added parameter to chimera.uchime

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 8febfe286c6b14b6d8dd2d373cec860a6f099897..6909f47b1235c72b67ae409907af97346dfa8007 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -40,7 +40,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                        
                        if (pid == 0) {
-                               positions = setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
+                               positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
 
                                //send file positions to all processes
                                for(int i = 1; i < processors; i++) { 
@@ -74,7 +74,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                if (temp.getName() != "") {
                                        templateSequences.push_back(temp);
                                        //save longest base
-                                       if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
+                                       if (temp.getUnaligned().length() >= longest)  { longest = temp.getUnaligned().length()+1; }
                                }
                        }
                        
@@ -84,21 +84,20 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                
        #else
                ifstream fastaFile;
-               openInputFile(fastaFileName, fastaFile);
+               m->openInputFile(fastaFileName, fastaFile);
 
                while (!fastaFile.eof()) {
-                       Sequence temp(fastaFile);  gobble(fastaFile);
+                       Sequence temp(fastaFile);  m->gobble(fastaFile);
                        
                        if (m->control_pressed) {  templateSequences.clear(); break;  }
                        
                        if (temp.getName() != "") {
                                templateSequences.push_back(temp);
                                //save longest base
-                               if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
+                               if (temp.getUnaligned().length() >= longest)  { longest = (temp.getUnaligned().length()+1); }
                        }
                }
                fastaFile.close();
-               
        #endif
        
                numSeqs = templateSequences.size();
@@ -124,13 +123,13 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                ifstream kmerFileTest(kmerDBName.c_str());
                                
                                if(kmerFileTest){       
-                                       bool GoodFile = checkReleaseVersion(kmerFileTest, m->getVersion());
+                                       bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
                                        if (GoodFile) {  needToGenerate = false;        }
                                }
                        #endif
                }
                else if(method == "suffix")             {       search = new SuffixDB(numSeqs);                                                         }
-               else if(method == "blast")              {       search = new BlastDB(gapOpen, gapExtend, match, misMatch);      }
+               else if(method == "blast")              {       search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);   }
                else {
                        m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
                        m->mothurOutEndLine();
@@ -154,7 +153,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                ifstream kmerFileTest(kmerDBName.c_str());
                                search->readKmerDB(kmerFileTest);       
                        }
-                       
+               
                        search->setNumSeqs(numSeqs);
                }
        }