X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=5a3027229bb8e91bdacfa25dea566a5273ca9d9d;hb=af27acb766f6947c45e1eb65438d878c7ea48ef3;hp=59405efe05963c8d153828d7f8f56976c440f197;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 59405ef..5a30272 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -14,30 +14,93 @@
 
 
 /**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string method, 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){		//	This assumes that the template database is in fasta format, may 
 	try {											//	need to alter this in the future?
 		m = MothurOut::getInstance();
 		longest = 0;
-
-		ifstream fastaFile;
-		openInputFile(fastaFileName, fastaFile);
+		method = s;
+		bool needToGenerate = true;
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t");	cout.flush();
 		
+		#ifdef USE_MPI	
+			int pid, processors;
+			vector<unsigned long int> positions;
+		
+			MPI_Status status; 
+			MPI_File inMPI;
+			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+			MPI_Comm_size(MPI_COMM_WORLD, &processors);
+			int tag = 2001;
+	
+			char inFileName[1024];
+			strcpy(inFileName, fastaFileName.c_str());
+	
+			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
+			
+			if (pid == 0) {
+				positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
+
+				//send file positions to all processes
+				for(int i = 1; i < processors; i++) { 
+					MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+					MPI_Send(&positions[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+				}
+			}else{
+				MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+				positions.resize(numSeqs+1);
+				MPI_Recv(&positions[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+			}
+		
+			//read file 
+			for(int i=0;i<numSeqs;i++){
+				
+				if (m->control_pressed) {  templateSequences.clear(); break;  }
+				
+				//read next sequence
+				int length = positions[i+1] - positions[i];
+				char* buf4 = new char[length];
+			
+				MPI_File_read_at(inMPI, positions[i], buf4, length, MPI_CHAR, &status);
+		
+				string tempBuf = buf4;
+				if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+				delete buf4;
+
+				istringstream iss (tempBuf,istringstream::in);
+		
+				Sequence temp(iss);  
+				if (temp.getName() != "") {
+					templateSequences.push_back(temp);
+					//save longest base
+					if (temp.getUnaligned().length() >= longest)  { longest = temp.getUnaligned().length()+1; }
+				}
+			}
+			
+			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+			
+			MPI_File_close(&inMPI);
+		
+	#else
+		ifstream 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); }
 			}
 		}
-		
-		numSeqs = templateSequences.size();
-		
 		fastaFile.close();
+	#endif
+	
+		numSeqs = templateSequences.size();
 		//all of this is elsewhere already!
 		
 		m->mothurOut("DONE.");
@@ -49,15 +112,21 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
 		emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
 		emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
 		
-		bool needToGenerate = true;
+		
 		string kmerDBName;
 		if(method == "kmer")			{	
 			search = new KmerDB(fastaFileName, kmerSize);			
 			
-			kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
-			ifstream kmerFileTest(kmerDBName.c_str());
-			
-			if(kmerFileTest){	needToGenerate = false;		}
+			#ifdef USE_MPI
+			#else
+				kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+				ifstream kmerFileTest(kmerDBName.c_str());
+				
+				if(kmerFileTest){	
+					bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
+					if (GoodFile) {  needToGenerate = false;	}
+				}
+			#endif
 		}
 		else if(method == "suffix")		{	search = new SuffixDB(numSeqs);								}
 		else if(method == "blast")		{	search = new BlastDB(gapOpen, gapExtend, match, misMatch);	}
@@ -67,20 +136,49 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
 			search = new KmerDB(fastaFileName, 8);
 		}
 		
-		if (needToGenerate) {
-		
-			//add sequences to search 
-			for (int i = 0; i < templateSequences.size(); i++) {
-				search->addSequence(templateSequences[i]);
+		if (!(m->control_pressed)) {
+			if (needToGenerate) {
+				//add sequences to search 
+				for (int i = 0; i < templateSequences.size(); i++) {
+					search->addSequence(templateSequences[i]);
+					
+					if (m->control_pressed) {  templateSequences.clear(); break;  }
+				}
+				
+				if (m->control_pressed) {  templateSequences.clear();  }
+				
+				search->generateDB();
+				
+			}else if ((method == "kmer") && (!needToGenerate)) {
+				ifstream kmerFileTest(kmerDBName.c_str());
+				search->readKmerDB(kmerFileTest);	
 			}
-			search->generateDB();
-			
-		}else if ((method == "kmer") && (!needToGenerate)) {
-			ifstream kmerFileTest(kmerDBName.c_str());
-			search->readKmerDB(kmerFileTest);	
+		
+			search->setNumSeqs(numSeqs);
 		}
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AlignmentDB", "AlignmentDB");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+AlignmentDB::AlignmentDB(string s){		 
+	try {											
+		m = MothurOut::getInstance();
+		method = s;
+		
+		if(method == "suffix")		{	search = new SuffixDB();	}
+		else if(method == "blast")	{	search = new BlastDB();		}
+		else						{	search = new KmerDB();		}
+
+				
+		//in case you delete the seqs and then ask for them
+		emptySequence = Sequence();
+		emptySequence.setName("no_match");
+		emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+		emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
 		
-		search->setNumSeqs(numSeqs);
 	}
 	catch(exception& e) {
 		m->errorOut(e, "AlignmentDB", "AlignmentDB");
@@ -109,3 +207,5 @@ Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
 
 
 
+
+