X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundfloatvector.cpp;h=9eeb0f21bf3626620806c49372ab36efd0ff0831;hp=8abf92023620096dd820dbf2f16fcfb1fe34464c;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f

diff --git a/sharedrabundfloatvector.cpp b/sharedrabundfloatvector.cpp
index 8abf920..9eeb0f2 100644
--- a/sharedrabundfloatvector.cpp
+++ b/sharedrabundfloatvector.cpp
@@ -48,7 +48,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		//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"
@@ -62,25 +62,45 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 				
 				//parse labels to save
 				istringstream iStringStream(label);
-				m->binLabelsInFile.clear();
+				m->sharedBinLabelsInFile.clear();
 				while(!iStringStream.eof()){
 					if (m->control_pressed) { break; }
 					string temp;
 					iStringStream >> temp;  m->gobble(iStringStream);
-					
-					m->binLabelsInFile.push_back(temp);
+                    
+					m->sharedBinLabelsInFile.push_back(temp);
 				}
 				
-				f >> label;
-			}
-		}else { label = m->saveNextLabel; }
+				f >> label >> groupN >> num;
+			}else {
+                //read in first row since you know there is at least 1 group.
+                f >> groupN >> num;
+                
+                //make binlabels because we don't have any
+                string snumBins = toString(num);
+                m->sharedBinLabelsInFile.clear();
+                for (int i = 0; i < num; i++) {  
+                    //if there is a bin label use it otherwise make one
+                    string binLabel = "Otu";
+                    string sbinNumber = toString(i+1);
+                    if (sbinNumber.length() < snumBins.length()) { 
+                        int diff = snumBins.length() - sbinNumber.length();
+                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                    }
+                    binLabel += sbinNumber;
+                    m->sharedBinLabelsInFile.push_back(binLabel);
+                }
+            }
+		}else { 
+            label = m->saveNextLabel; 
+            
+            //read in first row since you know there is at least 1 group.
+            f >> groupN >> num;
+        }
 		
 		//reset labels, currentLabels may have gotten changed as otus were eliminated because of group choices or sampling
-		m->currentBinLabels = m-> binLabelsInFile;
+		m->currentSharedBinLabels = m->sharedBinLabelsInFile;
 		
-		//read in first row since you know there is at least 1 group.
-		f >> groupN >> num;
-
 		holdLabel = label;
 		
 		//add new vector to lookup
@@ -108,6 +128,7 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		//read the rest of the groups info in
 		while ((nextLabel == holdLabel) && (f.eof() != true)) {
 			f >> groupN >> num;
+            
 			count++;
 			
 			allGroups.push_back(groupN);
@@ -131,7 +152,6 @@ SharedRAbundFloatVector::SharedRAbundFloatVector(ifstream& f) : DataVector(), ma
 		
 		m->saveNextLabel = nextLabel;
 		m->setAllGroups(allGroups);
-	
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedRAbundFloatVector", "SharedRAbundFloatVector");
@@ -171,6 +191,16 @@ float SharedRAbundFloatVector::getAbundance(int index){
 	return data[index].abundance;	
 }
 /***********************************************************************/
+//returns vector of abundances
+vector<float> SharedRAbundFloatVector::getAbundances(){
+    vector<float> abunds;
+    for (int i = 0; i < data.size(); i++) {
+        abunds.push_back(data[i].abundance);
+    }
+    
+	return abunds;
+}
+/***********************************************************************/
 individualFloat SharedRAbundFloatVector::get(int index){
 	return data[index];	
 }
@@ -265,7 +295,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber;
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
 			}
@@ -280,7 +310,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber;
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				output << binLabel << '\t'; 
 			}
@@ -288,7 +318,7 @@ void SharedRAbundFloatVector::printHeaders(ostream& output){
 			output << endl;
 		}
 		
-		m->printedHeaders = true;
+		m->printedSharedHeaders = true;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SharedRAbundVector", "printHeaders");
@@ -520,7 +550,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber; 
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				newBinLabels.push_back(binLabel);
 			}
@@ -529,7 +559,7 @@ int SharedRAbundFloatVector::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 		for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 		
 		thislookup = newLookup;
-		m->currentBinLabels = newBinLabels;
+		m->currentSharedBinLabels = newBinLabels;
 		
 		return 0;