added shhh.seqs command

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index edb6314427a423f216ab5ab6576305d8c0b51687..3711a1d52c796006a354e3a341e4ba250fd8cf20 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -14,6 +14,7 @@
 #include "onegapdist.h"
 #include "onegapignore.h"
 
+
 //**********************************************************************************************************************
 vector<string> DistanceCommand::getValidParameters(){  
        try {
@@ -48,7 +49,7 @@ vector<string> DistanceCommand::getRequiredParameters(){
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+               m->errorOut(e, "DistanceCommand", "getRequiredParameters");
                exit(1);
        }
 }
@@ -210,13 +211,7 @@ DistanceCommand::DistanceCommand(string option) {
 
 //**********************************************************************************************************************
 
-DistanceCommand::~DistanceCommand(){
-       
-       for(int i=0;i<lines.size();i++){
-               delete lines[i];
-       }
-       
-}
+DistanceCommand::~DistanceCommand(){}
        
 //**********************************************************************************************************************
 
@@ -319,7 +314,7 @@ int DistanceCommand::execute(){
                        //delete filename;
 
                        if (pid == 0) { //you are the root process 
-                       
+                               
                                //do your part
                                string outputMyPart;
                                
@@ -439,17 +434,18 @@ int DistanceCommand::execute(){
                        if (numDists < processors) { processors = numDists; }
                        
                        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);
                                }
-                               //cout << i << '\t' << lines[i]->start << '\t' << lines[i]->end << endl;
+                               
                        }
-
+                       
                        createProcesses(outputFile); 
                }
        #else
@@ -540,34 +536,35 @@ void DistanceCommand::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);  //create map from line number to pid so you can append files in correct order later
                                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. Error code: " + toString(pid)); m->mothurOutEndLine(); 
-                               for (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) { int temp = it->second; kill (temp, SIGINT); }
+                               perror(" : ");
+                               for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
                                exit(0);
                        }
                }
                
                //parent does its part
-               if (output != "square") {  driver(lines[0]->start, lines[0]->end, filename, cutoff); }
-               else { driver(lines[0]->start, lines[0]->end, filename, "square"); }
+               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 (map<int, int>::iterator it = processIDS.begin(); it != processIDS.end(); it++) {
-                       m->appendFiles((filename + toString(it->second) + ".temp"), filename);
-                       remove((filename + toString(it->second) + ".temp").c_str());
+               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
        }
@@ -1156,7 +1153,7 @@ bool DistanceCommand::sanityCheck() {
                
        }
        catch(exception& e) {
-               m->errorOut(e, "DistanceCommand", "m->appendFiles");
+               m->errorOut(e, "DistanceCommand", "sanityCheck");
                exit(1);
        }
 }