X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedordervector.cpp;h=80b8fb9bd45a8596e91afe30fdec3984b2411de6;hp=76eeafa4b519c02b25c8364e19d3d0397ffdcd96;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 76eeafa..80b8fb9 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;
@@ -39,14 +38,50 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 		individual newguy;
 		
 		//read in first row since you know there is at least 1 group.
-		f >> label >> groupN >> num;
+		//are we at the beginning of the file??
+		if (m->saveNextLabel == "") {  
+			f >> label; 
+			
+			//is this a shared file that has headers
+			if (label == "label") { 
+				//gets "group"
+				f >> label; m->gobble(f);
+				
+				//gets "numOtus"
+				f >> label; m->gobble(f);
+				
+				//eat rest of line
+				label = m->getline(f); m->gobble(f);
+				
+				//parse labels to save
+				istringstream iStringStream(label);
+				m->sharedBinLabelsInFile.clear();
+				while(!iStringStream.eof()){
+					if (m->control_pressed) { break; }
+					string temp;
+					iStringStream >> temp;  m->gobble(iStringStream);
+					
+					m->sharedBinLabelsInFile.push_back(temp);
+				}
+				
+				f >> label;
+			}
+		}else { label = m->saveNextLabel; }
+		
+		//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
+		m->currentSharedBinLabels = m->sharedBinLabelsInFile;
+		
+		//read in first row since you know there is at least 1 group.
+		f >> groupN >> num;
+		
 		holdLabel = label;
 		
-		if (globaldata->gGroupmap == NULL) { 
-			//save group in groupmap
-			groupmap->namesOfGroups.push_back(groupN);
-			groupmap->groupIndex[groupN] = 0;
-		}
+		
+		vector<string> allGroups;
+		//save group in groupmap
+		allGroups.push_back(groupN);
+		groupmap->groupIndex[groupN] = 0;
+		
 		
 		for(int i=0;i<num;i++){
 			f >> inputData;
@@ -57,18 +92,20 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 			}
 		}
 		
-		if (f.eof() != true) { f >> nextLabel; }
+		m->gobble(f); 
+		
+		if (!(f.eof())) { f >> nextLabel; }
 		
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (f.eof() != true)) {
 			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
+			allGroups.push_back(groupN);
+			groupmap->groupIndex[groupN] = count;
+			
 			
 			for(int i=0;i<num;i++){
 				f >> inputData;
@@ -79,21 +116,22 @@ SharedOrderVector::SharedOrderVector(ifstream& f) : DataVector() {  //reads in a
 				}
 			}
 			
+			m->gobble(f);
 				
 			if (f.eof() != true) { f >> nextLabel; }
 
 		}
 		
-		//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->saveNextLabel = nextLabel;
+			
+		groupmap->setNamesOfGroups(allGroups);
+		m->setAllGroups(allGroups);
 		
 		updateStats();
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "SharedOrderVector");
+		m->errorOut(e, "SharedOrderVector", "SharedOrderVector");
 		exit(1);
 	}
 }
@@ -163,16 +201,23 @@ 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 +260,7 @@ RAbundVector SharedOrderVector::getRAbundVector(){
 		return rav;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getRAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getRAbundVector");
 		exit(1);
 	}
 }
@@ -235,7 +280,7 @@ 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 +310,7 @@ SharedRAbundVector SharedOrderVector::getSharedRAbundVector(string group) {
 		return sharedRav;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
 		exit(1);
 	}
 }
@@ -276,13 +321,17 @@ vector<SharedRAbundVector*> SharedOrderVector::getSharedRAbundVector() {
 		util = new SharedUtil();
 		vector<SharedRAbundVector*> lookup;
 		
-		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-		util->getSharedVectors(globaldata->Groups, lookup, this);
+		vector<string> Groups = m->getGroups();
+		vector<string> allGroups = m->getAllGroups();
+		util->setGroups(Groups, allGroups);
+		util->getSharedVectors(Groups, lookup, this);
+		m->setGroups(Groups);
+		m->setAllGroups(allGroups);
 		
 		return lookup;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getSharedRAbundVector");
 		exit(1);
 	}
 }
@@ -295,7 +344,7 @@ SharedSAbundVector SharedOrderVector::getSharedSAbundVector(string group) {
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
+		m->errorOut(e, "SharedOrderVector", "getSharedSAbundVector");
 		exit(1);
 	}
 }
@@ -330,7 +379,7 @@ void SharedOrderVector::updateStats(){
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedOrderVector", "updateStats");
+		m->errorOut(e, "SharedOrderVector", "updateStats");
 		exit(1);
 	}
 }