#include "tree.h"
/*****************************************************************/
-Tree::Tree(int num, TreeMap* t) : tmap(t) {
+Tree::Tree(int num, CountTable* t) : ct(t) {
try {
m = MothurOut::getInstance();
}
}
/*****************************************************************/
-Tree::Tree(TreeMap* t) : tmap(t) {
+Tree::Tree(CountTable* t) : ct(t) {
try {
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;
tree.resize(numNodes);
//initialize groupNodeInfo
- for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
- groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
- }
+ vector<string> namesOfGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[i]].resize(0); }
//initialize tree with correct number of nodes, name and group info.
for (int i = 0; i < numNodes; i++) {
tree[i].setName(m->Treenames[i]);
//save group info
- string group = tmap->getGroup(m->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[group] = 1;
- tree[i].pGroups[group] = 1;
-
- //Treemap knows name, group and index to speed up search
- tmap->setIndex(m->Treenames[i], i);
-
+ int maxPars = 1;
+ vector<string> group;
+ vector<int> counts = ct->getGroupCounts(m->Treenames[i]);
+ for (int j = 0; j < namesOfGroups.size(); j++) {
+ if (counts[j] != 0) { //you have seqs from this group
+ groupNodeInfo[namesOfGroups[j]].push_back(i);
+ group.push_back(namesOfGroups[j]);
+ tree[i].pGroups[namesOfGroups[j]] = counts[j];
+ tree[i].pcount[namesOfGroups[j]] = counts[j];
+ //keep highest group
+ if(counts[j] > maxPars){ maxPars = counts[j]; }
+ }
+ }
+ tree[i].setGroup(group);
+ setIndex(m->Treenames[i], i);
+
+ 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
+
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setName("");
}
}
/*****************************************************************/
-Tree::Tree(TreeMap* t, vector< vector<double> >& sims) : tmap(t) {
+Tree::Tree(CountTable* t, vector< vector<double> >& sims) : ct(t) {
try {
m = MothurOut::getInstance();
tree.resize(numNodes);
//initialize groupNodeInfo
- for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
- groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
- }
+ vector<string> namesOfGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[i]].resize(0); }
//initialize tree with correct number of nodes, name and group info.
for (int i = 0; i < numNodes; i++) {
tree[i].setName(m->Treenames[i]);
//save group info
- string group = tmap->getGroup(m->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[group] = 1;
- tree[i].pGroups[group] = 1;
-
- //Treemap knows name, group and index to speed up search
- tmap->setIndex(m->Treenames[i], i);
+ int maxPars = 1;
+ vector<string> group;
+ vector<int> counts = ct->getGroupCounts(m->Treenames[i]);
+ for (int j = 0; j < namesOfGroups.size(); j++) {
+ if (counts[j] != 0) { //you have seqs from this group
+ groupNodeInfo[namesOfGroups[j]].push_back(i);
+ group.push_back(namesOfGroups[j]);
+ tree[i].pGroups[namesOfGroups[j]] = counts[j];
+ tree[i].pcount[namesOfGroups[j]] = counts[j];
+ //keep highest group
+ if(counts[j] > maxPars){ maxPars = counts[j]; }
+ }
+ }
+ tree[i].setGroup(group);
+ setIndex(m->Treenames[i], i);
+
+ 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
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setGroup(tempGroups);
}
}
+
//build tree from matrix
//initialize indexes
- map<int, int> indexes; //maps row in simMatrix to vector index in the tree
- for (int g = 0; g < numLeaves; g++) { indexes[g] = g; }
+ map<int, int> thisIndexes; //maps row in simMatrix to vector index in the tree
+ for (int g = 0; g < numLeaves; g++) { thisIndexes[g] = g; }
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
//set non-leaf node info and update leaves to know their parents
//non-leaf
- tree[numLeaves + i].setChildren(indexes[row], indexes[column]);
+ tree[numLeaves + i].setChildren(thisIndexes[row], thisIndexes[column]);
//parents
- tree[indexes[row]].setParent(numLeaves + i);
- tree[indexes[column]].setParent(numLeaves + i);
+ tree[thisIndexes[row]].setParent(numLeaves + i);
+ tree[thisIndexes[column]].setParent(numLeaves + i);
//blength = distance / 2;
float blength = ((1.0 - largest) / 2);
//branchlengths
- tree[indexes[row]].setBranchLength(blength - tree[indexes[row]].getLengthToLeaves());
- tree[indexes[column]].setBranchLength(blength - tree[indexes[column]].getLengthToLeaves());
+ tree[thisIndexes[row]].setBranchLength(blength - tree[thisIndexes[row]].getLengthToLeaves());
+ tree[thisIndexes[column]].setBranchLength(blength - tree[thisIndexes[column]].getLengthToLeaves());
//set your length to leaves to your childs length plus branchlength
- tree[numLeaves + i].setLengthToLeaves(tree[indexes[row]].getLengthToLeaves() + tree[indexes[row]].getBranchLength());
+ tree[numLeaves + i].setLengthToLeaves(tree[thisIndexes[row]].getLengthToLeaves() + tree[thisIndexes[row]].getBranchLength());
//update index
- indexes[row] = numLeaves+i;
- indexes[column] = numLeaves+i;
+ thisIndexes[row] = numLeaves+i;
+ thisIndexes[column] = numLeaves+i;
//remove highest value that caused the merge.
sims[row][column] = -1000.0;
}
/*****************************************************************/
Tree::~Tree() {}
-/*****************************************************************/
+/*****************************************************************
void Tree::addNamesToCounts(map<string, string> nameMap) {
try {
//ex. seq1 seq2,seq3,se4
m->errorOut(e, "Tree", "addNamesToCounts");
exit(1);
}
-}
+}*/
/*****************************************************************/
int Tree::getIndex(string searchName) {
try {
- //Treemap knows name, group and index to speed up search
- // getIndex function will return the vector index or -1 if seq is not found.
- int index = tmap->getIndex(searchName);
- return index;
-
+ map<string, int>::iterator itIndex = indexes.find(searchName);
+ if (itIndex != indexes.end()) {
+ return itIndex->second;
+ }
+ return -1;
}
catch(exception& e) {
m->errorOut(e, "Tree", "getIndex");
void Tree::setIndex(string searchName, int index) {
try {
- //set index in treemap
- tmap->setIndex(searchName, index);
+ map<string, int>::iterator itIndex = indexes.find(searchName);
+ if (itIndex == indexes.end()) {
+ indexes[searchName] = index;
+ }
}
catch(exception& e) {
m->errorOut(e, "Tree", "setIndex");
}
}
/*****************************************************************/
-int Tree::assembleTree(map<string, string> nameMap) {
- try {
- //save for later
- names = nameMap;
-
- //if user has given a names file we want to include that info in the pgroups and pcount info.
- if(nameMap.size() != 0) { addNamesToCounts(nameMap); }
-
+int Tree::assembleTree() {
+ 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; }
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) {
- m->errorOut(e, "Tree", "assembleTree");
- exit(1);
- }
-}
/*****************************************************************/
//assumes leaf node names are in groups and no names file - used by indicator command
void Tree::getSubTree(Tree* Ctree, vector<string> Groups) {
try {
//copy Tree since we are going to destroy it
- Tree* copy = new Tree(tmap);
+ Tree* copy = new Tree(ct);
copy->getCopy(Ctree);
- map<string, string> empty;
- copy->assembleTree(empty);
+ copy->assembleTree();
//we want to select some of the leaf nodes to create the output tree
//go through the input Tree starting at parents of leaves
+ //initialize groupNodeInfo
+ vector<string> namesOfGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[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(Groups[i]);
//save group info
- string group = tmap->getGroup(Groups[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[group] = 1;
- tree[i].pGroups[group] = 1;
-
- //Treemap knows name, group and index to speed up search
- tmap->setIndex(Groups[i], i);
-
- //intialize non leaf nodes
+ int maxPars = 1;
+ vector<string> group;
+ vector<int> counts = ct->getGroupCounts(Groups[i]);
+ for (int j = 0; j < namesOfGroups.size(); j++) {
+ if (counts[j] != 0) { //you have seqs from this group
+ groupNodeInfo[namesOfGroups[j]].push_back(i);
+ group.push_back(namesOfGroups[j]);
+ tree[i].pGroups[namesOfGroups[j]] = counts[j];
+ tree[i].pcount[namesOfGroups[j]] = counts[j];
+ //keep highest group
+ if(counts[j] > maxPars){ maxPars = counts[j]; }
+ }
+ }
+ tree[i].setGroup(group);
+ setIndex(Groups[i], i);
+
+ 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
+
+ //intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setName("");
vector<string> tempGroups;
tree[i].setGroup(tempGroups);
}
}
-
+
set<int> removedLeaves;
for (int i = 0; i < copy->getNumLeaves(); i++) {
exit(1);
}
}
-/*****************************************************************/
+/*****************************************************************
//assumes nameMap contains unique names as key or is empty.
//assumes numLeaves defined in tree constructor equals size of seqsToInclude and seqsToInclude only contains unique seqs.
int Tree::getSubTree(Tree* copy, vector<string> seqsToInclude, map<string, string> nameMap) {
return (index++);
}else { //you are a leaf
- int indexInNewTree = tmap->getIndex(oldtree[node].getName());
+ int indexInNewTree = getIndex(oldtree[node].getName());
return indexInNewTree;
}
}
}
}
/*****************************************************************/
+void Tree::getCopy(Tree* copy, bool subsample) {
+ try {
+
+ //for each node in the tree copy its info
+ for (int i = 0; i < numNodes; i++) {
+ //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());
+ }
+
+ //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 {
tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
//copy index in node and tmap
+ setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
tree[i].setIndex(copy->tree[i].getIndex());
- setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
//copy pGroups
tree[i].pGroups = copy->tree[i].pGroups;
try {
//initialize groupNodeInfo
- for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
- groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
+ for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
+ groupNodeInfo[(ct->getNamesOfGroups())[i]].resize(0);
}
for(int i = 0; i < numLeaves; i++){
/*************************************************************************************************/
void Tree::assembleRandomUnifracTree(vector<string> g) {
randomLabels(g);
- map<string, string> empty;
- assembleTree(empty);
+ assembleTree();
}
/*************************************************************************************************/
void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
randomLabels(temp);
- map<string, string> empty;
- assembleTree(empty);
+ assembleTree();
}
/*************************************************************************************************/
//for now it's just random topology but may become random labels as well later that why this is such a simple function now...
void Tree::assembleRandomTree() {
randomTopology();
- map<string, string> empty;
- assembleTree(empty);
+ assembleTree();
}
/**************************************************************************************************/
}
}
}else { //you are a leaf
- string leafGroup = tmap->getGroup(tree[node].getName());
+ vector<string> leafGroup = ct->getGroups(tree[node].getName());
if (mode == "branch") {
- out << leafGroup;
+ out << leafGroup[0];
//if there is a branch length then print it
if (tree[node].getBranchLength() != -1) {
out << ":" << tree[node].getBranchLength();
}
}else if (mode == "boot") {
- out << leafGroup;
+ out << leafGroup[0];
//if there is a label then print it
if (tree[node].getLabel() != -1) {
out << tree[node].getLabel();
}
}
}else { //you are a leaf
- string leafGroup = tmap->getGroup(theseNodes[node].getName());
+ vector<string> leafGroup = ct->getGroups(theseNodes[node].getName());
if (mode == "branch") {
- out << leafGroup;
+ out << leafGroup[0];
//if there is a branch length then print it
if (theseNodes[node].getBranchLength() != -1) {
out << ":" << theseNodes[node].getBranchLength();
}
}else if (mode == "boot") {
- out << leafGroup;
+ out << leafGroup[0];
//if there is a label then print it
if (theseNodes[node].getLabel() != -1) {
out << theseNodes[node].getLabel();
/*****************************************************************/
//this code is a mess and should be rethought...-slw
-void Tree::parseTreeFile() {
+int Tree::parseTreeFile() {
//only takes names from the first tree and assumes that all trees use the same names.
try {
//ifyou are not a nexus file
if((c = filehandle.peek()) != '#') {
- while((c = filehandle.peek()) != ';') {
+ while((c = filehandle.peek()) != ';') {
+ if (m->control_pressed) { filehandle.close(); return 0; }
while ((c = filehandle.peek()) != ';') {
+ if (m->control_pressed) { filehandle.close(); return 0; }
// get past comments
if(c == '[') {
comment = 1;
string holder = "";
// get past comments
- while(holder != "translate" && holder != "Translate"){
+ while(holder != "translate" && holder != "Translate"){
+ if (m->control_pressed) { filehandle.close(); return 0; }
if(holder == "[" || holder == "[!"){
comment = 1;
}
string number, name, h;
h = ""; // so it enters the loop the first time
- while((h != ";") && (number != ";")) {
+ while((h != ";") && (number != ";")) {
+ if (m->control_pressed) { filehandle.close(); return 0; }
filehandle >> number;
filehandle >> name;
}
}
filehandle.close();
-
+ return 0;
//for (int i = 0; i < globaldata->Treenames.size(); i++) {
//cout << globaldata->Treenames[i] << endl; }
//cout << globaldata->Treenames.size() << endl;
int c;
string name; //, k
- while((c = filehandle.peek()) != ';') {
+ while((c = filehandle.peek()) != ';') {
+ if (m->control_pressed) { return 0; }
//k = c;
//cout << " at beginning of while " << k << endl;
if(c == ')') {
c = filehandle.get();
//k = c;
//cout << k << endl;
- while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
name += c;
c = filehandle.get();
//k = c;
}
//cout << "name = " << name << endl;
- m->Treenames.push_back(name);
+ if (name != "\r" ) {
+ m->Treenames.push_back(name); } //cout << m->Treenames.size() << '\t' << name << endl;
+
filehandle.putback(c);
//k = c;
//cout << " after putback" << k << endl;
projects / mothur.git / blobdiff