else {
//valid paramters for this command
- string Array[] = {"fasta", "phylip", "calc", "countends", "cutoff", "processors"};
+ string Array[] = {"fasta", "phylip", "calc", "countends", "cutoff", "processors", "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 it2;
//check to make sure all parameters are valid for command
- for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
+ for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
+ //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;
+ it2 = parameters.find("fasta");
+ //user has given a template file
+ if(it2 != parameters.end()){
+ path = hasPath(it2->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it2->second; }
+ }
+ }
+
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not found") { mothurOut("fasta is a required parameter for the dist.seqs command."); mothurOutEndLine(); abort = true; }
alignDB = SequenceDB(inFASTA);
inFASTA.close();
}
+
+ //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 += hasPath(fastafile); //if user entered a file with a path then preserve it
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
//doses the user want the phylip formatted file as well
if (isTrue(phylip) == true) {
- outputFile = getRootName(fastafile) + "phylip.dist";
+ outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
remove(outputFile.c_str());
//output numSeqs to phylip formatted dist file
}else { //user wants column format
- outputFile = getRootName(fastafile) + "dist";
+ outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "dist";
remove(outputFile.c_str());
}
- //# if defined (_WIN32)
- //figure out how to implement the fork and wait commands in windows
- // driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile, cutoff);
- //# endif
-
-
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//if you don't need to fork anything
if(processors == 1){
outFile << setprecision(4);
if(isTrue(phylip) && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
+
for(int i=startLine;i<endLine;i++){
- if(isTrue(phylip)) { outFile << alignDB.get(i).getName() << '\t'; }
+ if(isTrue(phylip)) {
+ string name = alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+ outFile << name << '\t';
+ }
for(int j=0;j<i;j++){
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
}
}
-/**************************************************************************************************/
+/**************************************************************************************************
void DistanceCommand::appendFiles(string temp, string filename) {
try{
ofstream output;