#include "parsimony.h"
/**************************************************************************************************/
+
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();
+
+ //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);
- data.resize(1,0);
+ 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++){
+
+ if (m->control_pressed) { return data; }
+
+ int lc = copyTree->tree[i].getLChild();
+ int rc = copyTree->tree[i].getRChild();
- int score = 0;
+ int iSize = copyTree->tree[i].pGroups.size();
+ int rcSize = copyTree->tree[rc].pGroups.size();
+ int lcSize = copyTree->tree[lc].pGroups.size();
- //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));
+ //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();
+ }
}
- for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
- int lc = t->tree[i].getLChild();
- int rc = t->tree[i].getRChild();
+ 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]);
+ }
+ }
- int iSize = t->tree[i].pGroups.size();
- int rcSize = t->tree[rc].pGroups.size();
- int lcSize = t->tree[lc].pGroups.size();
+ //copy users tree so that you can redo pgroups
+ copyTree->getCopy(t);
+ int score = 0;
- //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++;
+ //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));
}
- cout << i << ' ' << score << ": ";
- t->tree[i].printNode();
- }
- //string hold;
- //cin >> hold;
+// map<string,int>::iterator it;
+
+ for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
+
+ if (m->control_pressed) { return data; }
+
+ 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;
+
+ }
- data[0] = score;
+ delete copyTree;
return data;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Parsimony class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Parsimony", "getValues");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Parsimony class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/**************************************************************************************************/
projects / mothur.git / blobdiff