X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqnoise.cpp;h=8c712c3ab8bb08c8b8e9282e59e97b03c77d29fc;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=578daafffe4273fae5564781d1407ddc0bd869aa;hpb=e0dc0bcef2a0f7e1f63abb531dbb1ad533da98ca;p=mothur.git

diff --git a/seqnoise.cpp b/seqnoise.cpp
index 578daaf..8c712c3 100644
--- a/seqnoise.cpp
+++ b/seqnoise.cpp
@@ -9,6 +9,8 @@
 
 #include "seqnoise.h"
 #include "sequence.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
 
 #define MIN_DELTA 1.0e-6
 #define MIN_ITER 20
@@ -138,69 +140,132 @@ int seqNoise::getListData(string listFileName, double cutOff, vector<int>& otuDa
 		
 		ifstream listFile;
 		m->openInputFile(listFileName, listFile);
-		double threshold;
-		int numOTUs;
 		
-		if(listFile.peek() == 'u'){	m->getline(listFile);	}
+		bool adjustCutoff = true;
+        string lastLabel = "";
+        
+		while(!listFile.eof()){
+            
+            ListVector list(listFile); m->gobble(listFile); //10/18/13 - change to reading with listvector to accomodate changes to the listfiel format. ie. adding header labels.
+            
+            string thisLabel = list.getLabel();
+            lastLabel = thisLabel;
+            
+            if (thisLabel == "unique") {} //skip to next label in listfile
+            else {
+                double threshold;
+                m->mothurConvert(thisLabel, threshold);
+                
+                if(threshold < cutOff){} //skip to next label in listfile
+                else{
+                    adjustCutoff = false;
+                    int numOTUs = list.getNumBins();
+                    otuFreq.resize(numOTUs, 0);
+                    
+                    for(int i=0;i<numOTUs;i++){
+                        
+                        if (m->control_pressed) { return 0; }
+                        
+                        string otu = list.get(i);
+                        int count = 0;
+                        string number = "";
+                        
+                        for(int j=0;j<otu.size();j++){
+                            if(otu[j] != ','){
+                                number += otu[j];
+                            }
+                            else{
+                                int index = atoi(number.c_str());
+                                otuData[index] = i;
+                                count++;
+                                number = "";
+                            }
+                        }
+                        
+                        int index = atoi(number.c_str());
+                        otuData[index] = i;
+                        count++;
+                        
+                        otuFreq[i] = count;
+                    }
+                    
+                    otuBySeqLookUp.resize(numOTUs);
+                    
+                    int numSeqs = otuData.size();
+                    
+                    for(int i=0;i<numSeqs;i++){
+                        if (m->control_pressed) { return 0; }
+                        otuBySeqLookUp[otuData[i]].push_back(i);
+                    }
+                    for(int i=0;i<numOTUs;i++){
+                        if (m->control_pressed) { return 0; }
+                        for(int j=otuBySeqLookUp[i].size();j<numSeqs;j++){
+                            otuBySeqLookUp[i].push_back(0);
+                        }
+                    }
+                    
+                    break;
+                }
+            }
+		}
+		
+		listFile.close();
 		
-		while(listFile){
-			listFile >> threshold;
+		//the listfile does not contain a threshold greater than the cutoff so use highest value
+		if (adjustCutoff) {
+            
+            InputData input(listFileName, "list");
+            ListVector* list = input.getListVector(lastLabel);
+            
+            int numOTUs = list->getNumBins();
+            otuFreq.resize(numOTUs, 0);
 			
-			if(threshold < cutOff){
-				m->getline(listFile);	
-			}
-			else{
-				listFile >> numOTUs;
-				otuFreq.resize(numOTUs, 0);
+			for(int i=0;i<numOTUs;i++){
 				
-				for(int i=0;i<numOTUs;i++){
-					
-					if (m->control_pressed) { return 0; }
-					
-					string otu;
-					listFile >> otu;
-					
-					int count = 0;
-					
-					string number = "";
-					
-					for(int j=0;j<otu.size();j++){
-						if(otu[j] != ','){
-							number += otu[j];
-						}
-						else{
-							int index = atoi(number.c_str());
-							otuData[index] = i;
-							count++;
-							number = "";
-						}
-					}
-					
-					int index = atoi(number.c_str());
-					otuData[index] = i;
-					count++;
-					
-					otuFreq[i] = count;
-				}
+				if (m->control_pressed) { return 0; }
 				
-				otuBySeqLookUp.resize(numOTUs);
+				string otu = list->get(i);
 				
-				int numSeqs = otuData.size();
+				int count = 0;
+				string number = "";
 				
-				for(int i=0;i<numSeqs;i++){
-					if (m->control_pressed) { return 0; }
-					otuBySeqLookUp[otuData[i]].push_back(i);
-				}
-				for(int i=0;i<numOTUs;i++){
-					if (m->control_pressed) { return 0; }
-					for(int j=otuBySeqLookUp[i].size();j<numSeqs;j++){
-						otuBySeqLookUp[i].push_back(0);
+				for(int j=0;j<otu.size();j++){
+					if(otu[j] != ','){
+						number += otu[j];
+					}
+					else{
+						int index = atoi(number.c_str());
+						otuData[index] = i;
+						count++;
+						number = "";
 					}
 				}
 				
-				break;
+				int index = atoi(number.c_str());
+				otuData[index] = i;
+				count++;
+				
+				otuFreq[i] = count;
 			}
+			
+			otuBySeqLookUp.resize(numOTUs);
+			
+			int numSeqs = otuData.size();
+			
+			for(int i=0;i<numSeqs;i++){
+				if (m->control_pressed) { return 0; }
+				otuBySeqLookUp[otuData[i]].push_back(i);
+			}
+			for(int i=0;i<numOTUs;i++){
+				if (m->control_pressed) { return 0; }
+				for(int j=otuBySeqLookUp[i].size();j<numSeqs;j++){
+					otuBySeqLookUp[i].push_back(0);
+				}
+			}
+			
+            delete list;
 		}
+		
 		return 0;
 	}
 	catch(exception& e) {
@@ -956,4 +1021,4 @@ int main(int argc, char *argv[]){
 	return 0;
 }
 
-/**************************************************************************************************/
+**************************************************************************************************/