chimera.seqs pintail is working.

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index f2dd821acf896302bc4b265cdb3bd8a03e89428d..86bc7527b9ae1458ed1a9fb81be99faf1728343e 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -92,7 +92,7 @@ void Bellerophon::getChimeras() {
                distCalculator = new eachGapDist();
                
                //read in sequences
-               readSeqs();
+               //seqs = readSeqs(fastafile);
                
                int numSeqs = seqs.size();
                
@@ -173,6 +173,7 @@ cout << "increment = " << increment << endl;
                                vector<SeqMap> distMapLeft;
                                
                                // Create a data structure to quickly access the distance information.
+                               //this is from thallingers reimplementation on get.oturep
                                // It consists of a vector of distance maps, where each map contains
                                // all distances of a certain sequence. Vector and maps are accessed
                                // via the index of a sequence in the distance matrix
@@ -231,31 +232,6 @@ cout << "increment = " << increment << endl;
        }
 }
 
-//***************************************************************************************************************
-void Bellerophon::readSeqs(){
-       try {
-               ifstream inFASTA;
-               openInputFile(fastafile, inFASTA);
-               
-               //read in seqs and store in vector
-               while(!inFASTA.eof()){
-                       Sequence current(inFASTA);
-                       
-                       if (current.getAligned() == "") { current.setAligned(current.getUnaligned()); }
-                       
-                       seqs.push_back(current);
-                       
-                       gobble(inFASTA);
-               }
-               inFASTA.close();
-
-       }
-       catch(exception& e) {
-               errorOut(e, "Bellerophon", "readSeqs");
-               exit(1);
-       }
-}
-
 /***************************************************************************************************************/
 int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
        try {
@@ -272,8 +248,7 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
                                
                        }
                }
-                       
-       
+               
                return 1;
        }
        catch(exception& e) {