added MPI to dist.seqs command

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index b73bfab7caefdb0a97e5f7cc8f3271ec3e51cb57..3bd80a87fde16f95d1bf1f8ae9369c0f962eb181 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -44,13 +44,14 @@ Sequence::Sequence(istringstream& fastaString){
                initialize();
        cout << "after mothur initialize" << endl;
                fastaString >> name;
-       cout << "after name "  << endl;
+       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)     {       char c = fastaString.get(); if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
+                       while (!fastaString.eof())      {       char c = fastaString.get(); if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
                        sequence = getCommentString(fastaString);
                        
                        if (fastaString) {  
@@ -60,13 +61,13 @@ Sequence::Sequence(istringstream& fastaString){
                                name = "";
                                break;
                        }
+                       cout << pid << "in while comment" << endl;      
                }
-       cout << "after mothur comment" << endl; 
-               //read real sequence
-               while (fastaString)     {       char c = fastaString.get(); if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
-       cout << "after mothur name" << 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;    
                sequence = getSequenceString(fastaString);              
-       cout << "after mothur sequence" << endl;        
+       cout << pid << " after mothur sequence" << endl;        
                setAligned(sequence);   
                //setUnaligned removes any gap characters for us                                                
                setUnaligned(sequence);         
@@ -168,9 +169,11 @@ string Sequence::getSequenceString(istringstream& fastaFile) {
        try {
                char letter;
                string sequence = "";   
-               
-               while(fastaFile){
+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;