// 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) {
+map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
try {
int lc = tree[i].getLChild();
//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, globaldata->Groups) != true) { tree[lc].pGroups.erase(it->first); }
+ 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, globaldata->Groups) != true) { tree[rc].pGroups.erase(it->first); }
+ if (inUsersGroups(it->first, g) != true) { tree[rc].pGroups.erase(it->first); }
}
//set parsimony groups to left child
}
/**************************************************************************************************/
-void Tree::randomLabels() {
+void Tree::randomLabels(vector<string> g) {
try {
- //set up the groups the user wants to include
- setGroups();
-
for(int i = 0; i < numLeaves; i++){
int z;
//get random index to switch with
//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;
- treez = inUsersGroups(tree[z].getGroup(), globaldata->Groups);
- treei = inUsersGroups(tree[i].getGroup(), 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.
void Tree::randomLabels(string groupA, string groupB) {
try {
- for(int i = 0; i < numLeaves; i++) {
- int z;
- //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.
- if (((tree[z].getGroup() == groupA) || (tree[z].getGroup() == groupB)) && ((tree[i].getGroup() == groupA) || (tree[i].getGroup() == groupB))) {
- //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);
-
- 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);
+ 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());
- map<string,int> gcount_hold = tree[z].pcount;
- tree[z].pcount = (tree[i].pcount);
- tree[i].pcount = (gcount_hold);
+ 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);
}
}
/*************************************************************************************************/
-void Tree::assembleRandomUnifracTree() {
- randomLabels();
+void Tree::assembleRandomUnifracTree(vector<string> g) {
+ randomLabels(g);
assembleTree();
}
/*************************************************************************************************/
printBranch(tree[node].getRChild());
out << ")";
}else { //you are a leaf
- out << tree[node].getName() << ":" << tree[node].getBranchLength();
+ 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++){
projects / mothur.git / blobdiff