}
lookup.clear();
-
+
+ sort(Groups.begin(), Groups.end());
+
//create and initialize vector of sharedvectors, one for each group
for (int i = 0; i < Groups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
}
}
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";
+ m->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";
+ m->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, string mode) {
+void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
try {
+
+ sort(userGroups.begin(), userGroups.end());
+ sort(allGroups.begin(), allGroups.end());
+
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;
+ 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) {
+ m->mothurOut("You provided no valid groups. I will run the command using all the groups in your file."); m->mothurOutEndLine();
+ for (int i = 0; i < allGroups.size(); i++) {
+ userGroups.push_back(allGroups[i]);
+ }
+ }
}else{//user has enter "all" and wants the default groups
userGroups.clear();
}
}
- if (mode == "venn") {
- //if the user only entered invalid groups
- if (userGroups.size() == 0) {
- if (allGroups.size() > 4) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first four groups in your groupfile." << endl;
- for (int i = 0; i < 4; i++) {
- userGroups.push_back(allGroups[i]);
- }
- }else {
- 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;
- for (int i = 0; i < allGroups.size(); i++) {
- userGroups.push_back(allGroups[i]);
- }
- }
- }
-
- //check to make sure their are only 4 groups
- if (userGroups.size() > 4) {
- cout << "You may only use up to 4 groups at a time with this command. I will choose the first four and disregard the rest." << endl;
- for (int i = 4; i < userGroups.size(); i++) {
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedUtil", "setGroups");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+//need to have mode because different commands require different number of valid groups
+void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string mode) {
+ try {
+
+ sort(userGroups.begin(), userGroups.end());
+ sort(allGroups.begin(), allGroups.end());
+
+ 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) {
+ 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--;
}
}
- }else if (mode == "heat") {
- //if the user only entered invalid groups
- if (userGroups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < allGroups.size(); i++) {
- userGroups.push_back(allGroups[i]);
- }
+
+ }else{//user has enter "all" and wants the default groups
+ userGroups.clear();
+ for (int i = 0; i < allGroups.size(); i++) {
+ userGroups.push_back(allGroups[i]);
}
- }else if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
+ }
+ }else { //the user has not entered groups
+ for (int i = 0; i < allGroups.size(); i++) {
+ userGroups.push_back(allGroups[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;
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->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);
- }
-
}
+
/**************************************************************************************/
//for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string& label, int& numGroups, string mode){ //globaldata->Groups, your tree or group map, allgroups, mode
try {
+ sort(userGroups.begin(), userGroups.end());
+ sort(allGroups.begin(), allGroups.end());
+
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;
+ 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--;
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
- label += allGroups[i] + "-";
}
}
}
}else { //the user has not entered groups
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
- label += allGroups[i] + "-";
if (mode == "weighted") {
userGroups.push_back(allGroups[i]);
}else {
numGroups = 1;
+ label += allGroups[i] + "-";
}
}
}
+ //rip extra - off allgroups
+ label = label.substr(0, label.length()-1);
+ if ((mode != "weighted") && (allGroups.size() > 10)) { label = "merged"; }
}
-
if (mode == "weighted") {
//if the user only entered invalid groups
if (userGroups.size() == 0) {
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;
+ 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) {
- 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;
+ 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)) {
- 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;
+ 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]);
- label += allGroups[i] + "-";
}
}
- }else {
- for (int i = 0; i < userGroups.size(); i++) {
- label += userGroups[i] + "-";
- }
}
- //rip extra - off allgroups
- label = label.substr(0, label.length()-1);
-
if (numGroups != 1) { numGroups = userGroups.size(); }
-
}
}
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";
+ m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
/**************************************************************************************/
void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups, int& numComp) { //groupcomb, globaldata->Groups, numcomb
try {
+ sort(userGroups.begin(), userGroups.end());
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
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) {
- 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";
+ m->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";
+ m->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";
+ m->errorOut(e, "SharedUtil", "updateGroupIndex");
exit(1);
}
}
+/**************************************************************************************/
+
+
projects / mothur.git / blobdiff