venn command with up to 4 groups

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index c8a7dbf36548cf915d64fbe7717ff82484a1e84e..85dcd93c33d9b1df4baf8dcbef8bf16e2677154b 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -141,10 +141,18 @@ void VennCommand::setGroups() {
                        
                                //if the user only entered invalid groups
                                if (globaldata->Groups.size() == 0) { 
-                                       cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first three groups in your groupfile." << endl; 
-                                       for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-                                               globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+                                       if (globaldata->gGroupmap->namesOfGroups.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++) {
+                                                       globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[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 < globaldata->gGroupmap->namesOfGroups.size(); i++) {
+                                                       globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+                                               }
                                        }
+
                                }
                        }else{//user has enter "all" and wants the default groups
                                globaldata->Groups.clear();
@@ -161,9 +169,9 @@ void VennCommand::setGroups() {
                
                
                //check to make sure their are only 3 groups
-               if (globaldata->Groups.size() > 3) {
-                       cout << "You may only use 3 groups at a time with this command.  I will choose the first three and disregard the rest." << endl;
-                       for (int i = 3; i < globaldata->Groups.size(); i++) {
+               if (globaldata->Groups.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 < globaldata->Groups.size(); i++) {
                                globaldata->Groups.erase(globaldata->Groups.begin()+i);
                        }
                }