//**********************************************************************************************************************
-vector<string> PairwiseSeqsCommand::getValidParameters(){
+vector<string> PairwiseSeqsCommand::setParameters(){
try {
- string AlignArray[] = {"fasta","align","match","mismatch","gapopen","gapextend", "processors","calc","compress","cutoff","countends","output","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> PairwiseSeqsCommand::getRequiredParameters(){
- try {
- string AlignArray[] = {"fasta"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ 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 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, "PairwiseSeqsCommand", "getRequiredParameters");
+ m->errorOut(e, "PairwiseSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> PairwiseSeqsCommand::getRequiredFiles(){
+string PairwiseSeqsCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n";
+ helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n";
+ helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+ helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
+ helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
+ helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
+ helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
+ helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\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 compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
+ helpString += "The pairwise.seqs command should be in the following format: \n";
+ helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
+ helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "PairwiseSeqsCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
PairwiseSeqsCommand::PairwiseSeqsCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
-
- //valid paramters for this command
- string AlignArray[] = {"fasta","align","match","mismatch","gapopen","gapextend", "processors","cutoff","compress","calc","countends","output","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
if (inputDir == "not found"){ inputDir = ""; }
fastaFileName = validParameter.validFile(parameters, "fasta", false);
- if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the pairwise.seqs command."); m->mothurOutEndLine(); abort = true; }
+ if (fastaFileName == "not found") {
+ //if there is a current fasta file, use it
+ string filename = m->getFastaFile();
+ if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else {
m->splitAtDash(fastaFileName, fastaFileNames);
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
convert(temp, gapExtend);
- 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, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
convert(temp, cutoff);
exit(1);
}
}
-//**********************************************************************************************************************
-PairwiseSeqsCommand::~PairwiseSeqsCommand(){}
-//**********************************************************************************************************************
-
-void PairwiseSeqsCommand::help(){
- try {
- m->mothurOut("The pairwise.seqs command reads a fasta file and creates distance matrix.\n");
- m->mothurOut("The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n");
- m->mothurOut("The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
- m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
- m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
- m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
- m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\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 compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n");
- m->mothurOut("The pairwise.seqs command should be in the following format: \n");
- m->mothurOut("pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n");
- m->mothurOut("Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "help");
- exit(1);
- }
-}
-
-
//**********************************************************************************************************************
int PairwiseSeqsCommand::execute(){
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