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

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 7ab00a7822f7a7fc7ddd1ef0de00d2d24b8c51de..e6e616a3a5d3f4b7a81ef1ab91a974a9c993074c 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -263,7 +263,7 @@ int FilterSeqsCommand::filterSequences() {
                                MPI_Status status; 
                                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
-       cout << pid << "is in create filter " << endl;                  
+                               
                                MPI_File outMPI;
                                MPI_File tempMPI;
                                MPI_File inMPI;
@@ -494,7 +494,14 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
                                        out << '>' << seq.getName() << endl << filterSeq << endl;
                                }
                                gobble(in);
+                               
+                       //report progress
+                       if((i+1) % 100 == 0){   m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
                }
+               
+               //report progress
+               if((line->num) % 100 != 0){     m->mothurOut(toString(line->num)); m->mothurOutEndLine();               }
+               
                out.close();
                in.close();
                
@@ -853,13 +860,27 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
                
                //loop through and create all the processes you want
                while (process != processors) {
-                       int pid = vfork();
+                       int pid = fork();
                        
                        if (pid > 0) {
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
                                driverCreateFilter(F, filename, lines[process]);
+                               
+                               //write out filter counts to file
+                               filename += toString(getpid()) + "filterValues.temp";
+                               ofstream out;
+                               openOutputFile(filename, out);
+                               
+                               for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
+                               for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
+                               for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
+                               for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
+                               for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
+                               
+                               out.close();
+                               
                                exit(0);
                        }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
                }
@@ -870,6 +891,23 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
                        wait(&temp);
                }
                
+               //parent reads in and combine Filter info
+               for (int i = 0; i < processIDS.size(); i++) {
+                       string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
+                       ifstream in;
+                       openInputFile(tempFilename, in);
+                       
+                       int temp;
+                       for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           gobble(in);
+                       for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           gobble(in);
+                       for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           gobble(in);
+                       for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           gobble(in);
+                       for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } gobble(in);
+                               
+                       in.close();
+                       remove(tempFilename.c_str());
+               }
+               
                return exitCommand;
 #endif         
        }