working on pam

[mothur.git] / seqnoise.cpp

diff --git a/seqnoise.cpp b/seqnoise.cpp
index 8e7a4395fbf20009d135502fde3774b2592a9440..8c712c3ab8bb08c8b8e9282e59e97b03c77d29fc 100644 (file)
--- 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
@@ -138,91 +140,93 @@ int seqNoise::getListData(string listFileName, double cutOff, vector<int>& otuDa
                
                ifstream listFile;
                m->openInputFile(listFileName, listFile);
-               double threshold;
-               int numOTUs;
-               string line = "";
-               bool adjustCutoff = true;
-               
-               if(listFile.peek() == 'u'){     m->getline(listFile);   }
                
-               while(listFile){
-                       listFile >> threshold;
-                       
-                       if(threshold < cutOff){
-                               line = m->getline(listFile); m->gobble(listFile);
-                       }
-                       else{
-                               adjustCutoff = false;
-                               listFile >> numOTUs;
-                               otuFreq.resize(numOTUs, 0);
-                               
-                               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;
-                               }
-                               
-                               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;
-                       }
+               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();
                
                //the listfile does not contain a threshold greater than the cutoff so use highest value
                if (adjustCutoff) {
-                       istringstream iss (line,istringstream::in);
-                       
-                       iss >> numOTUs;
-                       otuFreq.resize(numOTUs, 0);
+            
+            InputData input(listFileName, "list");
+            ListVector* list = input.getListVector(lastLabel);
+            
+            int numOTUs = list->getNumBins();
+            otuFreq.resize(numOTUs, 0);
                        
                        for(int i=0;i<numOTUs;i++){
                                
                                if (m->control_pressed) { return 0; }
                                
-                               string otu;
-                               iss >> otu;
+                               string otu = list->get(i);
                                
                                int count = 0;
-                               
                                string number = "";
                                
                                for(int j=0;j<otu.size();j++){
@@ -259,6 +263,7 @@ int seqNoise::getListData(string listFileName, double cutOff, vector<int>& otuDa
                                }
                        }
                        
+            delete list;
                }
                
                return 0;