X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classify.cpp;h=212e563f94c4ae7af3ba0916d1040afd9b0e11fa;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=7770999e779917996a916e87836a03c3a2a8f26b;hpb=65b6a38d00b3a72021611211e7c25392022c69ed;p=mothur.git

diff --git a/classify.cpp b/classify.cpp
index 7770999..212e563 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -47,7 +47,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				}
 			}
 			else if(method == "suffix")		{	database = new SuffixDB(numSeqs);								}
-			else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);	}
+			else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID);	}
 			else if(method == "distance")	{	database = new DistanceDB();	}
 			else {
 				m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
@@ -89,7 +89,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 			m->mothurOut("Generating search database...    "); cout.flush();
 	#ifdef USE_MPI	
 				int pid, processors;
-				vector<unsigned long int> positions;
+				vector<unsigned long long> positions;
 				int tag = 2001;
 			
 				MPI_Status status; 
@@ -123,7 +123,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				//create database
 				if(method == "kmer")			{	database = new KmerDB(tempFile, kmerSize);			}
 				else if(method == "suffix")		{	database = new SuffixDB(numSeqs);								}
-				else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);	}
+				else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", pid);	}
 				else if(method == "distance")	{	database = new DistanceDB();	}
 				else {
 					m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8."); m->mothurOutEndLine();
@@ -176,7 +176,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				}
 			}
 			else if(method == "suffix")		{	database = new SuffixDB(numSeqs);								}
-			else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);	}
+			else if(method == "blast")		{	database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID);	}
 			else if(method == "distance")	{	database = new DistanceDB();	}
 			else {
 				m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
@@ -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) {
@@ -249,10 +249,11 @@ 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 int> positions;
+		vector<unsigned long long> positions;
 		int tag = 2001;
 		
 		MPI_Status status; 
@@ -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);