X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=3d667227ae2219347f2523ee1ff8286988299423;hb=74d3aaf0f85080ea3cfb1f1871e706bab9f48392;hp=f09aa997a506076b99584228c2b2272a6530a6fc;hpb=8f909cf6870cc2e4d8ed8cff69a203f6f83a160b;p=mothur.git

diff --git a/distancecommand.cpp b/distancecommand.cpp
index f09aa99..3d66722 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -14,6 +14,7 @@
 #include "onegapdist.h"
 #include "onegapignore.h"
 
+
 //**********************************************************************************************************************
 vector<string> DistanceCommand::getValidParameters(){	
 	try {
@@ -29,7 +30,7 @@ vector<string> DistanceCommand::getValidParameters(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["phylip"] = tempOutNames;
 		outputTypes["column"] = tempOutNames;
@@ -47,7 +48,7 @@ vector<string> DistanceCommand::getRequiredParameters(){
 		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+		m->errorOut(e, "DistanceCommand", "getRequiredParameters");
 		exit(1);
 	}
 }
@@ -65,11 +66,11 @@ vector<string> DistanceCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(string option) {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		Estimators.clear();
 				
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -209,13 +210,7 @@ DistanceCommand::DistanceCommand(string option) {
 
 //**********************************************************************************************************************
 
-DistanceCommand::~DistanceCommand(){
-	
-	for(int i=0;i<lines.size();i++){
-		delete lines[i];
-	}
-	
-}
+DistanceCommand::~DistanceCommand(){}
 	
 //**********************************************************************************************************************
 
@@ -246,7 +241,7 @@ void DistanceCommand::help(){
 int DistanceCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		int startTime = time(NULL);
 		
@@ -318,7 +313,7 @@ int DistanceCommand::execute(){
 			//delete filename;
 
 			if (pid == 0) { //you are the root process 
-			
+				
 				//do your part
 				string outputMyPart;
 				
@@ -422,28 +417,35 @@ 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 +527,7 @@ 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 +535,36 @@ 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 +1150,11 @@ 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);
 	}
 }