//**********************************************************************************************************************
-DistanceCommand::DistanceCommand(){
+DistanceCommand::DistanceCommand(string option){
try {
globaldata = GlobalData::getInstance();
- validCalculator = new ValidCalculators();
- countends = globaldata->getCountEnds();
- convert(globaldata->getProcessors(), processors);
- convert(globaldata->getCutOff(), cutoff);
- phylip = globaldata->getPhylipFile();
+ abort = false;
+ Estimators.clear();
- //open file
- string filename = globaldata->getFastaFile();
- openInputFile(filename, in);
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
-
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "phylip", "calc", "countends", "cutoff", "processors"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
- int i;
- if (isTrue(countends) == true) {
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "nogaps") {
- distCalculator = new ignoreGaps();
- }else if (globaldata->Estimators[i] == "eachgap") {
- distCalculator = new eachGapDist();
- }else if (globaldata->Estimators[i] == "onegap") {
- distCalculator = new oneGapDist(); }
- }
+ //check to make sure all parameters are valid for command
+ for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
+ if (validParameter->isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
- }else {
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "nogaps") {
- distCalculator = new ignoreGaps();
- }else if (globaldata->Estimators[i] == "eachgap") {
- distCalculator = new eachGapIgnoreTermGapDist();
- }else if (globaldata->Estimators[i] == "onegap") {
- distCalculator = new oneGapIgnoreTermGapDist();
+
+ //check for required parameters
+ fastafile = validParameter->validFile(parameters, "fasta", true);
+ if (fastafile == "not found") { cout << "fasta is a required parameter for the dist.seqs command." << endl; abort = true; }
+ else if (fastafile == "not open") { abort = true; }
+ else {
+ globaldata->setFastaFile(fastafile);
+ openInputFile(fastafile, in);
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ calc = validParameter->validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "onegap"; }
+ else {
+ if (calc == "default") { calc = "onegap"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter->validFile(parameters, "countends", false); if (temp == "not found") { temp = "T"; }
+ convert(temp, countends);
+
+ temp = validParameter->validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
+ convert(temp, cutoff);
+
+ temp = validParameter->validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, processors);
+
+ phylip = validParameter->validFile(parameters, "phylip", false); if (phylip == "not found") { phylip = "F"; }
+
+ delete validParameter;
+
+ validCalculator = new ValidCalculators();
+
+ int i;
+ if (isTrue(countends) == true) {
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") {
+ distCalculator = new ignoreGaps();
+ }else if (Estimators[i] == "eachgap") {
+ distCalculator = new eachGapDist();
+ }else if (Estimators[i] == "onegap") {
+ distCalculator = new oneGapDist(); }
+ }
+ }
+ }else {
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") {
+ distCalculator = new ignoreGaps();
+ }else if (Estimators[i] == "eachgap") {
+ distCalculator = new eachGapIgnoreTermGapDist();
+ }else if (Estimators[i] == "onegap") {
+ distCalculator = new oneGapIgnoreTermGapDist();
+ }
}
}
}
+
+ delete validCalculator;
}
-
- //reset calc for next command
- globaldata->setCalc("");
+
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function DistanceCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
}
//**********************************************************************************************************************
+void DistanceCommand::help(){
+ try {
+ cout << "The dist.seqs command reads a file containing sequences and creates a distance file." << "\n";
+ cout << "The dist.seqs command parameters are fasta, calc, countends, cutoff and processors. " << "\n";
+ cout << "The fasta parameter is required." << "\n";
+ cout << "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap." << "\n";
+ cout << "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T." << "\n";
+ cout << "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0." << "\n";
+ cout << "The processors parameter allows you to specify number of processors to use. The default is 1." << "\n";
+ cout << "The dist.seqs command should be in the following format: " << "\n";
+ cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
+ cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3)." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the DistanceCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+
int DistanceCommand::execute(){
try {
+ if (abort == true) { return 0; }
+
//reads fasta file and fills sequenceDB
- if(globaldata->getFastaFile() != "") { seqDB = new SequenceDB(in); }
- else { cout << "Error no fasta file." << endl; return 0; }
+ seqDB = new SequenceDB(in);
int numSeqs = seqDB->getNumSeqs();
cutoff += 0.005;
//doses the user want the phylip formatted file as well
if (isTrue(phylip) == true) {
- outputFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
+ outputFile = getRootName(fastafile) + "phylip.dist";
remove(outputFile.c_str());
//output numSeqs to phylip formatted dist file
outFile << numSeqs << endl;
outFile.close();
}else { //user wants column format
- outputFile = getRootName(globaldata->getFastaFile()) + "dist";
+ outputFile = getRootName(fastafile) + "dist";
remove(outputFile.c_str());
}
projects / mothur.git / blobdiff