X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedordervector.cpp;h=37cd28315a5c1928e965f7be8eef7ae0ef408692;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=76eeafa4b519c02b25c8364e19d3d0397ffdcd96;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 76eeafa..37cd283 100644
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -28,10 +28,9 @@ SharedOrderVector::SharedOrderVector(string id, vector<individual>  ov) :
 
 SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a shared file
 	try {
-		globaldata = GlobalData::getInstance();
 		maxRank = 0; numBins = 0; numSeqs = 0;
-		
-		if (globaldata->gGroupmap == NULL) {  groupmap = new GroupMap(); }
+				
+		groupmap = new GroupMap(); 
 		
 		int num, inputData, count;
 		count = 0;  numSeqs = 0;
@@ -42,11 +41,11 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 		f >> label >> groupN >> num;
 		holdLabel = label;
 		
-		if (globaldata->gGroupmap == NULL) { 
-			//save group in groupmap
-			groupmap->namesOfGroups.push_back(groupN);
-			groupmap->groupIndex[groupN] = 0;
-		}
+		
+		//save group in groupmap
+		groupmap->namesOfGroups.push_back(groupN);
+		groupmap->groupIndex[groupN] = 0;
+		
 		
 		for(int i=0;i<num;i++){
 			f >> inputData;
@@ -57,6 +56,8 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 			}
 		}
 		
+		m->gobble(f); 
+		
 		if (f.eof() != true) { f >> nextLabel; }
 		
 		//read the rest of the groups info in
@@ -64,11 +65,11 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 			f >> groupN >> num;
 			count++;
 			
-			if (globaldata->gGroupmap == NULL) { 
-				//save group in groupmap
-				groupmap->namesOfGroups.push_back(groupN);
-				groupmap->groupIndex[groupN] = count;
-			}
+			
+			//save group in groupmap
+			groupmap->namesOfGroups.push_back(groupN);
+			groupmap->groupIndex[groupN] = count;
+			
 			
 			for(int i=0;i<num;i++){
 				f >> inputData;
@@ -79,6 +80,7 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 				}
 			}
 			
+			m->gobble(f);
 				
 			if (f.eof() != true) { f >> nextLabel; }
 
@@ -87,13 +89,13 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 		//put file pointer back since you are now at a new distance label
 		for (int i = 0; i < nextLabel.length(); i++) { f.unget();  }
 	
-		if (globaldata->gGroupmap == NULL) { globaldata->gGroupmap = groupmap; }
+		m->namesOfGroups = groupmap->namesOfGroups;
 		
 		updateStats();
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "SharedOrderVector");
+		m->errorOut(e, "SharedOrderVector", "SharedOrderVector");
 		exit(1);
 	}
 }
@@ -163,16 +165,23 @@ void SharedOrderVector::print(ostream& output){
 		output << endl;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "print");
+		m->errorOut(e, "SharedOrderVector", "print");
 		exit(1);
 	}
 }
 
+/***********************************************************************/
 
+void SharedOrderVector::clear(){
+	numBins = 0;
+	maxRank = 0;
+	numSeqs = 0;
+	data.clear();
+}
 /***********************************************************************/
 
 void SharedOrderVector::resize(int){
-	mothurOut("resize() did nothing in class SharedOrderVector");
+	m->mothurOut("resize() did nothing in class SharedOrderVector");
 }
 
 /***********************************************************************/
@@ -215,7 +224,7 @@ RAbundVector SharedOrderVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getRAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -235,7 +244,7 @@ OrderVector SharedOrderVector::getOrderVector(map<string,int>* nameMap = NULL) {
 		return ov;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getOrderVector");
+		m->errorOut(e, "SharedOrderVector", "getOrderVector");
 		exit(1);
 	}
 }
@@ -265,7 +274,7 @@ SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
 		return sharedRav;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
 		exit(1);
 	}
 }
@@ -276,13 +285,13 @@ vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
 		util = new SharedUtil();
 		vector<SharedRAbundVector*> lookup;
 		
-		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-		util->getSharedVectors(globaldata->Groups, lookup, this);
+		util->setGroups(m->Groups, m->namesOfGroups);
+		util->getSharedVectors(m->Groups, lookup, this);
 		
 		return lookup;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
 		exit(1);
 	}
 }
@@ -295,7 +304,7 @@ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
 		exit(1);
 	}
 }
@@ -330,7 +339,7 @@ void SharedOrderVector::updateStats(){
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "updateStats");
+		m->errorOut(e, "SharedOrderVector", "updateStats");
 		exit(1);
 	}
 }