}
/***********************************************************************/
-SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, string t, int p, string output){
+SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float cu, string t, int p, string output){
m = MothurOut::getInstance();
fastafile = ffile;
namefile = name;
taxFile = tax;
- cutoff = c;
+ cutoff = c; //tax level cutoff
+ distCutoff = cu; //for fasta method if you are creating distance matrix you need a cutoff for that
method = t;
processors = p;
outputDir = output;
//process each distance file
for (int i = 0; i < numGroups; i++) {
- string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(cutoff);
+ string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
Command* command = new DistanceCommand(options);
command->execute();
for(int i=0;i<numGroups;i++){
string tempNameFile = namefile + "." + toString(i) + ".temp";
+ if (outputDir == "") { outputDir = m->hasPath(fastafile); }
string tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
//if there are valid distances