T = globaldata->gTree;
tmap = globaldata->gTreemap;
- unweightedFile = globaldata->getTreeFile() + ".unweighted";
- openOutputFile(unweightedFile, out);
- //column headers
- out << "Comb" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-
sumFile = globaldata->getTreeFile() + ".uwsummary";
openOutputFile(sumFile, outSum);
- //column headers
- outSum << "Tree#" << '\t' << "Comb" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
setGroups(); //sets users groups to analyze
convert(globaldata->getIters(), iters); //how many random trees to generate
userData.resize(numComp,0); //data[0] = unweightedscore
randomData.resize(numComp,0); //data[0] = unweightedscore
//create new tree with same num nodes and leaves as users
- randT = new Tree();
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
+ unweightedFile = globaldata->getTreeFile() + toString(i+1) + ".unweighted";
+ unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
+ //column headers
+ outSum << "Tree# " << i+1 << endl;
+ outSum << "Comb" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
+
//get unweighted for users tree
rscoreFreq.resize(numComp);
- uscoreFreq.resize(numComp);
rCumul.resize(numComp);
- uCumul.resize(numComp);
validScores.resize(numComp);
utreeScores.resize(numComp);
UWScoreSig.resize(numComp);
cout << "Processing tree " << i+1 << endl;
- outSum << "Tree#" << i+1 << endl;
- out << "Tree#" << i+1 << endl;
userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore
//output scores for each combination
for(int k = 0; k < numComp; k++) {
- //update uscoreFreq
- it = uscoreFreq[k].find(userData[k]);
- if (it == uscoreFreq[k].end()) {//new score
- uscoreFreq[k][userData[k]] = 1;
- }else{ uscoreFreq[k][userData[k]]++; }
-
//add users score to valid scores
validScores[k][userData[k]] = userData[k];
utreeScores[k].push_back(userData[k]);
}
- //copy T[i]'s info.
- randT->getCopy(T[i]);
-
//get unweighted scores for random trees
for (int j = 0; j < iters; j++) {
//we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
- randomData = unweighted->getValues(randT, "", "");
+ randomData = unweighted->getValues(T[i], "", "");
for(int k = 0; k < numComp; k++) {
-cout << "iter " << j << " comp " << k << " = " << randomData[k] << endl;
+//cout << "iter " << j << " comp " << k << " = " << randomData[k] << endl;
//add trees unweighted score to map of scores
it2 = rscoreFreq[k].find(randomData[k]);
if (it2 != rscoreFreq[k].end()) {//already have that score
}
for(int a = 0; a < numComp; a++) {
- float ucumul = 1.0000;
float rcumul = 1.0000;
//this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
- it2 = uscoreFreq[a].find(it->first);
- //make uCumul map
- uCumul[a][it->first] = ucumul;
- //user data has that score
- if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul-= it2->second; }
- else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
-
//make rscoreFreq map and rCumul
it2 = rscoreFreq[a].find(it->first);
rCumul[a][it->first] = rcumul;
printUnweightedFile();
printUWSummaryFile();
- rscoreFreq.clear();
- uscoreFreq.clear();
+ rscoreFreq.clear();
rCumul.clear();
- uCumul.clear();
validScores.clear();
utreeScores.clear();
UWScoreSig.clear();
}
//reset groups parameter
globaldata->Groups.clear(); globaldata->setGroups("");
-
- delete randT;
+ outSum.close();
return 0;
/***********************************************************/
void UnifracUnweightedCommand::printUnweightedFile() {
try {
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ vector<double> data;
for(int a = 0; a < numComp; a++) {
+ initFile(groupComb[a]);
//print each line
for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
- out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t' << uscoreFreq[a][it->first] << '\t' << uCumul[a][it->first] << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl;
+ data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ output(data);
+ data.clear();
}
+ resetFile();
}
+
out.close();
+ inFile.close();
+ remove(unweightedFileout.c_str());
}
catch(exception& e) {
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
//print each line
- for (int i = 0; i< T.size(); i++) {
- for(int a = 0; a < numComp; a++) {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
- }
+ for(int a = 0; a < numComp; a++) {
+ outSum << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
}
- outSum.close();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
/*****************************************************************/
+void UnifracUnweightedCommand::initFile(string label){
+ try {
+ if(counter != 0){
+ openOutputFile(unweightedFileout, out);
+ openInputFile(unweightedFile, inFile);
+
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ out << inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }else{
+ openOutputFile(unweightedFileout, out);
+ out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ }
+
+ out.setf(ios::fixed, ios::floatfield);
+ out.setf(ios::showpoint);
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+void UnifracUnweightedCommand::output(vector<double> data){
+ try {
+ if(counter != 0){
+ string inputBuffer;
+ getline(inFile, inputBuffer);
+
+ out << inputBuffer << setprecision(6) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+ else{
+ out << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+};
+
+/***********************************************************************/
+
+void UnifracUnweightedCommand::resetFile(){
+ try {
+ if(counter != 0){
+ out.close();
+ inFile.close();
+ }
+ else{
+ out.close();
+ }
+ counter = 1;
+
+ remove(unweightedFile.c_str());
+ rename(unweightedFileout.c_str(), unweightedFile.c_str());
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
private:
GlobalData* globaldata;
vector<Tree*> T; //user trees
- Tree* randT; //random tree
TreeMap* tmap;
Unweighted* unweighted;
- string sumFile, unweightedFile;
+ string sumFile, unweightedFile, unweightedFileout;
vector<string> groupComb; // AB. AC, BC...
- int iters, numGroups, numComp;
+ int iters, numGroups, numComp, counter;
EstOutput userData; //unweighted score info for user tree
EstOutput randomData; //unweighted score info for random trees
vector< vector<float> > utreeScores; //scores for users trees for each comb.
vector< vector<float> > UWScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or higher.
vector< map<float, float> > validScores; //map contains scores from both user and random
vector< map<float, float> > rscoreFreq; //map <unweighted score, number of random trees with that score.> -vector entry for each combination.
- vector< map<float, float> > uscoreFreq; //map <unweighted score, number of user trees with that score.> -vector entry for each combination.
vector< map<float, float> > rCumul; //map <unweighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each combination.
- vector< map<float, float> > uCumul; //map <unweighted score, cumulative percentage of number of user trees with that score or higher.> -vector entry for each combination. map<float, float>::iterator it;
map<float, float>::iterator it2;
map<float, float>::iterator it;
ofstream outSum, out;
+ ifstream inFile;
void printUWSummaryFile();
void printUnweightedFile();
- void setGroups();
+ void setGroups();
+ void initFile(string);
+ void output(vector<double>);
+ void resetFile();
+
};
//if the users enters no groups then give them the score of all groups
int numGroups = globaldata->Groups.size();
-cout << "NumGroups = " << numGroups << endl;
+
//calculate number of comparsions
int numComp = 0;
for (int r=0; r<numGroups; r++) {
//swap labels in the groups you want to compare
copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
-
+
+ //copyTree->createNewickFile("random"+groupA+toString(count));
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ int lc = copyTree->tree[i].getLChild(); //lc = vector index of left child
+ int rc = copyTree->tree[i].getRChild(); //rc = vector index of right child
/**********************************************************************/
//This section adds in all lengths that are non leaf
- copyIpcount = t->tree[i].pcount;
+ copyIpcount = copyTree->tree[i].pcount;
for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first); }
}
//if i's children are from the same group then i's pcount size will be 1
//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
if (copyIpcount.size() == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += copyTree->tree[i].getBranchLength(); }
//add i's BL to total if it is from the groups the user wants
- if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += t->tree[i].getBranchLength();
+ if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
+ totalBL += copyTree->tree[i].getBranchLength();
}
/**********************************************************************/
//This section adds in all lengths that are leaf
//if i's chidren are leaves
- if (t->tree[rc].getRChild() == -1) {
+ if (copyTree->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
- if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[rc].getBranchLength();
+ totalBL += copyTree->tree[rc].getBranchLength();
}
}
- if (t->tree[lc].getLChild() == -1) {
+ if (copyTree->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
- if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[lc].getBranchLength();
+ totalBL += copyTree->tree[lc].getBranchLength();
}
}
//swap labels in all the groups you want to compare
copyTree->assembleRandomUnifracTree(groups);
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ int lc = copyTree->tree[i].getLChild(); //lc = vector index of left child
+ int rc = copyTree->tree[i].getRChild(); //rc = vector index of right child
/**********************************************************************/
//This section adds in all lengths that are non leaf
- copyIpcount = t->tree[i].pcount;
+ copyIpcount = copyTree->tree[i].pcount;
for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first); }
}
//if i's children are from the same group then i's pcount size will be 1
//if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
if (copyIpcount.size() == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) { UniqueBL += copyTree->tree[i].getBranchLength(); }
//add i's BL to total if it is from the groups the user wants
- if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
- totalBL += t->tree[i].getBranchLength();
+ if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
+ totalBL += copyTree->tree[i].getBranchLength();
}
/**********************************************************************/
//This section adds in all lengths that are leaf
//if i's chidren are leaves
- if (t->tree[rc].getRChild() == -1) {
+ if (copyTree->tree[rc].getRChild() == -1) {
//if rc is a valid group and rc has a BL
- if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[rc].getBranchLength();
+ totalBL += copyTree->tree[rc].getBranchLength();
}
}
- if (t->tree[lc].getLChild() == -1) {
+ if (copyTree->tree[lc].getLChild() == -1) {
//if lc is a valid group and lc has a BL
- if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+ if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[lc].getBranchLength();
+ totalBL += copyTree->tree[lc].getBranchLength();
}
}
projects / mothur.git / commitdiff