X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.cpp;h=212e563f94c4ae7af3ba0916d1040afd9b0e11fa;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=c92d9fdc6526788df19d9e6f487ffb641bbaca44;hpb=5eca3348fe3962b8965236ca877ef6f52e8fb104;p=mothur.git

diff --git a/classify.cpp b/classify.cpp
index c92d9fd..212e563 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -61,7 +61,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 					names.push_back(temp.getName());
 					database->addSequence(temp);	
 				}
-//				database->generateDB();
+				database->generateDB();
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
 				database->readKmerDB(kmerFileTest);	
@@ -150,7 +150,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 					}
 				}
 				
-//				database->generateDB();
+				database->generateDB();
 				MPI_File_close(&inMPI);
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 		#else
@@ -200,7 +200,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				}
 				fastaFile.close();
 
-//				database->generateDB();
+				database->generateDB();
 				
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
@@ -223,9 +223,9 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 			database->setNumSeqs(names.size());
 			
 			//sanity check
-			//bool okay = phyloTree->ErrorCheck(names);
+			bool okay = phyloTree->ErrorCheck(names);
 			
-			//if (!okay) { m->control_pressed = true; }
+			if (!okay) { m->control_pressed = true; }
 			
 			m->mothurOut("DONE."); m->mothurOutEndLine();
 			m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
@@ -238,7 +238,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 	}
 }
 /**************************************************************************************************/
-Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	}
+Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	flipped=false; }
 /**************************************************************************************************/
 
 int Classify::readTaxonomy(string file) {
@@ -249,7 +249,8 @@ int Classify::readTaxonomy(string file) {
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Reading in the " + file + " taxonomy...\t");	cout.flush();
-
+        if (m->debug) { m->mothurOut("[DEBUG]: Taxonomies read in...\n"); }
+        
 #ifdef USE_MPI	
 		int pid, num, processors;
 		vector<unsigned long long> positions;
@@ -296,30 +297,21 @@ int Classify::readTaxonomy(string file) {
 			delete buf4;
 
 			istringstream iss (tempBuf,istringstream::in);
-			iss >> name >> taxInfo;
+			iss >> name; m->gobble(iss);
+            iss >> taxInfo;
+            if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
 			taxonomy[name] = taxInfo;
 			phyloTree->addSeqToTree(name, taxInfo);
 		}
 		
 		MPI_File_close(&inMPI);
 		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-#else				
-		ifstream inTax;
-		m->openInputFile(file, inTax);
-	
-		//read template seqs and save
-		while (!inTax.eof()) {
-			inTax >> name >> taxInfo;
-			
-			taxonomy[name] = taxInfo;
-			
-			phyloTree->addSeqToTree(name, taxInfo);
-		
-			m->gobble(inTax);
-		}
-		inTax.close();
+#else	
+        
+        taxonomy.clear(); 
+        m->readTax(file, taxonomy);
+        for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {  phyloTree->addSeqToTree(itTax->first, itTax->second);  }
 #endif	
-	
 		phyloTree->assignHeirarchyIDs(0);
 		
 		phyloTree->setUp(file);