added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index ebbf686e20ce080f2889cb91d9e5063c63592579..114f545aa26eb326f078b6ab7e1b18e024ecdcb5 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -212,23 +212,23 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        string temp;
                        temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
-                       convert(temp, match);  
+                       m->mothurConvert(temp, match);  
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, misMatch);  
+                       m->mothurConvert(temp, misMatch);  
                        
                        temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
-                       convert(temp, gapOpen);  
+                       m->mothurConvert(temp, gapOpen);  
                        
                        temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
-                       convert(temp, gapExtend); 
+                       m->mothurConvert(temp, gapExtend); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);           if(temp == "not found"){        temp = "1.0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        temp = validParameter.validFile(parameters, "countends", false);        if(temp == "not found"){        temp = "T";     }
                        countends = m->isTrue(temp); 
@@ -385,7 +385,7 @@ int PairwiseSeqsCommand::execute(){
                                
                                        //do your part
                                        string outputMyPart;
-                                       unsigned long int mySize;
+                                       unsigned long long mySize;
                                        
                                        if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
                                        else { driverMPI(start, end, outputFile, mySize, output); }
@@ -403,7 +403,7 @@ int PairwiseSeqsCommand::execute(){
 
                                        //wait on chidren
                                        for(int b = 1; b < processors; b++) { 
-                                               unsigned long int fileSize;
+                                               unsigned long long fileSize;
                                                
                                                if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  m->mothurRemove(outputFile);  delete distCalculator;  return 0; }
                                                
@@ -431,7 +431,7 @@ int PairwiseSeqsCommand::execute(){
                                        MPI_File_close(&outMPI);
                                }else { //you are a child process
                                        //do your part
-                                       unsigned long int size;
+                                       unsigned long long size;
                                        if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
                                        else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
                                        
@@ -782,7 +782,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI,
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
        try {
                MPI_Status status;
                
@@ -858,7 +858,7 @@ int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsi
 }
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
        try {
                MPI_Status status;