X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.cpp;h=459c90f9ddd769628b0fc9061e7bd504a88b2900;hb=96dbe925073caefaed6e6db85659c144a806aeb1;hp=2d01183479a504c798a18071df045f723643f850;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/classify.cpp b/classify.cpp
index 2d01183..459c90f 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -61,7 +61,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 					names.push_back(temp.getName());
 					database->addSequence(temp);	
 				}
-				database->generateDB();
+				if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); }
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
 				database->readKmerDB(kmerFileTest);	
@@ -200,7 +201,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				}
 				fastaFile.close();
 
-				database->generateDB();
+                if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); } 
 				
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
@@ -249,7 +251,8 @@ 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;
@@ -259,9 +262,6 @@ int Classify::readTaxonomy(string file) {
 		MPI_File inMPI;
 		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 		MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
-		//char* inFileName = new char[file.length()];
-		//memcpy(inFileName, file.c_str(), file.length());
 		
 		char inFileName[1024];
 		strcpy(inFileName, file.c_str());
@@ -298,30 +298,19 @@ int Classify::readTaxonomy(string file) {
 			istringstream iss (tempBuf,istringstream::in);
 			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; m->gobble(inTax);
-            inTax >> 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);