}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "getSharedVectors");
exit(1);
}
}
for (int j = 0; j < lookup.size(); j++) {
delete lookup[j];
}
-
lookup.clear();
//create and initialize vector of sharedvectors, one for each group
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
exit(1);
}
}
//need to have mode because different commands require different number of valid groups
void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
try {
-//cout << "groups size" << userGroups.size() << endl;
if (userGroups.size() != 0) {
if (userGroups[0] != "all") {
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
+ mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
// erase the invalid group from userGroups
userGroups.erase(userGroups.begin()+i);
i--;
//if the user only entered invalid groups
if (userGroups.size() == 0) {
- cout << "You provided no valid groups. I will run the command using all the groups in your groupfile." << endl;
+ mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/**************************************************************************************************/
//need to have mode because different commands require different number of valid groups
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
+ mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); 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)) {
- 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;
+ 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();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
-
}
try {
numGroups = 0;
label = "";
+
//if the user has not entered specific groups to analyze then do them all
if (userGroups.size() != 0) {
if (userGroups[0] != "all") {
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
- cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
+ mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); mothurOutEndLine();
// erase the invalid group from globaldata->Groups
userGroups.erase(userGroups.begin()+i);
i--;
userGroups.push_back(allGroups[i]);
}
}
- 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;
+ 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();
}else if (userGroups.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;
+ 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();
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)) {
- cout << "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." << endl;
+ 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();
for (int i = 0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "getCombos");
exit(1);
}
}
return false;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "isValidGroup");
exit(1);
}
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedUtil class function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedUtil", "updateGroupIndex");
exit(1);
}
}
projects / mothur.git / blobdiff