}
}
//**********************************************************************************************************************
+string AlignCheckCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "aligncheck") { outputFileName = "align.check"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(){
try {
abort = true; calledHelp = true;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
+ if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") {
fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " 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->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
-
+
+ if ((namefile == "") && (fastafile != "")){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
}
}
m->openInputFile(fastafile, in);
ofstream out;
- string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+ string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
m->openOutputFile(outfile, out);
int count = 0;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
in.close();
out.close();
- if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
sort(pound.begin(), pound.end());
sort(dash.begin(), dash.end());
int ptile97_5 = int(size * 0.975);
int ptile100 = size - 1;
- if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
m->mothurOutEndLine();
m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();