#include "onegapdist.h"
#include "onegapignore.h"
-
//**********************************************************************************************************************
-vector<string> DistanceCommand::getValidParameters(){
+vector<string> DistanceCommand::setParameters(){
try {
- string Array[] = {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir","compress"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(pcolumn);
+ CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn",false,false); parameters.push_back(poldfasta);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "",false,false); parameters.push_back(pcalc);
+ CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pcountends);
+ CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcompress);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "getValidParameters");
+ m->errorOut(e, "DistanceCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-DistanceCommand::DistanceCommand(){
+string DistanceCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["phylip"] = tempOutNames;
- outputTypes["column"] = tempOutNames;
+ string helpString = "";
+ helpString += "The dist.seqs command reads a file containing sequences and creates a distance file.\n";
+ helpString += "The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors. \n";
+ helpString += "The fasta parameter is required, unless you have a valid current fasta file.\n";
+ helpString += "The oldfasta and column parameters allow you to append the distances calculated to the column file.\n";
+ helpString += "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";
+ helpString += "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";
+ helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
+ helpString += "The processors parameter allows you to specify number of processors to use. The default is 1.\n";
+ helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
+ helpString += "The dist.seqs command should be in the following format: \n";
+ helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
+ helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "DistanceCommand");
+ m->errorOut(e, "DistanceCommand", "getHelpString");
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(){
+DistanceCommand::DistanceCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "getRequiredFiles");
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
exit(1);
}
}
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir","compress"};
-
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the dist.seqs command."); m->mothurOutEndLine(); abort = true; }
- else if (fastafile == "not open") { abort = true; }
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
+ ifstream inFASTA;
+ m->openInputFile(fastafile, inFASTA);
+ alignDB = SequenceDB(inFASTA);
+ inFASTA.close();
+ }else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else if (fastafile == "not open") { abort = true; }
else{
ifstream inFASTA;
m->openInputFile(fastafile, inFASTA);
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);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
convert(temp, compress);
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-DistanceCommand::~DistanceCommand(){}
-
-//**********************************************************************************************************************
-
-void DistanceCommand::help(){
- try {
- m->mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
- m->mothurOut("The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors. \n");
- m->mothurOut("The fasta parameter is required.\n");
- m->mothurOut("The oldfasta and column parameters allow you to append the distances calculated to the column file.\n");
- m->mothurOut("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");
- m->mothurOut("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");
- m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
- m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
- m->mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
- m->mothurOut("The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n");
- m->mothurOut("The dist.seqs command should be in the following format: \n");
- m->mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
- m->mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "help");
- exit(1);
- }
-}
//**********************************************************************************************************************
int DistanceCommand::execute(){
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