else {
//valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport", "accnos", "list"};
+ string Array[] = {"fasta","name", "group", "alignreport", "accnos", "list","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //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 = ""; }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("alignreport");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["alignreport"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("accnos");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["accnos"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+ }
+
+
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "not open") { abort = true; }
if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "")) { mothurOut("You must provide one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; }
- if (parameters.size() > 2) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; }
+ int okay = 2;
+ if (outputDir != "") { okay++; }
+
+ if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; }
}
}
//**********************************************************************************************************************
void GetSeqsCommand::readFasta(){
try {
- string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile);
+ if (outputDir == "") { outputDir += hasPath(fastafile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile);
ofstream out;
openOutputFile(outputFileName, out);
//**********************************************************************************************************************
void GetSeqsCommand::readList(){
try {
- string outputFileName = getRootName(listfile) + "pick" + getExtension(listfile);
+ if (outputDir == "") { outputDir += hasPath(listfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" + getExtension(listfile);
ofstream out;
openOutputFile(outputFileName, out);
//**********************************************************************************************************************
void GetSeqsCommand::readName(){
try {
-
- string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
+ if (outputDir == "") { outputDir += hasPath(namefile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
ofstream out;
openOutputFile(outputFileName, out);
//**********************************************************************************************************************
void GetSeqsCommand::readGroup(){
try {
-
- string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
+ if (outputDir == "") { outputDir += hasPath(groupfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
ofstream out;
openOutputFile(outputFileName, out);
//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
void GetSeqsCommand::readAlign(){
try {
- string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
+ if (outputDir == "") { outputDir += hasPath(alignfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
ofstream out;
openOutputFile(outputFileName, out);