/***********************************************************************/
-ReadCluster::ReadCluster(string distfile, float c){
+ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
globaldata = GlobalData::getInstance();
m = MothurOut::getInstance();
distFile = distfile;
cutoff = c;
+ outputDir = o;
+ sortWanted = s;
+ list = NULL;
}
/***********************************************************************/
if (m->control_pressed) { return 0; }
- OutPutFile = sortFile(distFile);
+ if (sortWanted) { OutPutFile = sortFile(distFile, outputDir); }
+ else { OutPutFile = distFile; } //for use by clusters splitMatrix to convert a phylip matrix to column
return 0;
ofstream out;
string tempFile = distFile + ".column.temp";
- openInputFile(distFile, in);
+ openInputFile(distFile, in); gobble(in);
openOutputFile(tempFile, out);
float distance;
list->setLabel("0");
in.close();
out.close();
-
+
if(nameMap == NULL){
nameMap = new NameAssignment();
for(int i=0;i<matrixNames.size();i++){
remove(tempFile.c_str());
distFile = outputFile;
-
+
if (m->control_pressed) { remove(outputFile.c_str()); }
return 0;