fixed bug in read.tree updates help and validparameters strings, added ability for...

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 0a4c7facec93938af068ebad350307ab6f5d4c0d..c2584eabfe07975d103c17c6d93e96e2ae1770e2 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -227,11 +227,14 @@ int UnifracWeightedCommand::findIndex(float score, int index) {
 /***********************************************************/
 void UnifracWeightedCommand::setGroups() {
        try {
+               numGroups = 0;
                //if the user has not entered specific groups to analyze then do them all
                if (globaldata->Groups.size() == 0) {
-                       numGroups = tmap->getNumGroups();
-                       for (int i=0; i < numGroups; i++) { 
-                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                       for (int i=0; i < tmap->getNumGroups(); i++) { 
+                               if (tmap->namesOfGroups[i] != "xxx") {
+                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                       numGroups++;
+                               }
                        }
                }else {
                        if (globaldata->getGroups() != "all") {
@@ -246,25 +249,31 @@ void UnifracWeightedCommand::setGroups() {
                        
                                //if the user only entered invalid groups
                                if (globaldata->Groups.size() == 0) { 
-                                       numGroups = tmap->getNumGroups();
-                                       for (int i=0; i < numGroups; i++) { 
-                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                       for (int i=0; i < tmap->getNumGroups(); i++) { 
+                                               if (tmap->namesOfGroups[i] != "xxx") {
+                                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                                       numGroups++;
+                                               }
                                        }
                                        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();
-                                       for (int i=0; i < numGroups; i++) { 
-                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                       for (int i=0; i < tmap->getNumGroups(); i++) { 
+                                               if (tmap->namesOfGroups[i] != "xxx") {
+                                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                                       numGroups++;
+                                               }
                                        }
                                }else { numGroups = globaldata->Groups.size(); }
                        }else { //users wants all groups
-                               numGroups = tmap->getNumGroups();
                                globaldata->Groups.clear();
                                globaldata->setGroups("");
-                               for (int i=0; i < numGroups; i++) { 
-                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                               for (int i=0; i < tmap->getNumGroups(); i++) { 
+                                       if (tmap->namesOfGroups[i] != "xxx") {
+                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+                                               numGroups++;
+                                       }
                                }
                        }
                }