#include "onegapdist.h"
#include "onegapignore.h"
-//**********************************************************************************************************************
+//**********************************************************************************************************************
+vector<string> DistanceCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir","compress"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DistanceCommand::DistanceCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DistanceCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DistanceCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
DistanceCommand::DistanceCommand(string option) {
try {
abort = false;
if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
//**********************************************************************************************************************
-DistanceCommand::~DistanceCommand(){
-
- for(int i=0;i<lines.size();i++){
- delete lines[i];
- }
-
-}
+DistanceCommand::~DistanceCommand(){}
//**********************************************************************************************************************
if (output == "lt") { //does the user want lower triangle phylip formatted file
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
- remove(outputFile.c_str());
+ remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+ outputTypes["column"].push_back(outputFile);
//so we don't accidentally overwrite
if (outputFile == column) {
}else { //assume square
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
remove(outputFile.c_str());
+ outputTypes["phylip"].push_back(outputFile);
}
//delete filename;
if (pid == 0) { //you are the root process
-
+
//do your part
string outputMyPart;
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
char buf[5];
MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
//do your part
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
char buf[5];
strcpy(buf, "done");
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
- if (m->control_pressed) { delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; return 0; }
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
for(int b = 1; b < processors; b++) {
unsigned long int fileSize;
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
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;
#endif
#endif
- if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
}
#endif
- if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
delete distCalculator;
m->mothurOut("Compressing..."); m->mothurOutEndLine();
m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
system(("gzip -v " + outputFile).c_str());
- }
+ outputNames.push_back(outputFile + ".gz");
+ }else { outputNames.push_back(outputFile); }
return 0;
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
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("unable to spawn the necessary processes."); m->mothurOutEndLine(); 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);
+ }
}
-
+
+ //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) {
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);
}
}