working on nmds command

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 98b6681d5091ffbb30b80172c0a36d12a531d130..65b5956cce5c0a6418d5d9524218b35b0b335aa8 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -267,7 +267,7 @@ int ScreenSeqsCommand::execute(){
                int start = time(NULL);
                
 #ifdef USE_MPI 
-                       int pid, end, numSeqsPerProcessor; 
+                       int pid, numSeqsPerProcessor; 
                        int tag = 2001;
                        vector<unsigned long int> MPIPos;
                        
@@ -507,13 +507,13 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
                
                ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
-       
+               
                while(!inputNames.eof()){
                        if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 
                        inputNames >> seqName >> seqList;
                        it = badSeqNames.find(seqName);
-                       
+                               
                        if(it != badSeqNames.end()){
                                badSeqNames.erase(it);
                                
@@ -558,7 +558,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                                if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); remove(goodNameFile.c_str());  remove(goodGroupFile.c_str()); return 0; }
 
                                inputGroups >> seqName >> group;
-
+                               
                                it = badSeqGroups.find(seqName);
                                
                                if(it != badSeqGroups.end()){
@@ -580,7 +580,8 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                                }
                        }
                }
-                       
+               
+               
                return 0;
        
        }