EstOutput Parsimony::getValues(Tree* t) {
try {
globaldata = GlobalData::getInstance();
+ vector<string> groups;
copyTree = new Tree();
//if the users enters no groups then give them the score of all groups
int numGroups = globaldata->Groups.size();
- if (numGroups == 0) {
- numGroups++;
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }
//calculate number of comparsions
int numComp = 0;
//numComp+1 for AB, AC, BC, ABC
data.resize(numComp+1,0);
- vector<string> groups;
int count = 0;
for (int a=0; a<numGroups; a++) {
}
}
- //get score for all users groups
-
- //copy users tree so that you can redo pgroups
- copyTree->getCopy(t);
- int score = 0;
+ if (numComp != 1) {
+ if (numGroups == 0) {
+ //get score for all users groups
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups.push_back(globaldata->Groups[i]);
+ }
+ }
+
+ //copy users tree so that you can redo pgroups
+ copyTree->getCopy(t);
+ int score = 0;
- //create pgroups that reflect the groups the user want to use
- for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, globaldata->Groups));
- }
+ //create pgroups that reflect the groups the user want to use
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+ copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
+ }
- for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- int lc = copyTree->tree[i].getLChild();
- int rc = copyTree->tree[i].getRChild();
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+ int lc = copyTree->tree[i].getLChild();
+ int rc = copyTree->tree[i].getRChild();
- int iSize = copyTree->tree[i].pGroups.size();
- int rcSize = copyTree->tree[rc].pGroups.size();
- int lcSize = copyTree->tree[lc].pGroups.size();
+ int iSize = copyTree->tree[i].pGroups.size();
+ int rcSize = copyTree->tree[rc].pGroups.size();
+ int lcSize = copyTree->tree[lc].pGroups.size();
- //if isize are 0 then that branch is to be ignored
- if (iSize == 0) { }
- else if ((rcSize == 0) || (lcSize == 0)) { }
- //if you have more groups than either of your kids then theres been a change.
- else if(iSize > rcSize || iSize > lcSize){
- score++;
- }
- }
+ //if isize are 0 then that branch is to be ignored
+ if (iSize == 0) { }
+ else if ((rcSize == 0) || (lcSize == 0)) { }
+ //if you have more groups than either of your kids then theres been a change.
+ else if(iSize > rcSize || iSize > lcSize){
+ score++;
+ }
+ }
- data[count] = score;
+ data[count] = score;
+ }
return data;
}
//output scores for each combination
for(int k = 0; k < numComp; k++) {
- cout << "Tree " << i+1 << " Combination " << groupComb[k] << " parsimony score = " << userData[k] << endl;
//update uscoreFreq
it = uscoreFreq[k].find(userData[k]);
if (it == uscoreFreq[k].end()) {//new score
}
printParsimonyFile();
- if (randomtree != "") { printUSummaryFile(); }
+ if (randomtree == "") { printUSummaryFile(); }
//reset globaldata's treemap if you just did random distrib
- if (randomtree == "") { globaldata->gTreemap = savetmap; }
+ if (randomtree != "") { globaldata->gTreemap = savetmap; }
//reset randomTree parameter to ""
globaldata->setRandomTree("");
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' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
}
}
}
//ABC
- groupComb.push_back(allGroups);
- numComp++;
+ if (numComp != 1) {
+ groupComb.push_back(allGroups);
+ numComp++;
+ }
}
catch(exception& e) {
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);
- distFile = globaldata->getTreeFile() + ".uwdistrib";
- openOutputFile(distFile, outDist);
+ //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
unweighted = new Unweighted(tmap);
/***********************************************************/
int UnifracUnweightedCommand::execute() {
try {
-
- //get unweighted for users tree
- userData.resize(1,0); //data[0] = unweightedscore
- randomData.resize(1,0); //data[0] = unweightedscore
-
- //format output
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
-
- outDist << "Groups Used ";
- for (int m = 0; m < globaldata->Groups.size(); m++) {
- outDist << globaldata->Groups[m] << " ";
- }
- outDist << endl;
-
- outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
-
+
+ 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++) {
+ //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
- //update uscoreFreq
- it = uscoreFreq.find(userData[0]);
- if (it == uscoreFreq.end()) {//new score
- uscoreFreq[userData[0]] = 1;
- }else{ uscoreFreq[userData[0]]++; }
+ //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[userData[0]] = userData[0];
+ //add users score to valid scores
+ validScores[k][userData[k]] = userData[k];
- //saves users score
- utreeScores.push_back(userData[0]);
+ //saves users score
+ 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++) {
- //create a random tree with same topology as T[i], but different labels
- randT->assembleRandomUnifracTree();
- //get pscore of random tree
- randomData = unweighted->getValues(randT);
+ int count = 0;
+ for (int r=0; r<numGroups; r++) {
+ for (int l = r+1; l < numGroups; l++) {
+ //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, "", "");
- //add trees unweighted score to map of scores
- it2 = rscoreFreq.find(randomData[0]);
- if (it2 != rscoreFreq.end()) {//already have that score
- rscoreFreq[randomData[0]]++;
- }else{//first time we have seen this score
- rscoreFreq[randomData[0]] = 1;
- }
+ //add trees unweighted score to map of scores
+ it2 = rscoreFreq[count].find(randomData[count]);
+ if (it2 != rscoreFreq[count].end()) {//already have that score
+ rscoreFreq[count][randomData[count]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[count][randomData[count]] = 1;
+ }
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
-
- //output info to uwdistrib file
- outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl;
+ //add randoms score to validscores
+ validScores[count][randomData[count]] = randomData[count];
+ count++;
+ }
+ }
}
-
- saveRandomScores(); //save all random scores for unweighted file
-
- //find the signifigance of the score
+
+ for(int a = 0; a < numComp; a++) {
+ float ucumul = 1.0000;
float rcumul = 1.0000;
- for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
- rCumul[it->first] = rcumul;
+ //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;
//get percentage of random trees with that info
- rscoreFreq[it->first] /= iters;
- rcumul-= it->second;
+ if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
+ else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
}
-
- //save the signifigance of the users score for printing later
- UWScoreSig.push_back(rCumul[userData[0]]);
-
-
- //clear random data
- rscoreFreq.clear(); //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees.
- rCumul.clear();
- }
-
- 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.begin(); it != validScores.end(); it++) {
- it2 = uscoreFreq.find(it->first);
- //make uCumul map
- uCumul[it->first] = ucumul;
- //user data has that score
- if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul-= it2->second; }
- else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
-
- //make rscoreFreq map and rCumul
- it2 = totalrscoreFreq.find(it->first);
- rCumul[it->first] = rcumul;
- //get percentage of random trees with that info
- if (it2 != totalrscoreFreq.end()) { totalrscoreFreq[it->first] /= (iters*T.size()); rcumul-= it2->second; }
- else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score
-
+ UWScoreSig[a].push_back(rCumul[a][userData[a]]);
}
printUnweightedFile();
printUWSummaryFile();
+ rscoreFreq.clear();
+ uscoreFreq.clear();
+ rCumul.clear();
+ uCumul.clear();
+ validScores.clear();
+ utreeScores.clear();
+ UWScoreSig.clear();
+ }
//reset groups parameter
- globaldata->Groups.clear();
+ globaldata->Groups.clear(); globaldata->setGroups("");
delete randT;
/***********************************************************/
void UnifracUnweightedCommand::printUnweightedFile() {
try {
- //column headers
-
- out << "Groups Used ";
- for (int m = 0; m < globaldata->Groups.size(); m++) {
- out << globaldata->Groups[m] << " ";
- }
- out << endl;
-
- out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-
//format output
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
- //print each line
- for (it = validScores.begin(); it != validScores.end(); it++) {
- out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << totalrscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
- }
-
+ for(int a = 0; a < numComp; 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;
+ }
+ }
out.close();
}
/***********************************************************/
void UnifracUnweightedCommand::printUWSummaryFile() {
try {
- //column headers
-
- outSum << "Groups Used ";
- for (int m = 0; m < globaldata->Groups.size(); m++) {
- outSum << globaldata->Groups[m] << " ";
- }
- outSum << endl;
-
- outSum << "Tree#" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
-
+
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
//print each line
for (int i = 0; i< T.size(); i++) {
- outSum << setprecision(6) << i+1 << '\t' << '\t' << utreeScores[i] << '\t' << UWScoreSig[i] << endl;
+ 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;
+ }
}
outSum.close();
exit(1);
}
}
-/***********************************************************/
-void UnifracUnweightedCommand::saveRandomScores() {
- try {
- for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
- //does this score already exist in the total map
- it2 = totalrscoreFreq.find(it->first);
- //if yes then add them
- if (it2 != totalrscoreFreq.end()) {
- totalrscoreFreq[it->first] += rscoreFreq[it->first];
- }else{ //its a new score
- totalrscoreFreq[it->first] = rscoreFreq[it->first];
- }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
/***********************************************************/
void UnifracUnweightedCommand::setGroups() {
try {
+ string allGroups = "";
+ numGroups = 0;
//if the user has not entered specific groups to analyze then do them all
if (globaldata->Groups.size() != 0) {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
+ if (globaldata->Groups[0] != "all") {
+ //check that groups are valid
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
+ cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ // erase the invalid group from globaldata->Groups
+ globaldata->Groups.erase(globaldata->Groups.begin()+i);
+ }
}
- }
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
+ //if the user only entered invalid groups
+ if (globaldata->Groups.size() == 0) {
+ cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ allGroups += tmap->namesOfGroups[i];
+ }
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ allGroups += tmap->namesOfGroups[i];
+ numGroups++;
+ }
+ }
+ }else{//user has enter "all" and wants the default groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ allGroups += tmap->namesOfGroups[i];
}
+ globaldata->setGroups("");
}
-
}else {
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ allGroups += tmap->namesOfGroups[i];
}
+ numGroups = 1;
+ }
+
+ //calculate number of comparsions
+ numComp = 0;
+ for (int r=0; r<numGroups; r++) {
+ for (int l = r+1; l < numGroups; l++) {
+ groupComb.push_back(globaldata->Groups[r]+globaldata->Groups[l]);
+ numComp++;
+ }
+ }
+
+ //ABC
+ if (numComp != 1) {
+ groupComb.push_back(allGroups);
+ numComp++;
}
}
catch(exception& e) {
private:
GlobalData* globaldata;
vector<Tree*> T; //user trees
- vector<float> utreeScores; //user tree unweighted scores
- vector<float> UWScoreSig; //tree unweighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
Tree* randT; //random tree
TreeMap* tmap;
Unweighted* unweighted;
- string sumFile, distFile, unweightedFile;
- int iters;
+ string sumFile, unweightedFile;
+ vector<string> groupComb; // AB. AC, BC...
+ int iters, numGroups, numComp;
EstOutput userData; //unweighted score info for user tree
EstOutput randomData; //unweighted score info for random trees
- map<float, float> validScores; //contains scores from both user and random
- map<float, float> rscoreFreq; //unweighted score, number of random trees with that score.
- map<float, float> uscoreFreq; //unweighted, number of user trees with that score.
- map<float, float> totalrscoreFreq; //unweighted score, number of random trees with that score.
- map<float, float> rCumul; //unweighted score, cumulative percentage of number of random trees with that score or higher.
- map<float, float> uCumul; //unweighted, cumulative percentage of number of user trees with that score or higher .
- map<float, float>::iterator it;
+ 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, outDist, out;
+ ofstream outSum, out;
void printUWSummaryFile();
void printUnweightedFile();
- void saveRandomScores();
void setGroups();
};
T = globaldata->gTree;
tmap = globaldata->gTreemap;
- weightedFile = globaldata->getTreeFile() + ".weighted";
- openOutputFile(weightedFile, out);
+ //weightedFile = globaldata->getTreeFile() + ".weighted";
+ //openOutputFile(weightedFile, out);
//column headers
- out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ //out << "Group" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
sumFile = globaldata->getTreeFile() + ".wsummary";
openOutputFile(sumFile, outSum);
//copy T[i]'s info.
randT->getCopy(T[i]);
- if (globaldata->Groups.size() != 0) {
- //create a random tree with same topology as T[i], but different labels
- randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
- //get wscore of random tree
- randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
- }else {
- //create a random tree with same topology as T[i], but different labels
- randT->assembleRandomUnifracTree(tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
- //get wscore of random tree
- randomData = weighted->getValues(randT, tmap->namesOfGroups[r], tmap->namesOfGroups[l]);
- }
+ //create a random tree with same topology as T[i], but different labels
+ randT->assembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]);
+ //get wscore of random tree
+ randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]);
+
//save scores
rScores[count].push_back(randomData[0]);
validScores[count][randomData[0]] = randomData[0];
WScoreSig.push_back((iters-index)/(float)iters);
}
- out << "Tree# " << i << endl;
+ //out << "Tree# " << i << endl;
//printWeightedFile();
//clear data
//if the user has not entered specific groups to analyze then do them all
if (globaldata->Groups.size() == 0) {
numGroups = tmap->getNumGroups();
+ for (int i=0; i < numGroups; i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
}else {
if (globaldata->getGroups() != "all") {
//check that groups are valid
//if the user only entered invalid groups
if (globaldata->Groups.size() == 0) {
numGroups = tmap->getNumGroups();
+ for (int i=0; i < numGroups; i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
}else if (globaldata->Groups.size() == 1) {
cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
numGroups = tmap->getNumGroups();
globaldata->Groups.clear();
+ for (int i=0; i < numGroups; i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
}else { numGroups = globaldata->Groups.size(); }
}else { //users wants all groups
numGroups = tmap->getNumGroups();
globaldata->Groups.clear();
globaldata->setGroups("");
+ for (int i=0; i < numGroups; i++) {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ }
}
}
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
numComp = 0;
- int n = 1;
- for (int i=1; i<numGroups; i++) {
+ for (int i=0; i<numGroups; i++) {
numComp += i;
- for (int l = n; l < numGroups; l++) {
+ for (int l = i+1; l < numGroups; l++) {
//set group comparison labels
- if (globaldata->Groups.size() != 0) {
- groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
- }else {
- groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
- }
+ groupComb.push_back(globaldata->Groups[i]+globaldata->Groups[l]);
}
- n++;
}
}
catch(exception& e) {
try {
globaldata = GlobalData::getInstance();
- //clear out old values
- data.resize(1,0);
-
- double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- double totalBL = 0.00; //all branch lengths
- double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
-
+ vector<string> groups;
+ double UniqueBL; //a branch length is unique if it's chidren are from the same group
+ double totalBL; //all branch lengths
+ double UW; //Unweighted Value = UniqueBL / totalBL;
map<string, int>::iterator it; //iterator to traverse pgroups
map<string, int> copyIpcount;
+
+
+ //if the users enters no groups then give them the score of all groups
+ int numGroups = globaldata->Groups.size();
+
+ //calculate number of comparsions
+ int numComp = 0;
+ for (int r=0; r<numGroups; r++) {
+ for (int l = r+1; l < numGroups; l++) {
+ numComp++;
+ }
+ }
+
+ //numComp+1 for AB, AC, BC, ABC
+ data.resize(numComp+1,0);
+
+ int count = 0;
+ for (int a=0; a<numGroups; a++) {
+ for (int l = a+1; l < numGroups; l++) {
+ UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ totalBL = 0.00; //all branch lengths
+ UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ copyIpcount.clear();
+
+ //groups in this combo
+ groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ for(int i=t->getNumLeaves();i<t->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 = t->tree[i].getLChild(); //lc = vector index of left child
+ int rc = t->tree[i].getRChild(); //rc = vector index of right child
- /**********************************************************************/
- //This section adds in all lengths that are non leaf
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
- copyIpcount = t->tree[i].pcount;
- for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
- if (inUsersGroups(it->first, globaldata->Groups) != true) { copyIpcount.erase(it->first); }
- }
+ copyIpcount = t->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(); }
+ //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(); }
- //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();
- }
+ //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();
+ }
- /**********************************************************************/
- //This section adds in all lengths that are leaf
+ /**********************************************************************/
+ //This section adds in all lengths that are leaf
- //if i's chidren are leaves
- if (t->tree[rc].getRChild() == -1) {
- //if rc is a valid group and rc has a BL
- if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
- UniqueBL += t->tree[rc].getBranchLength();
- totalBL += t->tree[rc].getBranchLength();
+ //if i's chidren are leaves
+ if (t->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[rc].getBranchLength();
+ totalBL += t->tree[rc].getBranchLength();
+ }
+ }
+
+ if (t->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[lc].getBranchLength();
+ totalBL += t->tree[lc].getBranchLength();
+ }
+ }
+
+ /**********************************************************************/
}
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[count] = UW;
+ count++;
+ groups.clear();
}
-
- if (t->tree[lc].getLChild() == -1) {
- //if lc is a valid group and lc has a BL
- if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
- UniqueBL += t->tree[lc].getBranchLength();
- totalBL += t->tree[lc].getBranchLength();
+ }
+
+
+ if (numComp != 1) {
+ if (numGroups == 0) {
+ //get score for all users groups
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups.push_back(globaldata->Groups[i]);
}
}
+
+ UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ totalBL = 0.00; //all branch lengths
+ UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ copyIpcount.clear();
+
+ for(int i=t->getNumLeaves();i<t->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
+
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
+
+ copyIpcount = t->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(); }
- /**********************************************************************/
+ //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();
+ }
+
+ /**********************************************************************/
+ //This section adds in all lengths that are leaf
+
+ //if i's chidren are leaves
+ if (t->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[rc].getBranchLength();
+ totalBL += t->tree[rc].getBranchLength();
+ }
+ }
+
+ if (t->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[lc].getBranchLength();
+ totalBL += t->tree[lc].getBranchLength();
+ }
+ }
+
+ /**********************************************************************/
+ }
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[count] = UW;
}
+
+ return data;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/**************************************************************************************************/
+
+EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
+ try {
+ globaldata = GlobalData::getInstance();
+
+ vector<string> groups;
+ double UniqueBL; //a branch length is unique if it's chidren are from the same group
+ double totalBL; //all branch lengths
+ double UW; //Unweighted Value = UniqueBL / totalBL;
+ map<string, int>::iterator it; //iterator to traverse pgroups
+ map<string, int> copyIpcount;
+ copyTree = new Tree;
+
+ //if the users enters no groups then give them the score of all groups
+ int numGroups = globaldata->Groups.size();
+
+ //calculate number of comparsions
+ int numComp = 0;
+ for (int r=0; r<numGroups; r++) {
+ for (int l = r+1; l < numGroups; l++) {
+ numComp++;
+ }
+ }
+
+ //numComp+1 for AB, AC, BC, ABC
+ data.resize(numComp+1,0);
+
+ int count = 0;
+ for (int a=0; a<numGroups; a++) {
+ for (int l = a+1; l < numGroups; l++) {
+ UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ totalBL = 0.00; //all branch lengths
+ UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ copyIpcount.clear();
+
+ //copy random tree passed in
+ copyTree->getCopy(t);
+
+ //swap labels in the groups you want to compare
+ copyTree->assembleRandomUnifracTree(globaldata->Groups[a], globaldata->Groups[l]);
+
+ //groups in this combo
+ groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
+
+ for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
- UW = (UniqueBL / totalBL);
+ int lc = t->tree[i].getLChild(); //lc = vector index of left child
+ int rc = t->tree[i].getRChild(); //rc = vector index of right child
+
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
+
+ copyIpcount = t->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(); }
+
+ //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();
+ }
+
+ /**********************************************************************/
+ //This section adds in all lengths that are leaf
+
+ //if i's chidren are leaves
+ if (t->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[rc].getBranchLength();
+ totalBL += t->tree[rc].getBranchLength();
+ }
+ }
+
+ if (t->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[lc].getBranchLength();
+ totalBL += t->tree[lc].getBranchLength();
+ }
+ }
+
+ /**********************************************************************/
+ }
+
+ UW = (UniqueBL / totalBL);
- if (isnan(UW) || isinf(UW)) { UW = 0; }
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
- data[0] = UW;
+ data[count] = UW;
+ count++;
+ groups.clear();
+ }
+ }
+
+ if (numComp != 1) {
+ if (numGroups == 0) {
+ //get score for all users groups
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups.push_back(globaldata->Groups[i]);
+ }
+ }
+
+ UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ totalBL = 0.00; //all branch lengths
+ UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ copyIpcount.clear();
+
+ //copy random tree passed in
+ copyTree->getCopy(t);
+
+ //swap labels in all the groups you want to compare
+ copyTree->assembleRandomUnifracTree();
+
+ for(int i=t->getNumLeaves();i<t->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
+
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
+
+ copyIpcount = t->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(); }
+
+ //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();
+ }
+
+ /**********************************************************************/
+ //This section adds in all lengths that are leaf
+
+ //if i's chidren are leaves
+ if (t->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(t->tree[rc].getGroup(), globaldata->Groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[rc].getBranchLength();
+ totalBL += t->tree[rc].getBranchLength();
+ }
+ }
+
+ if (t->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(t->tree[lc].getGroup(), globaldata->Groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[lc].getBranchLength();
+ totalBL += t->tree[lc].getBranchLength();
+ }
+ }
+
+ /**********************************************************************/
+ }
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[count] = UW;
+ }
+
return data;
}
cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
-
}
+
+
+
Unweighted(TreeMap* t) : tmap(t) {};
~Unweighted() {};
EstOutput getValues(Tree*);
- EstOutput getValues(Tree*, string, string) { return data; };
+ EstOutput getValues(Tree*, string, string);
private:
GlobalData* globaldata;
+ Tree* copyTree;
EstOutput data;
TreeMap* tmap;
int numGroups;
vector<double> D;
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- }else {
- numGroups = globaldata->Groups.size();
- }
+ numGroups = globaldata->Groups.size();
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
- int n = 1;
int count = 0;
- for (int i=1; i<numGroups; i++) {
- for (int l = n; l < numGroups; l++) {
+ for (int i=0; i<numGroups; i++) {
+ for (int l = i+1; l < numGroups; l++) {
//initialize weighted scores
- if (globaldata->Groups.size() == 0) {
- WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] = 0.0;
- }else {
- WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] = 0.0;
- }
+ WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
D.push_back(0.0000); //initialize a spot in D for each combination
sum += t->tree[index].getBranchLength();
}
- if (globaldata->Groups.size() == 0) {
- //is this sum from a sequence which is in one of the users groups
- if (inUsersGroups(t->tree[v].getGroup(), tmap->namesOfGroups) == true) {
- //is this sum from a sequence which is in this groupCombo
- if ((t->tree[v].getGroup() == tmap->namesOfGroups[i-1]) || (t->tree[v].getGroup() == tmap->namesOfGroups[l])) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D[count] += sum;
- }
- }
- }else {
- //is this sum from a sequence which is in one of the users groups
- if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
- //is this sum from a sequence which is in this groupCombo
- if ((t->tree[v].getGroup() == globaldata->Groups[i-1]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
- sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
- D[count] += sum;
- }
+ //is this sum from a sequence which is in one of the users groups
+ if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) {
+ //is this sum from a sequence which is in this groupCombo
+ if ((t->tree[v].getGroup() == globaldata->Groups[i]) || (t->tree[v].getGroup() == globaldata->Groups[l])) {
+ sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()];
+ D[count] += sum;
}
}
}
/*********************************************************/
count++;
}
- n++;
}
data.clear(); //clear out old values
for(int i=0;i<t->getNumNodes();i++){
//calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC.
- n = 1;
- for (int b=1; b<numGroups; b++) {
- for (int l = n; l < numGroups; l++) {
+ for (int b=0; b<numGroups; b++) {
+ for (int l = b+1; l < numGroups; l++) {
//calculate a u value for each combo
double u;
- //the user has not entered specific groups
- if (globaldata->Groups.size() == 0) {
- //does this node have descendants from group b-1
- it = t->tree[i].pcount.find(tmap->namesOfGroups[b-1]);
- //if it does u = # of its descendants with a certain group / total number in tree with a certain group
- if (it != t->tree[i].pcount.end()) {
- u = (double) t->tree[i].pcount[tmap->namesOfGroups[b-1]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[b-1]];
- }else { u = 0.00; }
+ //does this node have descendants from group b-1
+ it = t->tree[i].pcount.find(globaldata->Groups[b]);
+ //if it does u = # of its descendants with a certain group / total number in tree with a certain group
+ if (it != t->tree[i].pcount.end()) {
+ u = (double) t->tree[i].pcount[globaldata->Groups[b]] / (double) tmap->seqsPerGroup[globaldata->Groups[b]];
+ }else { u = 0.00; }
- //does this node have descendants from group l
- it = t->tree[i].pcount.find(tmap->namesOfGroups[l]);
- //if it does subtract their percentage from u
- if (it != t->tree[i].pcount.end()) {
- u -= (double) t->tree[i].pcount[tmap->namesOfGroups[l]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[l]];
- }
-
- u = abs(u) * t->tree[i].getBranchLength();
-
- //save groupcombs u value
- WScore[tmap->namesOfGroups[b-1]+tmap->namesOfGroups[l]] += u;
-
- //the user has entered specific groups
- }else {
- //does this node have descendants from group b-1
- it = t->tree[i].pcount.find(globaldata->Groups[b-1]);
- //if it does u = # of its descendants with a certain group / total number in tree with a certain group
- if (it != t->tree[i].pcount.end()) {
- u = (double) t->tree[i].pcount[globaldata->Groups[b-1]] / (double) tmap->seqsPerGroup[globaldata->Groups[b-1]];
- }else { u = 0.00; }
-
- //does this node have descendants from group l
- it = t->tree[i].pcount.find(globaldata->Groups[l]);
- //if it does subtract their percentage from u
- if (it != t->tree[i].pcount.end()) {
- u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]];
- }
+ //does this node have descendants from group l
+ it = t->tree[i].pcount.find(globaldata->Groups[l]);
+ //if it does subtract their percentage from u
+ if (it != t->tree[i].pcount.end()) {
+ u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]];
+ }
- u = abs(u) * t->tree[i].getBranchLength();
+ u = abs(u) * t->tree[i].getBranchLength();
- //save groupcombs u value
- WScore[globaldata->Groups[b-1]+globaldata->Groups[l]] += u;
- }
+ //save groupcombs u value
+ WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u;
/*********************************************************/
}
- n++;
}
}
//calculate weighted score for each group combination
double UN;
- n = 1;
count = 0;
- for (int i=1; i<numGroups; i++) {
- for (int l = n; l < numGroups; l++) {
- //the user has not entered specific groups
- if (globaldata->Groups.size() == 0) {
- UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D[count]);
- }else {//they have entered specific groups
- UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D[count]);
- }
+ for (int i=0; i<numGroups; i++) {
+ for (int l = i+1; l < numGroups; l++) {
+ UN = (WScore[globaldata->Groups[i]+globaldata->Groups[l]] / D[count]);
+
if (isnan(UN) || isinf(UN)) { UN = 0; }
data.push_back(UN);
count++;
}
- n++;
}
return data;
}
projects / mothur.git / commitdiff