X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterclassic.cpp;h=0048dc6053d0bab06130eeaa6ab5d10b576aeb48;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=0e48690dc57059bb2ab1af1df3da5df0ea71efa4;hpb=89f19f9c6ab89c2f6c7c6921a328ae87bce6f8e3;p=mothur.git

diff --git a/clusterclassic.cpp b/clusterclassic.cpp
index 0e48690..0048dc6 100644
--- a/clusterclassic.cpp
+++ b/clusterclassic.cpp
@@ -11,7 +11,7 @@
 #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
 	
@@ -19,7 +19,6 @@ ClusterClassic::ClusterClassic(float c, string f) : method(f), smallDist(1e6), n
 		cutoff = c;
 		aboveCutoff = cutoff + 10000.0;
 		m = MothurOut::getInstance();
-		globaldata = GlobalData::getInstance();
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClusterClassic", "ClusterClassic");
@@ -102,7 +101,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
 										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;
@@ -124,7 +123,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
 										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; }
@@ -162,7 +161,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
 										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; }
@@ -185,7 +184,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
 										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; }
@@ -215,6 +214,8 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
 		rabund = new RAbundVector(list->getRAbundVector());
 		
 		fileHandle.close();
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ClusterClassic", "readPhylipFile");
@@ -279,10 +280,10 @@ void ClusterClassic::clusterBins(){
 
 		rabund->set(smallRow, rabund->get(smallRow)+rabund->get(smallCol));	
 		rabund->set(smallCol, 0);	
-		for (int i = smallCol+1; i < rabund->size(); i++) {
+		/*for (int i = smallCol+1; i < rabund->size(); i++) {
 			rabund->set((i-1), rabund->get(i));
 		}
-		rabund->resize((rabund->size()-1));
+		rabund->resize((rabund->size()-1));*/
 		rabund->setLabel(toString(smallDist));
 
 	//	cout << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol) << endl;
@@ -300,10 +301,10 @@ void ClusterClassic::clusterNames(){
 		
 		list->set(smallRow, list->get(smallRow)+','+list->get(smallCol));
 		list->set(smallCol, "");	
-		for (int i = smallCol+1; i < list->size(); i++) {
+		/*for (int i = smallCol+1; i < list->size(); i++) {
 			list->set((i-1), list->get(i));
 		}
-		list->resize((list->size()-1));
+		list->resize((list->size()-1));*/
 		list->setLabel(toString(smallDist));
 	
 	//	cout << '\t' << list->get(smallRow) << '\t' << list->get(smallCol) << endl;
@@ -356,7 +357,7 @@ void ClusterClassic::update(double& cutOFF){
 		clusterNames();
 		
 		//resize each row
-		for(int i=0;i<nseqs;i++){
+		/*for(int i=0;i<nseqs;i++){
 			for(int j=c+1;j<dMatrix[i].size();j++){
 				dMatrix[i][j-1]=dMatrix[i][j];
 			}
@@ -370,7 +371,7 @@ void ClusterClassic::update(double& cutOFF){
 		}	
 		
 		nseqs--;
-		dMatrix.pop_back();
+		dMatrix.pop_back();*/
 
 	}
 	catch(exception& e) {