m = MothurOut::getInstance();
if (m->runParse == true) { parseTreeFile(); m->runParse = false; }
- //for(int i = 0; i < globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl; }
numLeaves = m->Treenames.size();
numNodes = 2*numLeaves - 1;
//build tree from matrix
//initialize indexes
map<int, int> indexes; //maps row in simMatrix to vector index in the tree
- int numGroups = (tmap->getNamesOfGroups()).size();
- for (int g = 0; g < numGroups; g++) { indexes[g] = g; }
+ for (int g = 0; g < numLeaves; g++) { indexes[g] = g; }
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
- for (int i = 0; i < (numGroups - 1); i++) {
+ for (int i = 0; i < (numLeaves - 1); i++) {
float largest = -1000.0;
if (m->control_pressed) { break; }
//set non-leaf node info and update leaves to know their parents
//non-leaf
- tree[numGroups + i].setChildren(indexes[row], indexes[column]);
+ tree[numLeaves + i].setChildren(indexes[row], indexes[column]);
//parents
- tree[indexes[row]].setParent(numGroups + i);
- tree[indexes[column]].setParent(numGroups + i);
+ tree[indexes[row]].setParent(numLeaves + i);
+ tree[indexes[column]].setParent(numLeaves + i);
//blength = distance / 2;
float blength = ((1.0 - largest) / 2);
tree[indexes[column]].setBranchLength(blength - tree[indexes[column]].getLengthToLeaves());
//set your length to leaves to your childs length plus branchlength
- tree[numGroups + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
+ tree[numLeaves + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
//update index
- indexes[row] = numGroups+i;
- indexes[column] = numGroups+i;
+ indexes[row] = numLeaves+i;
+ indexes[column] = numLeaves+i;
//remove highest value that caused the merge.
sims[row][column] = -1000.0;
}
}
/*****************************************************************/
+void Tree::getCopy(Tree* copy, map<string, string> nameMap, vector<string> namesToInclude) {
+ try {
+
+ //for each node in the tree copy its info
+ for (int i = 0; i < numNodes; i++) {
+ //copy name
+ tree[i].setName(copy->tree[i].getName());
+
+ //copy group
+ vector<string> temp;
+ tree[i].setGroup(temp);
+
+ //copy branch length
+ tree[i].setBranchLength(copy->tree[i].getBranchLength());
+
+ //copy parent
+ tree[i].setParent(copy->tree[i].getParent());
+
+ //copy children
+ tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
+
+ //copy index in node and tmap
+ tree[i].setIndex(copy->tree[i].getIndex());
+ setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
+
+ //copy pGroups
+ tree[i].pGroups.clear();
+
+ //copy pcount
+ tree[i].pcount.clear();
+ }
+
+ groupNodeInfo.clear();
+
+ //now lets change prune the seqs not in namesToInclude by setting their group to "doNotIncludeMe"
+ for (int i = 0; i < numLeaves; i++) {
+
+ if (m->control_pressed) { break; }
+
+ string name = tree[i].getName();
+
+ map<string, string>::iterator itNames = nameMap.find(name);
+
+ if (itNames == nameMap.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
+ else {
+ vector<string> dupNames;
+ m->splitAtComma(nameMap[name], dupNames);
+
+ map<string, int>::iterator itCounts;
+ int maxPars = 1;
+ set<string> groupsAddedForThisNode;
+ for (int j = 0; j < dupNames.size(); j++) {
+
+ string group = tmap->getGroup(dupNames[j]);
+ bool includeMe = m->inUsersGroups(dupNames[j], namesToInclude);
+
+ if (!includeMe && (group != "doNotIncludeMe")) { m->mothurOut("[ERROR] : creating subtree in copy.\n"); m->control_pressed = true; }
+ else if (!includeMe) {
+ 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 (itCounts == tree[i].pcount.end()) { //new group, add it
+ tree[i].pcount[group] = 1;
+ }else {
+ tree[i].pcount[group]++;
+ }
+
+ //update pgroups
+ itCounts = tree[i].pGroups.find(group);
+ if (itCounts == tree[i].pGroups.end()) { //new group, add it
+ tree[i].pGroups[group] = 1;
+ }else{
+ tree[i].pGroups[group]++;
+ }
+
+ //keep highest group
+ if(tree[i].pGroups[group] > maxPars){
+ maxPars = tree[i].pGroups[group];
+ }
+ }
+ }//end for
+
+ if (maxPars > 1) { //then we have some more dominant groups
+ //erase all the groups that are less than maxPars because you found a more dominant group.
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+ if(it->second < maxPars){
+ tree[i].pGroups.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+ tree[i].pGroups[it->first] = 1;
+ }
+ }//end if
+
+ //update groups to reflect all the groups this node represents
+ vector<string> nodeGroups;
+ map<string, int>::iterator itGroups;
+ for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
+ nodeGroups.push_back(itGroups->first);
+ }
+ tree[i].setGroup(nodeGroups);
+
+ }//end else
+ }//end for
+
+
+ //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) { break; }
+
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "getCopy");
+ exit(1);
+ }
+}
+/*****************************************************************/
void Tree::getCopy(Tree* copy) {
try {
projects / mothur.git / blobdiff