if (columnfile != "") {
if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
}
-
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
//get user cutoff and precision or use defaults
else if (format == "matrix") {
groupMap = new GroupMap(groupfile);
groupMap->readMap();
+
if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
globaldata->gGroupmap = groupMap;
}
ReadDistCommand::~ReadDistCommand(){
if (abort == false) {
- if (format != "matrix") { delete read; delete nameMap; }
+ if (format != "matrix") {
+ delete read;
+ delete nameMap;
+ }
}
}
if (abort == true) { return 0; }
- //time_t start = time(NULL);
+ time_t start = time(NULL);
size_t numDists = 0;
if (format == "matrix") {
if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix; }
globaldata->gSparseMatrix = read->getMatrix();
numDists = globaldata->gSparseMatrix->getNNodes();
-
+
int lines = cutoff / (1.0/precision);
vector<float> dist_cutoff(lines+1,0);
for (int i = 0; i <= lines;i++) {
// }
//mothurOut(dist_string); mothurOutEndLine(); mothurOut(count_string); mothurOutEndLine();
}
- //mothurOut("It took " + toString(time(NULL) - start) + " secs to read " + toString(numDists) + " distances (cutoff: " + toString(cutoff) + ")"); mothurOutEndLine();
+ mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); mothurOutEndLine();
return 0;
}