added getline function to mothur and modified places where we use getline to use...

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index b451721ca8a0d951b8e01ed5b398dd3b94dbe22a..a334ea31ccc2a7fd0334f687d3f84c16c00d3494 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -9,6 +9,8 @@
 
 #include "chimeraseqscommand.h"
 #include "eachgapdist.h"
+#include "ignoregaps.h"
+#include "onegapdist.h"
 
 //***************************************************************************************************************
 
@@ -228,13 +230,22 @@ cout << "increment = " << increment << endl;
                
                delete distCalculator;
                
-               //find average pref score across windows
-               //if (increment != 0) {
-                
-                       //for (int i = 0; i < pref.size(); i++) {
-                               //pref[i].score[0] = pref[i].score[0] / iters;
-                       //}
-               //}
+               //rank preference score to eachother
+               float dme = 0.0;
+               float expectedPercent = 1 / (float) (pref.size());
+               
+               for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[0];  }
+       
+               for (int i = 0; i < pref.size(); i++) {
+
+                       //gives the actual percentage of the dme this seq adds
+                       pref[i].score[0] = pref[i].score[0] / dme;
+                       
+                       //how much higher or lower is this than expected
+                       pref[i].score[0] = pref[i].score[0] / expectedPercent;
+                       
+               }
+               
                
                //sort Preferences highest to lowest
                sort(pref.begin(), pref.end(), comparePref);
@@ -364,8 +375,8 @@ void ChimeraSeqsCommand::generatePreferences(vector<SeqMap> left, vector<SeqMap>
                                
                                itL = currentLeft.find(j);
                                itR = currentRight.find(j);
-cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
-cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
+//cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
+//cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
                                
                                //if you can find this entry update the preferences
                                if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
@@ -373,31 +384,31 @@ cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
                                        if (!correction) {
                                                pref[i].score[1] += abs((itL->second - itR->second));
                                                pref[j].score[1] += abs((itL->second - itR->second));
-cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
-cout << "abs = " << abs((itL->second - itR->second)) << endl;
-cout << i << " score = " << pref[i].score[1] << endl;
-cout << j << " score = " << pref[j].score[1] << endl;
+//cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
+//cout << "abs = " << abs((itL->second - itR->second)) << endl;
+//cout << i << " score = " << pref[i].score[1] << endl;
+//cout << j << " score = " << pref[j].score[1] << endl;
                                        }else {
                                                pref[i].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
                                                pref[j].score[1] += abs((sqrt(itL->second) - sqrt(itR->second)));
-cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
-cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
-cout << i << " score = " << pref[i].score[1] << endl;
-cout << j << " score = " << pref[j].score[1] << endl;
+//cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
+//cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
+//cout << i << " score = " << pref[i].score[1] << endl;
+//cout << j << " score = " << pref[j].score[1] << endl;
                                        }
-cout << "pref[" << i << "].closestLeft[1] = "  <<      pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;                        
+//cout << "pref[" << i << "].closestLeft[1] = "        <<      pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;                        
                                        //are you the closest left sequence
                                        if (itL->second < pref[i].closestLeft[1]) {  
 
                                                pref[i].closestLeft[1] = itL->second;
                                                pref[i].leftParent[1] = seqs[j].getName();
-cout << "updating closest left to " << pref[i].leftParent[1] << endl;
+//cout << "updating closest left to " << pref[i].leftParent[1] << endl;
                                        }
-cout << "pref[" << j << "].closestLeft[1] = "  <<      pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;        
+//cout << "pref[" << j << "].closestLeft[1] = "        <<      pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;        
                                        if (itL->second < pref[j].closestLeft[1]) { 
                                                pref[j].closestLeft[1] = itL->second;
                                                pref[j].leftParent[1] = seqs[i].getName();
-cout << "updating closest left to " << pref[j].leftParent[1] << endl;
+//cout << "updating closest left to " << pref[j].leftParent[1] << endl;
                                        }
                                        
                                        //are you the closest right sequence
@@ -418,22 +429,25 @@ cout << "updating closest left to " << pref[j].leftParent[1] << endl;
                
                  
                //calculate the dme
+               
                int count0 = 0;
                for (int i = 0; i < pref.size(); i++) {  dme += pref[i].score[1];  if (pref[i].score[1] == 0.0) { count0++; }  }
                
                float expectedPercent = 1 / (float) (pref.size() - count0);
-cout << endl << "dme = " << dme << endl;
+//cout << endl << "dme = " << dme << endl;
                //recalculate prefernences based on dme
                for (int i = 0; i < pref.size(); i++) {
-cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;  
+//cout << "unadjusted pref " << i << " = " << pref[i].score[1] << endl;        
                        // gives the actual percentage of the dme this seq adds
                        pref[i].score[1] = pref[i].score[1] / dme;
                        
                        //how much higher or lower is this than expected
                        pref[i].score[1] = pref[i].score[1] / expectedPercent;
                        
+                       //pref[i].score[1] = dme / (dme - 2 * pref[i].score[1]);
+                       
                        //so a non chimeric sequence would be around 1, and a chimeric would be signifigantly higher.
-cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;                                    
+//cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;                                  
                }
                
                //is this score bigger then the last score
@@ -449,8 +463,6 @@ cout << "adjusted pref " << i << " = " << pref[i].score[1] << endl;
                                pref[i].midpoint = mid;
                        }
                        
-                       //total of preference scores across windows
-                       //pref[i].score[0] += pref[i].score[1];
                }
 
        }