#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();
+
for (int i = 0; i < numLeaves; i++) {
string name = tree[i].getName();
if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
else {
vector<string> dupNames;
- splitAtComma(globaldata->names[name], dupNames);
+ m->splitAtComma(globaldata->names[name], dupNames);
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
tree[i].setGroup(nodeGroups);
}//end else
- }//end for
+ }//end for
+
+ //float B = clock();
+ //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;
+
}
catch(exception& e) {
m->errorOut(e, "Tree", "addNamesToCounts");
/*****************************************************************/
int Tree::assembleTree() {
try {
-
+ //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;
+ 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");
//loop through nodes groups removing the ones the user doesn't want
for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
- if (inUsersGroups(it->first, g) != true) {
+ if (m->inUsersGroups(it->first, g) != true) {
tree[lc].pGroups.erase(it++);
}else { it++; }
}
//loop through nodes groups removing the ones the user doesn't want
for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
- if (inUsersGroups(it->first, g) != true) {
+ if (m->inUsersGroups(it->first, g) != true) {
tree[rc].pGroups.erase(it++);
}else { it++; }
}
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;
//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(), g);
- treei = inUsersGroups(tree[i].getGroup(), g);
+ treez = m->inUsersGroups(tree[z].getGroup(), g);
+ treei = m->inUsersGroups(tree[i].getGroup(), g);
if ((treez == true) && (treei == true)) {
//switches node i and node z's info.
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");
}
/*************************************************************************************************/
void Tree::createNewickFile(string f) {
try {
int root = findRoot();
- //filename = getRootName(globaldata->getTreeFile()) + "newick";
+ //filename = m->getRootName(globaldata->getTreeFile()) + "newick";
filename = f;
- openOutputFile(filename, out);
+ m->openOutputFile(filename, out);
printBranch(root, out, "branch");
try {
string filename = globaldata->getTreeFile();
ifstream filehandle;
- openInputFile(filename, filehandle);
+ m->openInputFile(filename, filehandle);
int c, comment;
comment = 0;
int done = 1;
//cout << " at beginning of while " << k << endl;
if(c == ')') {
//to pass over labels in trees
- string label = readLabel(filehandle);
+ c=filehandle.get();
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+ filehandle.putback(c);
}
-
if(c == ';') { return 0; }
if(c == -1) { return 0; }
-
//if you are a name
if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
- name = readName(filehandle);
+ name = "";
+ c = filehandle.get();
+ //k = c;
+//cout << k << endl;
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ name += c;
+ c = filehandle.get();
+ //k = c;
+//cout << " in name while " << k << endl;
+ }
+
+//cout << "name = " << name << endl;
globaldata->Treenames.push_back(name);
+ filehandle.putback(c);
+//k = c;
+//cout << " after putback" << k << endl;
}
if(c == ':') { //read until you reach the end of the branch length
- string bl = readBranchLength(filehandle);
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+ c = filehandle.get();
+ //k = c;
+ //cout << " in branch while " << k << endl;
+ }
+ filehandle.putback(c);
}
c = filehandle.get();
}
/*******************************************************/
-string Tree::readLabel(ifstream& filehandle) {
- try {
-
- string label = "";
-
- //to pass over labels in trees
- int c=filehandle.get();
- while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ label += c; c=filehandle.get(); }
- filehandle.putback(c);
-
- return label;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Tree", "readLabel");
- exit(1);
- }
-}
-/*******************************************************/
-string Tree::readName(ifstream& filehandle) {
- try {
-
- string name = "";
- int c = filehandle.get();
-
- while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
- name += c;
- c = filehandle.get();
- }
-
-//cout << "name = " << name << endl;
- filehandle.putback(c);
-
- return name;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Tree", "readName");
- exit(1);
- }
-}
-/*******************************************************/
-string Tree::readBranchLength(ifstream& filehandle) {
- try {
-
- string br = "";
- int c;
- while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
- br += c;
- c = filehandle.get();
- }
- filehandle.putback(c);
-
- return br;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Tree", "readBranchLength");
- exit(1);
- }
-}
/*******************************************************/
-/*******************************************************/
projects / mothur.git / blobdiff