#include "nast.hpp"
#include "nastreport.hpp"
+#include "referencedb.h"
//**********************************************************************************************************************
vector<string> AlignCommand::setParameters(){
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
helpString += "The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.";
helpString += "The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.";
helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
+ helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
helpString += "The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.";
helpString += "The align.seqs command should be in the following format:";
helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
//**********************************************************************************************************************
AlignCommand::AlignCommand(string option) {
try {
- abort = false; calledHelp = false;
-
+ abort = false; calledHelp = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
+
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true;}
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
}
}
- //check for required parameters
- templateFileName = validParameter.validFile(parameters, "reference", true);
-
- if (templateFileName == "not found") {
- m->mothurOut("reference is a required parameter for the align.seqs command.");
- m->mothurOutEndLine();
- abort = true;
- }else if (templateFileName == "not open") { abort = true; }
-
candidateFileName = validParameter.validFile(parameters, "fasta", false);
if (candidateFileName == "not found") {
//if there is a current fasta file, use it
temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
flip = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ rdb->save = save;
+ if (save) { //clear out old references
+ rdb->clearMemory();
+ }
+
+ //this has to go after save so that if the user sets save=t and provides no reference we abort
+ templateFileName = validParameter.validFile(parameters, "reference", true);
+ if (templateFileName == "not found") {
+ //check for saved reference sequences
+ if (rdb->referenceSeqs.size() != 0) {
+ templateFileName = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }else if (templateFileName == "not open") { abort = true; }
+ else { if (save) { rdb->setSavedReference(templateFileName); } }
+
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
convert(temp, threshold);