exit(1);
}
}
+//**********************************************************************************************************************
+string CreateDatabaseCommand::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 == "database") { outputFileName = "database"; }
+ 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, "CreateDatabaseCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
CreateDatabaseCommand::CreateDatabaseCommand(){
try {
//names redundants to uniques. backwards to how we normally do it, but each bin is the list file will be a key entry in the map.
map<string, string> repNames;
- int numUniqueNamesFile = readNames(repNames);
+ int numUniqueNamesFile = m->readNames(repnamesfile, repNames);
//are there the same number of otus in the fasta and name files
if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
if (m->control_pressed) { delete list; if (groupfile != "") { delete groupmap; } return 0; }
if (outputDir == "") { outputDir += m->hasPath(listfile); }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + "database";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("database");
outputNames.push_back(outputFileName); outputTypes["database"].push_back(outputFileName);
ofstream out;
exit(1);
}
}
-/**********************************************************************************************************************/
-int CreateDatabaseCommand::readNames(map<string, string>& nameMap) {
- try {
-
- //open input file
- ifstream in;
- m->openInputFile(repnamesfile, in);
-
- while (!in.eof()) {
- if (m->control_pressed) { break; }
-
- string firstCol, secondCol;
- in >> firstCol >> secondCol; m->gobble(in);
-
- nameMap[secondCol] = firstCol;
- }
- in.close();
-
- return nameMap.size();
-
- }
- catch(exception& e) {
- m->errorOut(e, "CreateDatabaseCommand", "readNames");
- exit(1);
- }
-}
//**********************************************************************************************************************
ListVector* CreateDatabaseCommand::getList(){
try {