EstOutput Unweighted::getValues(Tree* t) {
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;
+
- //clear out old values
- data.resize(1,0);
- penalty.resize(t->getNumLeaves(), 0);
-
- map<string,double> unique; //group, total of all branch lengths of nodes with that group.
- double shared = 0.0000;
- double UW=0.0000;
-
- //add up the branch lengths for each group.
- for(int i=0;i<t->getNumLeaves();i++){
- if(t->tree[i].pGroups.size() > 0){
- unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+ //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 each non-leaf node
- 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
+
+ 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(), 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(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += t->tree[lc].getBranchLength();
+ totalBL += t->tree[lc].getBranchLength();
+ }
+ }
- //get penalty values
- if(t->tree[rc].pGroups.size() == 0 || t->tree[lc].pGroups.size() == 0){
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+ /**********************************************************************/
+ }
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[count] = UW;
+ count++;
+ groups.clear();
}
- else if(t->tree[i].pGroups.size() > t->tree[rc].pGroups.size() || t->tree[i].pGroups.size() > t->tree[lc].pGroups.size()){
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]+1);
+ }
+
+
+ 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]);
+ }
}
- else{
- penalty.push_back(penalty[t->tree[rc].getIndex()]+penalty[t->tree[lc].getIndex()]);
+
+ 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(), 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(), 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;
+ }
- //not sure when this would ever be true??? if your parent is root could be, but pGroups.size() should never be 0.
- if(t->tree[i].getParent() == -1 && (t->tree[lc].pGroups.size() == 0 || t->tree[rc].pGroups.size() == 0)){
- shared -= 1;
- }
- else if(penalty[i] != 0 && t->tree[i].pGroups.size() != 0){
- shared += t->tree[i].getBranchLength();
- }
- else if( t->tree[i].pGroups.size() != 0){
- unique[t->tree[i].pGroups.begin()->first] += t->tree[i].getBranchLength();
+ 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++;
}
}
-
- map<string,double>::iterator pos;
- for(pos=unique.begin();pos!=unique.end();pos++){
- if(pos->first!="xxx"){
- UW += unique[pos->first];
+
+ //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);
+
+ //groups in this combo
+ groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
+
+ //swap labels in the groups you want to compare
+ copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
+
+ //copyTree->createNewickFile("random"+groupA+toString(count));
+
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+
+ 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 = 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 ((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 ((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 (copyTree->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[rc].getBranchLength();
+ totalBL += copyTree->tree[rc].getBranchLength();
+ }
+ }
+
+ if (copyTree->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[lc].getBranchLength();
+ totalBL += copyTree->tree[lc].getBranchLength();
+ }
+ }
+
+ /**********************************************************************/
+ }
+
+ UW = (UniqueBL / totalBL);
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ 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(groups);
+
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+
+ 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 = 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 ((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 ((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 (copyTree->tree[rc].getRChild() == -1) {
+ //if rc is a valid group and rc has a BL
+ if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[rc].getBranchLength();
+ totalBL += copyTree->tree[rc].getBranchLength();
+ }
+ }
+
+ if (copyTree->tree[lc].getLChild() == -1) {
+ //if lc is a valid group and lc has a BL
+ if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
+ UniqueBL += copyTree->tree[lc].getBranchLength();
+ totalBL += copyTree->tree[lc].getBranchLength();
+ }
+ }
+
+ /**********************************************************************/
+ }
+
+ UW = (UniqueBL / totalBL);
- UW /= (UW + shared);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
- data[0] = UW;
+ data[count] = UW;
+ }
+
+ delete copyTree;
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);
}
-
}
-/**************************************************************************************************/
\ No newline at end of file
+
+
+
projects / mothur.git / blobdiff