}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "getSharedVectors");
+ m->errorOut(e, "SharedUtil", "getSharedVectors");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
+ m->errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
exit(1);
}
}
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+ m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from userGroups
userGroups.erase(userGroups.begin()+i);
i--;
//if the user only entered invalid groups
if (userGroups.size() == 0) {
- mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ m->mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "setGroups");
+ m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+ m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from userGroups
userGroups.erase(userGroups.begin()+i);
i--;
if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
//if the user only entered invalid groups
if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
- mothurOut("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."); mothurOutEndLine();
+ m->mothurOut("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."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "setGroups");
+ m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
+ m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from globaldata->Groups
userGroups.erase(userGroups.begin()+i);
i--;
}
//rip extra - off allgroups
label = label.substr(0, label.length()-1);
+ if ((mode != "weighted") && (allGroups.size() > 10)) { label = "merged"; }
}
if (mode == "weighted") {
userGroups.push_back(allGroups[i]);
}
}
- mothurOut("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."); mothurOutEndLine();
+ m->mothurOut("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."); m->mothurOutEndLine();
}else if (userGroups.size() == 1) {
- mothurOut("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."); mothurOutEndLine();
+ m->mothurOut("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."); m->mothurOutEndLine();
userGroups.clear();
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
}else if ((mode == "unweighted") || (mode == "parsimony")) {
//if the user only entered invalid groups
if ((userGroups.size() == 0) && (numGroups == 0)) {
- mothurOut("When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
+ m->mothurOut("When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "setGroups");
+ m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
numComp = 0;
for (int i=0; i< userGroups.size(); i++) {
numComp += i;
- for (int l = i+1; l < userGroups.size(); l++) {
- //set group comparison labels
- groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
+ for (int l = 0; l < i; l++) {
+ if (userGroups[i] > userGroups[l]) {
+ //set group comparison labels
+ groupComb.push_back(userGroups[l] + "-" + userGroups[i]);
+ }else{
+ groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
+ }
}
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "getCombos");
+ m->errorOut(e, "SharedUtil", "getCombos");
exit(1);
}
}
return false;
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "isValidGroup");
+ m->errorOut(e, "SharedUtil", "isValidGroup");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "SharedUtil", "updateGroupIndex");
+ m->errorOut(e, "SharedUtil", "updateGroupIndex");
exit(1);
}
}