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);
}
}
}
}
/*****************************************************************/
-
int Tree::getIndex(string searchName) {
try {
//Treemap knows name, group and index to speed up search
try {
int lc = tree[i].getLChild();
int rc = tree[i].getRChild();
-
+
//set parsimony groups to left child
map<string,int> parsimony = tree[lc].pGroups;
for(it=parsimony.begin();it!=parsimony.end();it++){
if(it->second == 1){
parsimony.erase(it->first);
- it--;
+// it--;
}
}
//set one remaining groups to 1
// 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
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);
- it--;
}
}
- //set one remaining groups to 1
- //so with our above example p[white] = 2 would be left and it would become p[white] = 1
for(it=parsimony.begin();it!=parsimony.end();it++){
parsimony[it->first] = 1;
}
+ }
- }
-
return parsimony;
}
catch(exception& e) {
}
/**************************************************************************************************/
-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::assembleRandomUnifracTree() {
- randomLabels();
+void Tree::assembleRandomUnifracTree(vector<string> g) {
+ randomLabels(g);
assembleTree();
}
/*************************************************************************************************/
/*****************************************************************/
-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++){
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