changes to dist.seqs and pairwise.seqs and cluster.classic no longer resizes

[mothur.git] / pairwiseseqscommand.cpp

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 18412fdeac778159551d32e8573edd1dddc321bf..f261dd91ff256f953fed82114e42e3d79ff7f5cc 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -442,27 +442,18 @@ int PairwiseSeqsCommand::execute(){
                        }else{ //you have multiple processors
                                
                                for (int i = 0; i < processors; i++) {
-                                       lines.push_back(new linePair());
+                                       distlinePair tempLine;
+                                       lines.push_back(tempLine);
                                        if (output != "square") {
-                                               lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
-                                               lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
+                                               lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
+                                               lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
                                        }else{
-                                               lines[i]->start = int ((float(i)/float(processors)) * numSeqs);
-                                               lines[i]->end = int ((float(i+1)/float(processors)) * numSeqs);
+                                               lines[i].start = int ((float(i)/float(processors)) * numSeqs);
+                                               lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
                                        }
                                }
-
-                               createProcesses(outputFile); 
-                       
-                               map<int, int>::iterator it = processIDS.begin();
-                               rename((outputFile + toString(it->second) + ".temp").c_str(), outputFile.c_str());
-                               it++;
                                
-                               //append and remove temp files
-                               for (; it != processIDS.end(); it++) {
-                                       m->appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
-                                       remove((outputFile + toString(it->second) + ".temp").c_str());
-                               }
+                               createProcesses(outputFile); 
                        }
                #else
                        //ifstream inFASTA;
@@ -522,7 +513,7 @@ int PairwiseSeqsCommand::execute(){
 void PairwiseSeqsCommand::createProcesses(string filename) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               int process = 0;
+               int process = 1;
                processIDS.clear();
                
                //loop through and create all the processes you want
@@ -530,24 +521,35 @@ void PairwiseSeqsCommand::createProcesses(string filename) {
                        int pid = fork();
                        
                        if (pid > 0) {
-                               processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
+                               processIDS.push_back(pid); 
                                process++;
                        }else if (pid == 0){
-                               if (output != "square") {  driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff); }
-                               else { driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", "square"); }
+                               if (output != "square") {  driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
+                               else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
                                exit(0);
                        }else { 
                                m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
-                               for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { int temp = it->second; kill (temp, SIGINT); }
+                               for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
                                exit(0);
                        }
                }
-       
+               
+               //parent do my part
+               if (output != "square") {  driver(lines[0].start, lines[0].end, filename, cutoff); }
+               else { driver(lines[0].start, lines[0].end, filename, "square"); }
+
+               
                //force parent to wait until all the processes are done
-               for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { 
-                       int temp = it->second;
+               for (int i=0;i<processIDS.size();i++) { 
+                       int temp = processIDS[i];
                        wait(&temp);
                }
+               
+               //append and remove temp files
+               for (int i=0;i<processIDS.size();i++) { 
+                       m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
+                       remove((filename + toString(processIDS[i]) + ".temp").c_str());
+               }
 #endif
        }
        catch(exception& e) {