worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa...

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index f261dd91ff256f953fed82114e42e3d79ff7f5cc..0a4edea92911866d4768328ed2f2e46cf4a089b3 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -61,8 +61,7 @@ vector<string> PairwiseSeqsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
                outputTypes["column"] = tempOutNames;
@@ -75,10 +74,10 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(){
 //**********************************************************************************************************************
 PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
        
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        
@@ -268,7 +267,7 @@ void PairwiseSeqsCommand::help(){
 
 int PairwiseSeqsCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int longestBase = 2000; //will need to update this in driver if we find sequences with more bases.  hardcoded so we don't have the pre-read user fasta file.
                
@@ -770,7 +769,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
 
-               int startTime = time(NULL);
+               
                
                string outputString = "";
                size = 0;
@@ -846,7 +845,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 
                MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
                
-               int startTime = time(NULL);
+               
                
                string outputString = "";
                size = 0;