//**********************************************************************************************************************
vector<string> ChimeraCheckCommand::setParameters(){
try {
- CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter psvg("svg", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psvg);
- CommandParameter pincrement("increment", "Number", "", "10", "", "", "",false,false); parameters.push_back(pincrement);
- CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
- CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter psvg("svg", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psvg);
+ CommandParameter pincrement("increment", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pincrement);
+ CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
-string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string ChimeraCheckCommand::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 == "chimera") { outputFileName = "chimeracheck.chimeras"; }
- 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, "ChimeraCcodeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "chimera") { pattern = "[filename],chimeracheck.chimeras"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCheckCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(){
if (m->control_pressed) { delete chimera; return 0; }
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]));
+ string outputFileName = getOutputFileName("chimera", variables);
outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
#ifdef USE_MPI
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
- count++;
+ if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); }
out.close();
inFASTA.close();
delete candidateSeq;
//report progress
- if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; }
}
//report progress
- if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); }
+ if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; }
return 0;
}