X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=f59c5db7d6e6ef2d039ccdda8b48a6ea3fb6428a;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=bac61c451854b96e256bae11545448fa38589ebd;hpb=783b9ef8e739307aed392f35970701f6b53390fb;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index bac61c4..f59c5db 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -13,19 +13,25 @@
 #include "blastdb.hpp"
 #include "referencedb.h"
 
-
 /**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){		//	This assumes that the template database is in fasta format, may 
+AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){		//	This assumes that the template database is in fasta format, may 
 	try {											//	need to alter this in the future?
 		m = MothurOut::getInstance();
 		longest = 0;
 		method = s;
 		bool needToGenerate = true;
 		ReferenceDB* rdb = ReferenceDB::getInstance();
+		bool silent = false;
+		threadID = tid;
+		
+		if (fastaFileName == "saved-silent") {
+			fastaFileName = "saved"; silent = true;
+		}
 		
 		if (fastaFileName == "saved") {
 			int start = time(NULL);
-			m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine();
+			
+			if (!silent) { m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine(); }
 
 			for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
 				templateSequences.push_back(rdb->referenceSeqs[i]);
@@ -35,7 +41,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			fastaFileName = rdb->getSavedReference();
 			
 			numSeqs = templateSequences.size();
-			m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  
+			if (!silent) { m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  }
 
 		}else {
 			int start = time(NULL);
@@ -44,7 +50,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			
 			#ifdef USE_MPI	
 				int pid, processors;
-				vector<unsigned long int> positions;
+				vector<unsigned long long> positions;
 			
 				MPI_Status status; 
 				MPI_File inMPI;
@@ -157,8 +163,9 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			#endif
 		}
 		else if(method == "suffix")		{	search = new SuffixDB(numSeqs);								}
-		else if(method == "blast")		{	search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "");	}
+		else if(method == "blast")		{	search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID);	}
 		else {
+			method = "kmer";
 			m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
 			m->mothurOutEndLine();
 			search = new KmerDB(fastaFileName, 8);
@@ -198,7 +205,7 @@ AlignmentDB::AlignmentDB(string s){
 		method = s;
 		
 		if(method == "suffix")		{	search = new SuffixDB();	}
-		else if(method == "blast")	{	search = new BlastDB("");		}
+		else if(method == "blast")	{	search = new BlastDB("", 0);		}
 		else						{	search = new KmerDB();		}