#include "tree.h"
-
+/*****************************************************************/
+Tree::Tree(string g) {
+ try {
+ globaldata = GlobalData::getInstance();
+ m = MothurOut::getInstance();
+
+ parseTreeFile(); globaldata->runParse = false;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "Tree - just parse");
+ exit(1);
+ }
+}
/*****************************************************************/
Tree::Tree() {
try {
numNodes = 2*numLeaves - 1;
tree.resize(numNodes);
+
+ //initialize groupNodeInfo
+ for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
+ groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+ }
//initialize tree with correct number of nodes, name and group info.
for (int i = 0; i < numNodes; i++) {
//initialize leaf nodes
if (i <= (numLeaves-1)) {
tree[i].setName(globaldata->Treenames[i]);
- vector<string> tempGroups; tempGroups.push_back(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+
+ //save group info
+ string group = globaldata->gTreemap->getGroup(globaldata->Treenames[i]);
+ vector<string> tempGroups; tempGroups.push_back(group);
tree[i].setGroup(tempGroups);
+ groupNodeInfo[group].push_back(i);
+
//set pcount and pGroup for groupname to 1.
- tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
- tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
+ tree[i].pcount[group] = 1;
+ tree[i].pGroups[group] = 1;
+
//Treemap knows name, group and index to speed up search
globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
//go through each leaf and update its pcounts and pgroups
- float A = clock();
+ //float A = clock();
for (int i = 0; i < numLeaves; i++) {
map<string, int>::iterator itCounts;
int maxPars = 1;
+ set<string> groupsAddedForThisNode;
for (int j = 0; j < dupNames.size(); j++) {
-
+
+ string group = globaldata->gTreemap->getGroup(dupNames[j]);
+
if (dupNames[j] != name) {//you already added yourself in the constructor
- string group = globaldata->gTreemap->getGroup(dupNames[j]);
+
+ if (groupsAddedForThisNode.count(group) == 0) { groupNodeInfo[group].push_back(i); groupsAddedForThisNode.insert(group); } //if you have not already added this node for this group, then add it
//update pcounts
itCounts = tree[i].pcount.find(group);
if(tree[i].pGroups[group] > maxPars){
maxPars = tree[i].pGroups[group];
}
- }//end if
+ }else { groupsAddedForThisNode.insert(group); } //add it so you don't add it to groupNodeInfo again
}//end for
if (maxPars > 1) { //then we have some more dominant groups
}//end else
}//end for
- float B = clock();
- cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;
+ //float B = clock();
+ //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;
}
catch(exception& e) {
/*****************************************************************/
int Tree::assembleTree() {
try {
- float A = clock();
+ //float A = clock();
//if user has given a names file we want to include that info in the pgroups and pcount info.
if(globaldata->names.size() != 0) { addNamesToCounts(); }
tree[i].pGroups = (mergeGroups(i));
tree[i].pcount = (mergeGcounts(i));
}
- float B = clock();
- cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
+ //float B = clock();
+ //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "assembleTree");
+ exit(1);
+ }
+}
+/*****************************************************************/
+int Tree::assembleTree(string n) {
+ try {
+
+ //build the pGroups in non leaf nodes to be used in the parsimony calcs.
+ for (int i = numLeaves; i < numNodes; i++) {
+ if (m->control_pressed) { return 1; }
+
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+ //float B = clock();
+ //cout << "assembleTree\t" << (B-A) / CLOCKS_PER_SEC << endl;
return 0;
}
catch(exception& e) {
exit(1);
}
}
+
/*****************************************************************/
void Tree::getCopy(Tree* copy) {
try {
tree[i].pcount = copy->tree[i].pcount;
}
+ groupNodeInfo = copy->groupNodeInfo;
+
}
catch(exception& e) {
m->errorOut(e, "Tree", "getCopy");
void Tree::randomLabels(vector<string> g) {
try {
+
+ //initialize groupNodeInfo
+ for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
+ groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+ }
for(int i = 0; i < numLeaves; i++){
int z;
tree[z].pcount = (tree[i].pcount);
tree[i].pcount = (gcount_hold);
}
+
+ for (int k = 0; k < (tree[i].getGroup()).size(); k++) { groupNodeInfo[(tree[i].getGroup())[k]].push_back(i); }
+ for (int k = 0; k < (tree[z].getGroup()).size(); k++) { groupNodeInfo[(tree[z].getGroup())[k]].push_back(z); }
}
}
catch(exception& e) {
/*************************************************************************************************/
void Tree::assembleRandomUnifracTree(vector<string> g) {
randomLabels(g);
- assembleTree();
+ assembleTree("noNameCounts");
}
/*************************************************************************************************/
void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
randomLabels(temp);
- assembleTree();
+ assembleTree("noNameCounts");
}
/*************************************************************************************************/