#include "progress.hpp"
/***********************************************************************/
-ClusterClassic::ClusterClassic(float c, string f) : method(f), smallDist(1e6), nseqs(0) {
+ClusterClassic::ClusterClassic(float c, string f, bool s) : method(f), smallDist(1e6), nseqs(0), sim(s) {
try {
mapWanted = false; //set to true by mgcluster to speed up overlap merge
cutoff = c;
aboveCutoff = cutoff + 10000.0;
m = MothurOut::getInstance();
- globaldata = GlobalData::getInstance();
}
catch(exception& e) {
m->errorOut(e, "ClusterClassic", "ClusterClassic");
fileHandle >> distance;
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
//if(distance < cutoff){
dMatrix[i][j] = distance;
if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
//if(distance < cutoff){
if (distance < smallDist) { smallDist = distance; }
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(j < i){
if (distance < smallDist) { smallDist = distance; }
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
if (distance == -1) { distance = 1000000; }
- else if (globaldata->sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(j < i){
if (distance < smallDist) { smallDist = distance; }
rabund = new RAbundVector(list->getRAbundVector());
fileHandle.close();
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "ClusterClassic", "readPhylipFile");