#include "onegapdist.h"
#include "onegapignore.h"
+
//**********************************************************************************************************************
vector<string> DistanceCommand::getValidParameters(){
try {
//**********************************************************************************************************************
DistanceCommand::DistanceCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+ m->errorOut(e, "DistanceCommand", "getRequiredParameters");
exit(1);
}
}
//**********************************************************************************************************************
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
//**********************************************************************************************************************
-DistanceCommand::~DistanceCommand(){
-
- for(int i=0;i<lines.size();i++){
- delete lines[i];
- }
-
-}
+DistanceCommand::~DistanceCommand(){}
//**********************************************************************************************************************
int DistanceCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int startTime = time(NULL);
//delete filename;
if (pid == 0) { //you are the root process
-
+
//do your part
string outputMyPart;
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
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();
}
//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
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);
}
}