try {
globaldata = GlobalData::getInstance();
- //clear out old values
- data.resize(1,0);
-
- float UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- float totalBL = 0.00; //all branch lengths
- float 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> copyLCpcount;
- map<string, int> copyRCpcount;
map<string, int> copyIpcount;
+
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
+ //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]);
- int lc = t->tree[i].getLChild(); //lc = vector index of left child
- int rc = t->tree[i].getRChild(); //rc = vector index of right child
+ for(int i=0;i<t->getNumNodes();i++){
+
+ copyIpcount = t->tree[i].pcount;
+ for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+ if (inUsersGroups(it->first, groups) != true) {
+ copyIpcount.erase(it++);
+ }else { it++; }
+ }
+
+ //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 += abs(t->tree[i].getBranchLength()); }
- /**********************************************************************/
- //This section adds in all lengths that are non leaf
+ //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 += abs(t->tree[i].getBranchLength());
+ }
- //copy left childs pGroups and remove groups that the user doesn't want
- copyIpcount = t->tree[i].pcount;
- for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
- if (inUsersGroups(it->first, globaldata->Groups) != true) { copyIpcount.erase(it->first); }
+ }
+
+ UW = (UniqueBL / totalBL);
+ //cout << globaldata->Groups[a] << globaldata->Groups[l] << '\t' << UniqueBL << '\t' << totalBL << endl;
+
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[count] = UW;
+ count++;
+ groups.clear();
}
-
- //copy left childs pGroups and remove groups that the user doesn't want
- copyLCpcount = t->tree[lc].pcount;
- for (it = copyLCpcount.begin(); it != copyLCpcount.end(); it++) {
- if (inUsersGroups(it->first, globaldata->Groups) != true) { copyLCpcount.erase(it->first); }
+ }
+
+
+ if (numComp != 1) {
+ if (numGroups == 0) {
+ //get score for all users groups
+ for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+ if (tmap->namesOfGroups[i] != "xxx") {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
+ }
+ }else {
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups.push_back(globaldata->Groups[i]);
+ }
}
-
- //copy right childs pGroups and remove groups that the user doesn't want
- copyRCpcount = t->tree[rc].pcount;
- for (it = copyRCpcount.begin(); it != copyRCpcount.end(); it++) {
- if (inUsersGroups(it->first, globaldata->Groups) != true) { copyRCpcount.erase(it->first); }
+
+ 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=0;i<t->getNumNodes();i++){
+
+ copyIpcount = t->tree[i].pcount;
+ for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+ if (inUsersGroups(it->first, groups) != true) {
+ copyIpcount.erase(it++);
+ }else { it++; }
+ }
+
+ //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 += abs(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 += abs(t->tree[i].getBranchLength());
+ }
+
}
+
+ UW = (UniqueBL / totalBL);
- //if i's children are from the same group and i has a BL then add i's length to unique
- //if copyRCpcount.size() = 0 && copyLCpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
- if ((copyRCpcount.size() == 0) && (copyLCpcount.size() == 0)) { }
- else {
- if ((copyRCpcount == copyLCpcount) && (t->tree[i].getBranchLength() != -1)) { UniqueBL += t->tree[i].getBranchLength(); }
- //if either childs groups = 0 then all of there groups were not valid making the parent unique
- else if (((copyRCpcount.size() == 0) || (copyLCpcount.size() == 0)) && (t->tree[i].getBranchLength() != -1)) { UniqueBL += t->tree[i].getBranchLength(); }
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
+
+ data[count] = UW;
+ }
+
+ return data;
+
+ }
+ catch(exception& e) {
+ errorOut(e, "Unweighted", "getValues");
+ 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);
+
+ //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=0;i<copyTree->getNumNodes();i++){
+
+ /**********************************************************************/
+ //This section adds in all lengths that are non leaf
+ copyIpcount = copyTree->tree[i].pcount;
+ for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+ if (inUsersGroups(it->first, groups) != true) {
+ copyIpcount.erase(it++);
+ }else { it++; }
+ }
- //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 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 += abs(copyTree->tree[i].getBranchLength()); }
- /**********************************************************************/
- //This section adds in all lengths that are leaf
+ //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 += abs(copyTree->tree[i].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();
}
+
+ 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++) {
+ if (tmap->namesOfGroups[i] != "xxx") {
+ 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();
- UW = (UniqueBL / totalBL);
+ //copy random tree passed in
+ copyTree->getCopy(t);
+
+ //swap labels in all the groups you want to compare
+ copyTree->assembleRandomUnifracTree(groups);
+
+ for(int i=0;i<copyTree->getNumNodes();i++){
+
+ copyIpcount = copyTree->tree[i].pcount;
+ for (it = copyIpcount.begin(); it != copyIpcount.end();) {
+ if (inUsersGroups(it->first, groups) != true) {
+ copyIpcount.erase(it++);
+ }else { it++; }
+ }
+
+ //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)) { abs(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 += abs(copyTree->tree[i].getBranchLength());
+ }
+
+ }
+
+ UW = (UniqueBL / totalBL);
- if (isnan(UW) || isinf(UW)) { UW = 0; }
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
- data[0] = UW;
+ data[count] = UW;
+ }
+
+ delete copyTree;
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";
+ errorOut(e, "Unweighted", "getValues");
exit(1);
}
-
}
+
+
+
projects / mothur.git / blobdiff