else {
//valid paramters for this command
- string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing"};
+ string Array[] = {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing","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;
}
globaldata->newRead();
+ //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("phylip");
+ //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["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //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["column"] = 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; }
+ }
+ }
+
+ //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 = ""; }
+
//check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
if (abort == false) {
-
- fileroot = getRootName(distfile);
+
+ if (outputDir == "") { outputDir += hasPath(distfile); }
+ fileroot = outputDir + getRootName(getSimpleName(distfile));
if (method == "furthest") { tag = "fn"; }
else if (method == "nearest") { tag = "nn"; }
print_start = true;
start = time(NULL);
-
- ifstream in;
- openInputFile(distfile, in);
- string firstName, secondName;
- float distance;
-
- cluster = new HCluster(rabund, list, method);
+
+ cluster = new HCluster(rabund, list, method, distfile, globaldata->nameMap, cutoff);
vector<seqDist> seqs; seqs.resize(1); // to start loop
while (seqs.size() != 0){
- seqs = cluster->getSeqs(in, globaldata->nameMap, cutoff);
+ seqs = cluster->getSeqs();
for (int i = 0; i < seqs.size(); i++) { //-1 means skip me
- if (print_start && isTrue(timing)) {
- mothurOut("Clustering (" + tag + ") dist " + toString(distance) + "/"
- + toString(roundDist(distance, precision))
- + "\t(precision: " + toString(precision) + ")");
- cout.flush();
- print_start = false;
- }
-
-
if (seqs[i].seq1 != seqs[i].seq2) {
cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
float rndDist = roundDist(seqs[i].dist, precision);
-
+
if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
printData("unique");
}
else if((rndDist != rndPreviousDist)){
printData(toString(rndPreviousDist, length-1));
}
-
+
previousDist = seqs[i].dist;
rndPreviousDist = rndDist;
oldRAbund = *rabund;
}
}
}
-
- in.close();
- if (print_start && isTrue(timing)) {
- //mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist)
- //+ "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
- cout.flush();
- print_start = false;
- }
-
if(previousDist <= 0.0000){
printData("unique");
}