try {
globaldata = GlobalData::getInstance();
- data.resize(1,0);
+ 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;
+ 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);
+ vector<string> groups;
+
+ int count = 0;
+ for (int a=0; a<numGroups; a++) {
+ for (int l = a+1; l < numGroups; l++) {
+ int score = 0;
+
+ //groups in this combo
+ groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
+
+ //copy users tree so that you can redo pgroups
+ copyTree->getCopy(t);
+
+ //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();
+ 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++;
+ }
+ }
+
+ data[count] = score;
+ count++;
+ groups.clear();
+ }
+ }
+
+ //get score for all users groups
+
+ //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=t->getNumLeaves();i<t->getNumNodes();i++){
- t->tree[i].pGroups = (t->mergeUserGroups(i));
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+ copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, globaldata->Groups));
}
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
- int lc = t->tree[i].getLChild();
- int rc = t->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 = t->tree[i].pGroups.size();
- int rcSize = t->tree[rc].pGroups.size();
- int lcSize = t->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) { }
}
}
-
- data[0] = score;
+ data[count] = score;
return data;
}
int ParsimonyCommand::execute() {
try {
- //get pscore for users tree
- userData.resize(1,0); //data[0] = pscore.
- randomData.resize(1,0); //data[0] = pscore.
-
+
if (randomtree == "") {
- copyUserTree = new Tree();
+ //get pscore for users tree
+ userData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
+ rscoreFreq.resize(numComp);
+ uscoreFreq.resize(numComp);
+ rCumul.resize(numComp);
+ uCumul.resize(numComp);
+ validScores.resize(numComp);
+ userTreeScores.resize(numComp);
+ UScoreSig.resize(numComp);
+
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
- //copy users tree so that you can redo pgroups
- copyUserTree->getCopy(T[i]);
cout << "Processing tree " << i+1 << endl;
- userData = pars->getValues(copyUserTree); //userData[0] = pscore
- cout << "Tree " << i+1 << " parsimony score = " << userData[0] << endl;
- //update uscoreFreq
- it = uscoreFreq.find(userData[0]);
- if (it == uscoreFreq.end()) {//new score
- uscoreFreq[userData[0]] = 1;
- }else{ uscoreFreq[userData[0]]++; }
-
- //add users score to valid scores
- validScores[userData[0]] = userData[0];
+ userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC.
- //save score for summary file
- userTreeScores.push_back(userData[0]);
-
+ //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
+ uscoreFreq[k][userData[k]] = 1;
+ }else{ uscoreFreq[k][userData[k]]++; }
+
+ //add users score to valid scores
+ validScores[k][userData[k]] = userData[k];
+
+ //save score for summary file
+ userTreeScores[k].push_back(userData[k]);
+ }
}
//get pscores for random trees
randT->assembleRandomTree();
//get pscore of random tree
randomData = pars->getValues(randT);
+
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ it2 = rscoreFreq[r].find(randomData[r]);
+ if (it2 != rscoreFreq[r].end()) {//already have that score
+ rscoreFreq[r][randomData[r]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[r][randomData[r]] = 1;
+ }
- //add trees pscore 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 randoms score to validscores
+ validScores[r][randomData[r]] = randomData[r];
}
-
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
delete randT;
}
randT->assembleRandomTree();
//get pscore of random tree
randomData = pars->getValues(randT);
+
+ for(int r = 0; r < numComp; r++) {
+ //add trees pscore to map of scores
+ it2 = rscoreFreq[r].find(randomData[r]);
+ if (it2 != rscoreFreq[r].end()) {//already have that score
+ rscoreFreq[r][randomData[r]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[r][randomData[r]] = 1;
+ }
- //add trees pscore 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 randoms score to validscores
+ validScores[r][randomData[r]] = randomData[r];
}
-
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
-
+
delete randT;
}
}
float rcumul = 0.0000;
float ucumul = 0.0000;
+ for(int a = 0; a < numComp; a++) {
//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++) {
- if (randomtree == "") {
- it2 = uscoreFreq.find(it->first);
- //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 uCumul map
- uCumul[it->first] = ucumul;
+ for (it = validScores[a].begin(); it != validScores[a].end(); it++) {
+ if (randomtree == "") {
+ it2 = uscoreFreq[a].find(it->first);
+ //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 uCumul map
+ uCumul[a][it->first] = ucumul-a;
+ }
+
+ //make rscoreFreq map and rCumul
+ it2 = rscoreFreq[a].find(it->first);
+ //get percentage of random trees with that info
+ 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
+ rCumul[a][it->first] = rcumul-a;
}
- //make rscoreFreq map and rCumul
- it2 = rscoreFreq.find(it->first);
- //get percentage of random trees with that info
- if (it2 != rscoreFreq.end()) { rscoreFreq[it->first] /= iters; rcumul+= it2->second; }
- else { rscoreFreq[it->first] = 0.0000; } //no random trees with that score
- rCumul[it->first] = rcumul;
+ //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
+ for (int h = 0; h < userTreeScores[a].size(); h++) {
+ UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
+ }
}
- //find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
- for (int h = 0; h < userTreeScores.size(); h++) {
- UScoreSig.push_back(rCumul[userTreeScores[h]]);
- }
-
printParsimonyFile();
printUSummaryFile();
try {
//column headers
if (randomtree == "") {
- out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ out << "Comb" << '\t' << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
}else {
- out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
+ out << "Comb" << '\t' << "Score" << '\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++) {
- if (randomtree == "") {
- out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << rscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
- }else{
- out << setprecision(6) << it->first << '\t' << '\t' << rscoreFreq[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++) {
+ if (randomtree == "") {
+ 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;
+ }else{
+ out << setprecision(6) << groupComb[a] << '\t' << it->first << '\t' << '\t' << rscoreFreq[a][it->first] << '\t' << rCumul[a][it->first] << endl;
+ }
+ }
+ }
out.close();
}
void ParsimonyCommand::printUSummaryFile() {
try {
//column headers
- outSum << "Tree#" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << endl;
+ outSum << "Tree#" << '\t' << "Comb" << '\t' << "ParsScore" << '\t' << '\t' << "ParsSig" << 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' << userTreeScores[i] << '\t' << UScoreSig[i] << endl;
+ 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;
+ }
}
outSum.close();
void ParsimonyCommand::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) {
if (globaldata->Groups[0] != "all") {
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);
+ globaldata->Groups.erase(globaldata->Groups.begin()+i);
}
}
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
+ groupComb.push_back(allGroups);
+ numComp++;
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
TreeMap* tmap;
TreeMap* savetmap;
Parsimony* pars;
+ vector<string> groupComb; // AB. AC, BC...
string parsFile, sumFile, randomtree;
- int iters, numGroups;
+ int iters, numGroups, numComp;
vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
- vector<float> userTreeScores; //scores for users trees
- vector<float> UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ vector< vector<float> > userTreeScores; //scores for users trees for each comb.
+ vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
EstOutput userData; //pscore info for user tree
EstOutput randomData; //pscore info for random trees
- map<int, float> validScores; //contains scores from both user and random
- map<int, float> rscoreFreq; //pscore, number of random trees with that score.
- map<int, float> uscoreFreq; //pscore, number of user trees with that score.
- map<int, float> rCumul; //pscore, cumulative percentage of number of random trees with that score or lower.
- map<int, float> uCumul; //pscore, cumulative percentage of number of user trees with that score or lower .
- map<int, float>::iterator it;
- map<int, float>::iterator it2;
+ vector< map<int, double> > validScores; //map contains scores from both user and random
+ vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
+ vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
+ vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
+ vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
+ map<int, double>::iterator it;
+ map<int, double>::iterator it2;
ofstream out, outSum;
projects / mothur.git / commitdiff