modified calculators to use doubles, added numotu and fontsize parameters to heatmap...

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index f19810e131b687ea372ae1914ecf3a02d03ef8d8..4641ed7f65a65374df52836bb6c9e6b943fa8e61 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -98,14 +98,6 @@ AlignCommand::AlignCommand(string option)  {
        
                                        int ableToOpen;
                                        ifstream in;
-                                       
-                                       #ifdef USE_MPI  
-                                               int pid;
-                                               MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
-                                               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-                               
-                                               if (pid == 0) {
-                                       #endif
 
                                        ableToOpen = openInputFile(candidateFileNames[i], in, "noerror");
                                
@@ -119,16 +111,6 @@ AlignCommand::AlignCommand(string option)  {
                                                }
                                        }
                                        in.close();                                     
-                                       #ifdef USE_MPI  
-                                                       for (int j = 1; j < processors; j++) {
-                                                               MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); 
-                                                       }
-                                               }else{
-                                                       MPI_Status status;
-                                                       MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
-                                               }
-                                               
-                                       #endif
 
                                        if (ableToOpen == 1) { 
                                                m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
@@ -263,7 +245,7 @@ int AlignCommand::execute(){
                                int tag = 2001;
                                vector<unsigned long int> MPIPos;
                                MPIWroteAccnos = false;
-                               
+                       
                                MPI_Status status; 
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
                                MPI_Comm_size(MPI_COMM_WORLD, &processors); 
@@ -580,7 +562,7 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
                                //if there is a possibility that this sequence should be reversed
                                if (candidateSeq->getNumBases() < numBasesNeeded) {
                                        
-                                       string wasBetter = "";
+                                       string wasBetter =  "";
                                        //if the user wants you to try the reverse
                                        if (flip) {
                                                //get reverse compliment
@@ -602,8 +584,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
                                                        delete nast;
                                                        nast = nast2;
                                                        needToDeleteCopy = true;
+                                                       wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
                                                }else{  
-                                                       wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
+                                                       wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
                                                        delete nast2;
                                                        delete copy;    
                                                }
@@ -678,7 +661,7 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
                        int length = MPIPos[start+i+1] - MPIPos[start+i];
 
                        char* buf4 = new char[length];
-                       memcpy(buf4, outputString.c_str(), length);
+                       //memcpy(buf4, outputString.c_str(), length);
 
                        MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
                        
@@ -687,9 +670,11 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
                        delete buf4;
 
                        if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
-                       istringstream iss (tempBuf,istringstream::in);
        
+                       istringstream iss (tempBuf,istringstream::in);
+
                        Sequence* candidateSeq = new Sequence(iss);  
+       
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
                        int numBasesNeeded = origNumBases * threshold;