modified mpi code to save ram by writing out every 10 seqs.

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index 3bd80a87fde16f95d1bf1f8ae9369c0f962eb181..4b5667584a07fd1ca5f6832efd16c192e04c5f1c 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -38,17 +38,12 @@ Sequence::Sequence(string newName, string sequence) {
 Sequence::Sequence(istringstream& fastaString){
        try {
                m = MothurOut::getInstance();
-       int pid;
-       MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-       cout << pid << " after mothur instance " << &name << endl;
+       
                initialize();
-       cout << "after mothur initialize" << endl;
                fastaString >> name;
-       cout << pid << " after name "  << name << endl;
                name = name.substr(1);
-
                string sequence;
-cout << pid << " name = "  << name << endl;            
+       
                //read comments
                while ((name[0] == '#') && fastaString) { 
                        while (!fastaString.eof())      {       char c = fastaString.get(); if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
@@ -61,13 +56,11 @@ cout << pid << " name = "  << name << endl;
                                name = "";
                                break;
                        }
-                       cout << pid << "in while comment" << endl;      
                }
-       cout << pid << "after mothur comment" << endl;  
-               while (!fastaString.eof())      {       char c = fastaString.get(); cout << pid << " char = " << int(c) << endl; if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
-       cout << pid << " after mothur name" << endl;    
+               
+               while (!fastaString.eof())      {       char c = fastaString.get();  if (c == 10 || c == 13){   break;  }       } // get rest of line if there's any crap there
+               
                sequence = getSequenceString(fastaString);              
-       cout << pid << " after mothur sequence" << endl;        
                setAligned(sequence);   
                //setUnaligned removes any gap characters for us                                                
                setUnaligned(sequence);         
@@ -169,11 +162,10 @@ string Sequence::getSequenceString(istringstream& fastaFile) {
        try {
                char letter;
                string sequence = "";   
-int pid;
-MPI_Comm_rank(MPI_COMM_WORLD, &pid);           
+               
                while(!fastaFile.eof()){
                        letter= fastaFile.get();
-       cout << pid << '\t' << letter << endl;
+       
                        if(letter == '>'){
                                fastaFile.putback(letter);
                                break;