last changes before move

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 86bc7527b9ae1458ed1a9fb81be99faf1728343e..5e219d49c9c6c0b41a80614d347fefbbf3470350 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -80,7 +80,7 @@ void Bellerophon::getChimeras() {
                
                //do soft filter
                if (filter)  {
-                       string optionString = "fasta=" + fastafile + ", soft=50, vertical=F";
+                       string optionString = "fasta=" + fastafile + ", soft=50";
                        filterSeqs = new FilterSeqsCommand(optionString);
                        filterSeqs->execute();
                        delete filterSeqs;
@@ -92,39 +92,39 @@ void Bellerophon::getChimeras() {
                distCalculator = new eachGapDist();
                
                //read in sequences
-               //seqs = readSeqs(fastafile);
+               seqs = readSeqs(fastafile);
                
                int numSeqs = seqs.size();
                
                if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); exit(1); }
                
                //set default window to 25% of sequence length
-               string seq0 = seqs[0].getAligned();
+               string seq0 = seqs[0]->getAligned();
                if (window == 0) { window = seq0.length() / 4;  }
                else if (window > (seq0.length() / 2)) {  
                        mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); mothurOutEndLine();
                        window = (seq0.length() / 2);
                }
                
-               if (increment > (seqs[0].getAlignLength() - (2*window))) { 
+               if (increment > (seqs[0]->getAlignLength() - (2*window))) { 
                        if (increment != 10) {
                        
                                mothurOut("You have selected a increment that is too large. I will use the default."); mothurOutEndLine();
                                increment = 10;
-                               if (increment > (seqs[0].getAlignLength() - (2*window))) {  increment = 0;  }
+                               if (increment > (seqs[0]->getAlignLength() - (2*window))) {  increment = 0;  }
                                
                        }else{ increment = 0; }
                }
 cout << "increment = " << increment << endl;           
                if (increment == 0) { iters = 1; }
-               else { iters = ((seqs[0].getAlignLength() - (2*window)) / increment); }
+               else { iters = ((seqs[0]->getAlignLength() - (2*window)) / increment); }
                
                //initialize pref
                pref.resize(numSeqs);  
                
                for (int i = 0; i < numSeqs; i++ ) { 
                        pref[i].leftParent.resize(2); pref[i].rightParent.resize(2); pref[i].score.resize(2);   pref[i].closestLeft.resize(2); pref[i].closestRight.resize(3);
-                       pref[i].name = seqs[i].getName();
+                       pref[i].name = seqs[i]->getName();
                        pref[i].score[0] = 0.0;  pref[i].score[1] = 0.0; 
                        pref[i].closestLeft[0] = 100000.0;  pref[i].closestLeft[1] = 100000.0;  
                        pref[i].closestRight[0] = 100000.0;  pref[i].closestRight[1] = 100000.0;  
@@ -140,16 +140,16 @@ cout << "increment = " << increment << endl;
                                for (int i = 0; i < seqs.size(); i++) {
 //cout << "whole = " << seqs[i].getAligned() << endl;
                                        //save left side
-                                       string seqLeft = seqs[i].getAligned().substr(midpoint-window, window);
+                                       string seqLeft = seqs[i]->getAligned().substr(midpoint-window, window);
                                        Sequence tempLeft;
-                                       tempLeft.setName(seqs[i].getName());
+                                       tempLeft.setName(seqs[i]->getName());
                                        tempLeft.setAligned(seqLeft);
                                        left.push_back(tempLeft);
 //cout << "left = " << tempLeft.getAligned() << endl;                  
                                        //save right side
-                                       string seqRight = seqs[i].getAligned().substr(midpoint, window);
+                                       string seqRight = seqs[i]->getAligned().substr(midpoint, window);
                                        Sequence tempRight;
-                                       tempRight.setName(seqs[i].getName());
+                                       tempRight.setName(seqs[i]->getName());
                                        tempRight.setAligned(seqRight);
                                        right.push_back(tempRight);
 //cout << "right = " << seqRight << endl;      
@@ -217,6 +217,8 @@ cout << "increment = " << increment << endl;
                        //how much higher or lower is this than expected
                        pref[i].score[0] = pref[i].score[0] / expectedPercent;
                        
+                       
+                       
                }
                
                
@@ -310,24 +312,24 @@ void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right,
                                        if (itL->second < pref[i].closestLeft[1]) {  
 
                                                pref[i].closestLeft[1] = itL->second;
-                                               pref[i].leftParent[1] = seqs[j].getName();
+                                               pref[i].leftParent[1] = seqs[j]->getName();
 //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;        
                                        if (itL->second < pref[j].closestLeft[1]) { 
                                                pref[j].closestLeft[1] = itL->second;
-                                               pref[j].leftParent[1] = seqs[i].getName();
+                                               pref[j].leftParent[1] = seqs[i]->getName();
 //cout << "updating closest left to " << pref[j].leftParent[1] << endl;
                                        }
                                        
                                        //are you the closest right sequence
                                        if (itR->second < pref[i].closestRight[1]) {   
                                                pref[i].closestRight[1] = itR->second;
-                                               pref[i].rightParent[1] = seqs[j].getName();
+                                               pref[i].rightParent[1] = seqs[j]->getName();
                                        }
                                        if (itR->second < pref[j].closestRight[1]) {   
                                                pref[j].closestRight[1] = itR->second;
-                                               pref[j].rightParent[1] = seqs[i].getName();
+                                               pref[j].rightParent[1] = seqs[i]->getName();
                                        }
                                        
                                }