X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=5a3027229bb8e91bdacfa25dea566a5273ca9d9d;hb=1b49ed179327150ebf24d77b33d9b3e6872cc8c0;hp=8febfe286c6b14b6d8dd2d373cec860a6f099897;hpb=050220fe7822cc660615972a0054cf4a83eefbe4;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 8febfe2..5a30272 100644
--- 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();
@@ -124,7 +123,7 @@ 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
@@ -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);
 		}
 	}