fixed bugs

diff --git a/globaldata.cpp b/globaldata.cpp
index 4005f40d8cb32bc5f293c97f32386029be08c1f3..0078d69997e8cd15f57e527a6db1cc3e0d430139 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -28,7 +28,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        gGroupmap = NULL;
                        gTree.clear();
                        Treenames.clear();
-                       labels.clear(); lines.clear(); groups.clear();
+                       labels.clear(); lines.clear(); Groups.clear();
                        allLines = 1;
                }
                

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index fd0595de079b588a53e5b11c23d89c5a56687d78..5776b3685c06b6eb7fe8e419c791b3ee6a4ecde6 100644 (file)
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -111,6 +111,7 @@ void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<S
 //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

diff --git a/validcommands.cpp b/validcommands.cpp
index 7f7acc2e61044c7ef8f2e8948a112dfd3184cfaf..230d80083d2d19cd7307fc2e6952f424656db55d 100644 (file)
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -17,7 +17,6 @@ ValidCommands::ValidCommands() {
                commands["read.dist"]                   = "read.dist"; 
                commands["read.otu"]                    = "read.otu";
                commands["read.tree"]                   = "read.tree"; 
-               commands["read.seqs"]           = "read.seqs";
                commands["bin.seqs"]                    = "bin.seqs"; 
                commands["get.oturep"]                  = "get.oturep";
                commands["cluster"]                             = "cluster";