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();
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();
+ //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++){
-
- 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();
- }
+ for(int i=0;i<t->getNumNodes();i++){
+ if (m->control_pressed) { return data; }
+
+ //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
+ //pcountSize = 2, not unique to one group
+ //pcountSize = 1, unique to one group
+
+ int pcountSize = 0;
+ for (int j = 0; j < groups.size(); j++) {
+ map<string, int>::iterator itGroup = t->tree[i].pcount.find(groups[j]);
+ if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
+
+ if (pcountSize == 0) { }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].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();
- }
+ if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
+ totalBL += abs(t->tree[i].getBranchLength());
}
-
- /**********************************************************************/
}
UW = (UniqueBL / totalBL);
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- groups.push_back(tmap->namesOfGroups[i]);
+ if (tmap->namesOfGroups[i] != "xxx") {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
}
}else {
for (int i = 0; i < globaldata->Groups.size(); 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
+ for(int i=0;i<t->getNumNodes();i++){
- //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 (m->control_pressed) { return data; }
+
+ //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
+ //pcountSize = 2, not unique to one group
+ //pcountSize = 1, unique to one group
+
+ int pcountSize = 0;
+ for (int j = 0; j < groups.size(); j++) {
+ map<string, int>::iterator itGroup = t->tree[i].pcount.find(groups[j]);
+ if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
-
- 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();
- }
+
+ if (pcountSize == 0) { }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
+
+ if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
+ totalBL += abs(t->tree[i].getBranchLength());
}
-
- /**********************************************************************/
}
UW = (UniqueBL / totalBL);
}
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";
+ m->errorOut(e, "Unweighted", "getValues");
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);
- }
-
}
/**************************************************************************************************/
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++) {
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(globaldata->Groups[a], globaldata->Groups[l]);
+ copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
- //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++){
-
- 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();
+ if (m->control_pressed) { delete copyTree; return data; }
+
+ for(int i=0;i<copyTree->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+
+ //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
+ //pcountSize = 2, not unique to one group
+ //pcountSize = 1, unique to one group
+
+ int pcountSize = 0;
+ for (int j = 0; j < groups.size(); j++) {
+ map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
+ if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
-
- /**********************************************************************/
- //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 (pcountSize == 0) { }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
+
+ if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
+ totalBL += abs(copyTree->tree[i].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; }
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- groups.push_back(tmap->namesOfGroups[i]);
+ if (tmap->namesOfGroups[i] != "xxx") {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
}
}else {
for (int i = 0; i < globaldata->Groups.size(); 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
+ copyTree->assembleRandomUnifracTree(groups);
- 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 (m->control_pressed) { delete copyTree; return data; }
+
+ for(int i=0;i<copyTree->getNumNodes();i++){
- //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 (m->control_pressed) { return data; }
+
+ //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
+ //pcountSize = 2, not unique to one group
+ //pcountSize = 1, unique to one group
+
+ int pcountSize = 0;
+ for (int j = 0; j < groups.size(); j++) {
+ map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
+ if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
-
- 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();
- }
+
+ if (pcountSize == 0) { }
+ else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
+
+ if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
+ totalBL += abs(copyTree->tree[i].getBranchLength());
}
-
- /**********************************************************************/
}
UW = (UniqueBL / totalBL);
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";
+ m->errorOut(e, "Unweighted", "getValues");
exit(1);
}
}
projects / mothur.git / blobdiff