removed various build warnings

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index f09aa997a506076b99584228c2b2272a6530a6fc..a3cebe27ac3a0dec63f8b21b3d1a446864350d28 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -14,6 +14,7 @@
 #include "onegapdist.h"
 #include "onegapignore.h"
 
+
 //**********************************************************************************************************************
 vector<string> DistanceCommand::getValidParameters(){  
        try {
@@ -29,6 +30,7 @@ vector<string> DistanceCommand::getValidParameters(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){    
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
@@ -47,7 +49,7 @@ vector<string> DistanceCommand::getRequiredParameters(){
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+               m->errorOut(e, "DistanceCommand", "getRequiredParameters");
                exit(1);
        }
 }
@@ -209,13 +211,7 @@ DistanceCommand::DistanceCommand(string option) {
 
 //**********************************************************************************************************************
 
-DistanceCommand::~DistanceCommand(){
-       
-       for(int i=0;i<lines.size();i++){
-               delete lines[i];
-       }
-       
-}
+DistanceCommand::~DistanceCommand(){}
        
 //**********************************************************************************************************************
 
@@ -318,7 +314,7 @@ int DistanceCommand::execute(){
                        //delete filename;
 
                        if (pid == 0) { //you are the root process 
-                       
+                               
                                //do your part
                                string outputMyPart;
                                
@@ -422,28 +418,35 @@ int DistanceCommand::execute(){
                        else { driver(0, numSeqs, outputFile, "square");  }
                }else{ //you have multiple processors
                        
+                       unsigned long int numDists = 0;
+                       
+                       if (output == "square") {
+                                numDists = numSeqs * numSeqs;
+                       }else {
+                               for(int i=0;i<numSeqs;i++){
+                                       for(int j=0;j<i;j++){
+                                               numDists++;
+                                               if (numDists > processors) { break; }
+                                       }
+                               }
+                       }
+                       
+                       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);
                                }
+                               
                        }
-
-                       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;
@@ -525,7 +528,7 @@ int DistanceCommand::execute(){
 void DistanceCommand::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
@@ -533,20 +536,36 @@ 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(); 
+                               perror(" : ");
+                               for (int i=0;i<processIDS.size();i++) {  int temp = processIDS[i]; kill (temp, SIGINT); }
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); 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"); }
+               
+               
                //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) {
@@ -1132,9 +1151,11 @@ bool DistanceCommand::sanityCheck() {
                        remove(outputFile.c_str()); //temp file is bad because file mismatch above
                }
                
+               return good;
+               
        }
        catch(exception& e) {
-               m->errorOut(e, "DistanceCommand", "m->appendFiles");
+               m->errorOut(e, "DistanceCommand", "sanityCheck");
                exit(1);
        }
 }