openOutputFile(sumFile, outSum);
distFile = globaldata->getTreeFile() + ".wdistrib";
openOutputFile(distFile, outDist);
-
- numGroups = tmap->getNumGroups();
+
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() == 0) {
+ numGroups = tmap->getNumGroups();
+ }else {
+ //check that groups are valid
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ 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);
+ }
+ }
+
+ //if the user only entered invalid groups
+ if (globaldata->Groups.size() == 0) {
+ numGroups = tmap->getNumGroups();
+ cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+ }else if (globaldata->Groups.size() == 1) {
+ cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+ numGroups = tmap->getNumGroups();
+ globaldata->Groups.clear();
+ }else { numGroups = globaldata->Groups.size(); }
+ }
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
numComp = 0;
numComp += i;
for (int l = n; l < numGroups; l++) {
//set group comparison labels
- groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
+ if (globaldata->Groups.size() != 0) {
+ groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
+ }else {
+ groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
+ }
}
n++;
}
//reset randomTree parameter to 0
globaldata->setRandomTree("0");
+ //clear out users groups
+ globaldata->Groups.clear();
delete randT;