//**********************************************************************************************************************
vector<string> AlignCheckCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
- CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","aligncheck",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pmap);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount);
+ 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); }
}
}
//**********************************************************************************************************************
-string AlignCheckCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string AlignCheckCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //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);
- }
+ if (type == "aligncheck") { pattern = "[filename],align.check"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "AlignCheckCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(){
if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, false);
nameMap = ct.getNameMap();
}
m->openInputFile(fastafile, in);
ofstream out;
- string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outfile = getOutputFileName("aligncheck",variables);
m->openOutputFile(outfile, out);
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outfile); m->mothurOutEndLine(); outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
m->mothurOutEndLine();