X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=9b8aa3f8abc87ef9ff93520a80b3da9169d406f4;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=e5d8427200aed0a61aaf04a0e7084ed0e17a0a78;hpb=4b54ce99af7db8019ea907cd7c2edf789369ada9;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index e5d8427..9b8aa3f 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -317,6 +317,10 @@ string GroupMap::getGroup(string sequenceName) {
 	if (it != groupmap.end()) { //sequence name was in group file
 		return it->second;	
 	}else {
+        //look for it in names of groups to see if the user accidently used the wrong file
+        if (m->inUsersGroups(sequenceName, namesOfGroups)) {
+            m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine(); 
+        }
 		return "not found";
 	}
 }
@@ -368,6 +372,22 @@ bool GroupMap::isValidGroup(string groupname) {
 	}
 }
 /************************************************************/
+int GroupMap::getCopy(GroupMap* g) {
+	try {
+        vector<string> names = g->getNamesSeqs();
+        for (int i = 0; i < names.size(); i++) {
+            if (m->control_pressed) { break; }
+            string group = g->getGroup(names[i]);
+            setGroup(names[i], group);
+        }
+        return names.size();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "getCopy");
+		exit(1);
+	}
+}
+/************************************************************/
 int GroupMap::getNumSeqs(string group) {
 	try {
 		
@@ -385,7 +405,66 @@ int GroupMap::getNumSeqs(string group) {
 		exit(1);
 	}
 }
-
+/************************************************************/
+int GroupMap::renameSeq(string oldName, string newName) {
+	try {
+		
+		map<string, string>::iterator itName;
+		
+		itName = groupmap.find(oldName);
+		
+		if (itName == groupmap.end()) {
+            m->mothurOut("[ERROR]: cannot find " + toString(oldName) + " in group file");
+            m->control_pressed = true;
+            return 0;
+        }else {
+            string group = itName->second;
+            groupmap.erase(itName);
+            groupmap[newName] = group;
+        }
+        
+        return 0;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "renameSeq");
+		exit(1);
+	}
+}
+/************************************************************/
+int GroupMap::print(ofstream& out) {
+	try {
+		
+		for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+            out << itName->first << '\t' << itName->second << endl;
+        }
+             
+        return 0;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "print");
+		exit(1);
+	}
+}
+/************************************************************/
+int GroupMap::print(ofstream& out, vector<string> userGroups) {
+	try {
+		
+		for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+            if (m->inUsersGroups(itName->second, userGroups)) {
+                out << itName->first << '\t' << itName->second << endl;
+            }
+        }
+        
+        return 0;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "print");
+		exit(1);
+	}
+}
 /************************************************************/
 vector<string> GroupMap::getNamesSeqs(){
 	try {