Checks group names in file file

#37

source/commands/getmimarkspackagecommand.cpp

@@ -467,6 +467,7 @@ int GetMIMarksPackageCommand::readFile(){
                 thisFileName1 = pieces[1];
                 thisFileName2 = pieces[2];
                 group = pieces[0];
+                m->checkGroupName(group);
             }else if (pieces.size() == 4) {
                 if (!setOligosParameter) { m->mothurOut("[ERROR]: You must have an oligosfile with the index file option. Aborting. \n"); m->control_pressed = true; }
                 thisFileName1 = pieces[0];

source/commands/makecontigscommand.cpp

@@ -2940,6 +2940,7 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
                 rindex = "";
             }else if (pieces.size() == 3) {
                 group = pieces[0];
+                m->checkGroupName(group);
                 forward = pieces[1];
                 reverse = pieces[2];
                 findex = "";

source/commands/parsefastaqcommand.cpp

@@ -1018,6 +1018,7 @@ vector< vector<string> > ParseFastaQCommand::readFile(){
                 if (oligosfile != "") { m->mothurOut("[ERROR]: You cannot have an oligosfile and 3 column file option at the same time. Aborting. \n"); m->control_pressed = true; }
                 if (groupfile != "") { m->mothurOut("[ERROR]: You cannot have an groupfile and 3 column file option at the same time. Aborting. \n"); m->control_pressed = true; }
                 group = pieces[0];
+                m->checkGroupName(group);
                 forward = pieces[1];
                 reverse = pieces[2];
                 findex = "";

source/commands/renameseqscommand.cpp

@@ -771,6 +771,7 @@ vector<map<string, string> > RenameSeqsCommand::readFiles(){
             }else if (pieces.size() == 3) {
                 thisFileName = pieces[0]+"-"+pieces[1];
                 group = pieces[2];
+                m->checkGroupName(group);
             }else {
                 m->mothurOut("[ERROR]: Your file contains " + toString(pieces.size()) + " columns. TThe file option allows you to provide a 2 or 3 column file. The first column contains the file type: fasta or qfile. The second column is the filename, and the optional third column can be a group name. If there is a third column, all sequences in the file will be assigned to that group.  This can be helpful when renaming data separated into samples.\n"); m->control_pressed = true;
             }

source/commands/sracommand.cpp

@@ -963,6 +963,7 @@ int SRACommand::readFile(map<string, vector<string> >& files){
                 thisFileName1 = pieces[1];
                 thisFileName2 = pieces[2];
                 group = pieces[0];
+                m->checkGroupName(group);
                 if (setOligosParameter) { m->mothurOut("[ERROR]: You cannot have an oligosfile and 3 column file option at the same time. Aborting. \n"); m->control_pressed = true; }
                 if ((thisFileName2 != "none") && (thisFileName2 != "NONE" )) {  if (!using3NONE) { libLayout = "paired"; } else { m->mothurOut("[ERROR]: You cannot have a 3 column file with paired and unpaired files at the same time. Aborting. \n"); m->control_pressed = true; } }
                 else {  thisFileName2 = ""; libLayout = "single"; using3NONE = true; }

source/mothurout.cpp

@@ -2979,6 +2979,28 @@ int MothurOut::checkName(string& name) {
 		exit(1);
 	}
 }
+/************************************************************/
+bool MothurOut::checkGroupName(string name) {
+    try {
+        
+        bool goodName = true;
+        for (int i = 0; i < name.length(); i++) {
+            if (name[i] == ':') {  goodName = false; break;  }
+            else if (name[i] == '-') {  goodName = false; break;  }
+            else if (name[i] == '/') {  goodName = false; break;  }
+        }
+        
+        if (!goodName) {
+            mothurOut("[ERROR]: group " + name + " contains illegal characters in the name. Group names cannot include :, -, or / characters.  The ':' character is a special character used in trees. Using ':' will result in your tree being unreadable by tree reading software.  The '-' character is a special character used by mothur to parse group names.  Using the '-' character will prevent you from selecting groups. The '/' character will created unreadable filenames when mothur includes the group in an output filename.\n"); control_pressed = true;
+        }
+        
+        return goodName;
+    }
+    catch(exception& e) {
+        errorOut(e, "MothurOut", "checkGroupName");
+        exit(1);
+    }
+}
 /**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) { 
 	try {

source/mothurout.h

@@ -193,6 +193,7 @@ class MothurOut {
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
         int checkName(string&);
+    bool checkGroupName(string name);
         map<string, vector<string> > parseClasses(string);
         string addUnclassifieds(string tax, int maxlevel, bool probs);