X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedcommand.cpp;h=4cc0ea73b6a4a561ce0a511ca5cbb5da4b9d581c;hb=818dcf9513122fa52616a7722f4893f77685a621;hp=efc45c191482cc191fa204e526758a81af4bf910;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index efc45c1..4cc0ea7 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -65,7 +65,7 @@ int SharedCommand::execute(){
 		//lookup.clear();
 		string errorOff = "no error";
 		//errorOff = "";
-cout << globaldata->inputFileName << endl;			
+		
 		//read in listfile
 		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
@@ -101,7 +101,7 @@ cout << globaldata->inputFileName << endl;
 				groups += globaldata->Groups[i] + ".";
 			}
 		
-			string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
+			string newGroupFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + groups + "groups";
 			ofstream outGroups;
 			openOutputFile(newGroupFile, outGroups);
 		
@@ -199,7 +199,13 @@ cout << globaldata->inputFileName << endl;
 			delete it3->second;
 		}
 
+		
+		//change format to shared  to speed up commands
+		globaldata->setFormat("sharedfile");
+		globaldata->setListFile("");
+		globaldata->setGroupFile("");
 		globaldata->setSharedFile(filename);
+
 		
 		return 0;
 	}
@@ -274,7 +280,7 @@ void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 void SharedCommand::createMisMatchFile() {
 	try {
 		ofstream outMisMatch;
-		string outputMisMatchName = getRootName(globaldata->inputFileName);
+		string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
 		
 		//you have sequences in your list file that are not in your group file
 		if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
@@ -283,6 +289,9 @@ void SharedCommand::createMisMatchFile() {
 			
 			openOutputFile(outputMisMatchName, outMisMatch);
 			
+			map<string, string> listNames;
+			map<string, string>::iterator itList;
+			
 			//go through list and if group returns "not found" output it
 			for (int i = 0; i < SharedList->getNumBins(); i++) {
 			
@@ -292,13 +301,22 @@ void SharedCommand::createMisMatchFile() {
 					string name = names.substr(0,names.find_first_of(','));
 					names = names.substr(names.find_first_of(',')+1, names.length());
 					string group = groupMap->getGroup(name);
-				
+					
 					if(group == "not found") {	outMisMatch << name << endl;  }
+					
+					itList = listNames.find(name);
+					if (itList != listNames.end()) {  mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+					else { listNames[name] = name; }
 				}
 			
 				//get last name
 				string group = groupMap->getGroup(names);
-				if(group == "not found") {	outMisMatch << names << endl;  }				
+				if(group == "not found") {	outMisMatch << names << endl;  }	
+				
+				itList = listNames.find(names);
+				if (itList != listNames.end()) {  mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+				else { listNames[names] = names; }
+
 			}
 			
 			outMisMatch.close();
@@ -310,6 +328,7 @@ void SharedCommand::createMisMatchFile() {
 			mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
 			
 			map<string, string> namesInList;
+			map<string, string>::iterator itList;
 			
 			//go through listfile and get names
 			for (int i = 0; i < SharedList->getNumBins(); i++) {
@@ -320,9 +339,16 @@ void SharedCommand::createMisMatchFile() {
 					string name = names.substr(0,names.find_first_of(','));
 					names = names.substr(names.find_first_of(',')+1, names.length());
 					
+					itList = namesInList.find(name);
+					if (itList != namesInList.end()) {  mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+
 					namesInList[name] = name;
+					
 				}
 				
+				itList = namesInList.find(names);
+				if (itList != namesInList.end()) {  mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+
 				//get last name
 				namesInList[names] = names;				
 			}