inUsersGroups(it->first, g) != true) { tree[lc].pGroups.erase(it->first); }
+ }
+
+ //loop through nodes groups removing the ones the user doesn't want
+ for (it = tree[rc].pGroups.begin(); it != tree[rc].pGroups.end(); it++) {
+ if (inUsersGroups(it->first, g) != true) { tree[rc].pGroups.erase(it->first); }
+ }
+
+ //set parsimony groups to left child
+ map<string,int> parsimony = tree[lc].pGroups;
+
+ int maxPars = 1;
+
+ //look at right child groups and update maxPars if right child has something higher for that group.
+ for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
+ it2 = parsimony.find(it->first);
+ if (it2 != parsimony.end()) {
+ parsimony[it->first]++;
+ }else {
+ parsimony[it->first] = 1;
+ }
+
+ if(parsimony[it->first] > maxPars){
+ maxPars = parsimony[it->first];
+ }
+ }
+
+ // this is true if right child had a greater parsimony for a certain group
+ if(maxPars > 1){
+ //erase all the groups that are only 1 because you found something with 2.
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ if(it->second == 1){
+ parsimony.erase(it->first);
+ }
+ }
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ parsimony[it->first] = 1;
+ }
+ }
+
+ return parsimony;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function mergeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
/**************************************************************************************************/
}
/**************************************************************************************************/
-void Tree::randomLabels() {
+void Tree::randomLabels(vector<string> g) {
try {
- //set up the groups the user wants to include
- setGroups();
-
- for(int i=numLeaves-1;i>=0;i--){
- if(tree[i].pGroups.size() == 0){
- continue;
- }
-
- int escape = 1;
+ for(int i = 0; i < numLeaves; i++){
int z;
-
- while(escape == 1){
- //get random index to switch with
- z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
-
- if(tree[z].pGroups.size() != 0){
- escape = 0;
- }
- }
+ //get random index to switch with
+ z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
//you only want to randomize the nodes that are from a group the user wants analyzed, so
//if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
bool treez, treei;
-
- //leaves have only one group so you can just set it to begin()
- it = tree[z].pGroups.begin();
- treez = inUsersGroups(it->first, globaldata->Groups);
-
- it = tree[i].pGroups.begin();
- treei = inUsersGroups(it->first, globaldata->Groups);
+
+ treez = inUsersGroups(tree[z].getGroup(), g);
+ treei = inUsersGroups(tree[i].getGroup(), g);
if ((treez == true) && (treei == true)) {
//switches node i and node z's info.
map<string,int> lib_hold = tree[z].pGroups;
tree[z].pGroups = (tree[i].pGroups);
tree[i].pGroups = (lib_hold);
-
- tree[z].setGroup(tree[z].pGroups.begin()->first);
- tree[i].setGroup(tree[i].pGroups.begin()->first);
-
+
+ string zgroup = tree[z].getGroup();
+ tree[z].setGroup(tree[i].getGroup());
+ tree[i].setGroup(zgroup);
+
+ string zname = tree[z].getName();
+ tree[z].setName(tree[i].getName());
+ tree[i].setName(zname);
+
map<string,int> gcount_hold = tree[z].pcount;
tree[z].pcount = (tree[i].pcount);
tree[i].pcount = (gcount_hold);
}
/**************************************************************************************************/
+void Tree::randomLabels(string groupA, string groupB) {
+ try {
+ int numSeqsA = globaldata->gTreemap->seqsPerGroup[groupA];
+ int numSeqsB = globaldata->gTreemap->seqsPerGroup[groupB];
+
+ vector<string> randomGroups(numSeqsA+numSeqsB, groupA);
+ for(int i=numSeqsA;i<randomGroups.size();i++){
+ randomGroups[i] = groupB;
+ }
+ random_shuffle(randomGroups.begin(), randomGroups.end());
+
+ int randomCounter = 0;
+ for(int i=0;i<numLeaves;i++){
+ if(tree[i].getGroup() == groupA || tree[i].getGroup() == groupB){
+ tree[i].setGroup(randomGroups[randomCounter]);
+ tree[i].pcount.clear();
+ tree[i].pcount[randomGroups[randomCounter]] = 1;
+ tree[i].pGroups.clear();
+ tree[i].pGroups[randomGroups[randomCounter]] = 1;
+ randomCounter++;
+ }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Tree class function randomLabels. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
void Tree::randomBlengths() {
try {
for(int i=numNodes-1;i>=0;i--){
}
}
/*************************************************************************************************/
-void Tree::assembleRandomUnifracTree() {
- randomLabels();
+void Tree::assembleRandomUnifracTree(vector<string> g) {
+ randomLabels(g);
+ assembleTree();
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
+ randomLabels(groupA, groupB);
assembleTree();
}
/*****************************************************************/
// This prints out the tree in Newick form.
-void Tree::createNewickFile() {
+void Tree::createNewickFile(string f) {
try {
int root = findRoot();
- filename = getRootName(globaldata->getTreeFile()) + "newick";
+ //filename = getRootName(globaldata->getTreeFile()) + "newick";
+ filename = f;
openOutputFile(filename, out);
printBranch(root);
// you are at the end of the tree
out << ";" << endl;
+ out.close();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function createNewickFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
printBranch(tree[node].getRChild());
out << ")";
}else { //you are a leaf
- tree[node].printNode(out); //prints out name and branch length
+ out << tree[node].getGroup() << ":" << tree[node].getBranchLength();
}
}
}
/*****************************************************************/
-void Tree::setGroups() {
- try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (globaldata->gTreemap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
- }
- }
-
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gTreemap->namesOfGroups[i]);
- }
- }
-
- }else {
- for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(globaldata->gTreemap->namesOfGroups[i]);
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the Tree class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
+void Tree::printTree() {
+
+ for(int i=0;i<numNodes;i++){
+ cout << i << '\t';
+ tree[i].printNode();
+ }
+
}
+/*****************************************************************/
+
+
projects / mothur.git / blobdiff