X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classify.cpp;h=5f97c7ec693a97997554683188a013b1054eb3d7;hp=c3e52abc5bcd9347853945346ee12cf641a268e3;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=a61980e36d61937acccadc41be260165a1e389f4

diff --git a/classify.cpp b/classify.cpp
index c3e52ab..5f97c7e 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -1,272 +1,389 @@
-/*
- *  classify.cpp
- *  Mothur
- *
- *  Created by westcott on 11/3/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "classify.h"
-#include "sequence.hpp"
-#include "kmerdb.hpp"
-#include "suffixdb.hpp"
-#include "blastdb.hpp"
-#include "distancedb.hpp"
-
-/**************************************************************************************************/
-Classify::Classify(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch) : taxFile(tfile), templateFile(tempFile) {		
-	try {	
-		m = MothurOut::getInstance();									
-		readTaxonomy(taxFile);	
-		
-		int start = time(NULL);
-		int numSeqs = 0;
-		
-		m->mothurOut("Generating search database...    "); cout.flush();
-#ifdef USE_MPI	
-			int pid;
-			vector<long> positions;
-		
-			MPI_Status status; 
-			MPI_File inMPI;
-			MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
-			//char* inFileName = new char[tempFile.length()];
-			//memcpy(inFileName, tempFile.c_str(), tempFile.length());
-			
-			char inFileName[1024];
-			strcpy(inFileName, tempFile.c_str());
-
-			MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
-			//delete inFileName;
-
-			if (pid == 0) { //only one process needs to scan file
-				positions = setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
-
-				//send file positions to all processes
-				MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-				MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos	
-			}else{
-				MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
-				positions.resize(numSeqs);
-				MPI_Bcast(&positions[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
-			}
-			
-			//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(gapOpen, gapExtend, match, misMatch);	}
-			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();
-				database = new KmerDB(tempFile, 8);
-			}
-
-			//read file 
-			for(int i=0;i<numSeqs;i++){
-				//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() != "") {
-					names.push_back(temp.getName());
-					database->addSequence(temp);	
-				}
-			}
-			
-			database->generateDB();
-			MPI_File_close(&inMPI);
-	#else
-		
-		//need to know number of template seqs for suffixdb
-		if (method == "suffix") {
-			ifstream inFASTA;
-			openInputFile(tempFile, inFASTA);
-			numSeqs = count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
-			inFASTA.close();
-		}
-
-		bool needToGenerate = true;
-		string kmerDBName;
-		if(method == "kmer")			{	
-			database = new KmerDB(tempFile, kmerSize);			
-			
-			kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
-			ifstream kmerFileTest(kmerDBName.c_str());
-			if(kmerFileTest){	needToGenerate = false;		}
-		}
-		else if(method == "suffix")		{	database = new SuffixDB(numSeqs);								}
-		else if(method == "blast")		{	database = new BlastDB(gapOpen, gapExtend, match, misMatch);	}
-		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();
-			database = new KmerDB(tempFile, 8);
-		}
-		
-		if (needToGenerate) {
-			ifstream fastaFile;
-			openInputFile(tempFile, fastaFile);
-			
-			while (!fastaFile.eof()) {
-				Sequence temp(fastaFile);
-				gobble(fastaFile);
-			
-				names.push_back(temp.getName());
-								
-				database->addSequence(temp);	
-			}
-			fastaFile.close();
-
-			database->generateDB();
-			
-		}else if ((method == "kmer") && (!needToGenerate)) {	
-			ifstream kmerFileTest(kmerDBName.c_str());
-			database->readKmerDB(kmerFileTest);	
-			
-			ifstream fastaFile;
-			openInputFile(tempFile, fastaFile);
-			
-			while (!fastaFile.eof()) {
-				Sequence temp(fastaFile);
-				gobble(fastaFile);
-			
-				names.push_back(temp.getName());
-			}
-			fastaFile.close();
-		}
-#endif		
-		database->setNumSeqs(names.size());
-		
-		m->mothurOut("DONE."); m->mothurOutEndLine();
-		m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
-
-	}
-	catch(exception& e) {
-		m->errorOut(e, "Classify", "Classify");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-void Classify::readTaxonomy(string file) {
-	try {
-		
-		phyloTree = new PhyloTree();
-		string name, taxInfo;
-		
-		m->mothurOutEndLine();
-		m->mothurOut("Reading in the " + file + " taxonomy...\t");	cout.flush();
-
-#ifdef USE_MPI	
-		int pid, num;
-		vector<long> positions;
-		
-		MPI_Status status; 
-		MPI_File inMPI;
-		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
-		//char* inFileName = new char[file.length()];
-		//memcpy(inFileName, file.c_str(), file.length());
-		
-		char inFileName[1024];
-		strcpy(inFileName, file.c_str());
-
-		MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
-		//delete inFileName;
-
-		if (pid == 0) {
-			positions = setFilePosEachLine(file, num);
-			
-			//send file positions to all processes
-			MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-			MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos	
-		}else{
-			MPI_Bcast(&num, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
-			positions.resize(num);
-			MPI_Bcast(&positions[0], (num+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
-		}
-	
-		//read file 
-		for(int i=0;i<num;i++){
-			//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);
-			iss >> name >> taxInfo;
-			taxonomy[name] = taxInfo;
-			phyloTree->addSeqToTree(name, taxInfo);
-		}
-		
-		MPI_File_close(&inMPI);
-#else				
-		ifstream inTax;
-		openInputFile(file, inTax);
-	
-		//read template seqs and save
-		while (!inTax.eof()) {
-			inTax >> name >> taxInfo;
-			
-			taxonomy[name] = taxInfo;
-			
-			phyloTree->addSeqToTree(name, taxInfo);
-		
-			gobble(inTax);
-		}
-		inTax.close();
-#endif	
-	
-		phyloTree->assignHeirarchyIDs(0);
-		
-		m->mothurOut("DONE.");
-		m->mothurOutEndLine();	cout.flush();
-	
-	}
-	catch(exception& e) {
-		m->errorOut(e, "Classify", "readTaxonomy");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
-vector<string> Classify::parseTax(string tax) {
-	try {
-		vector<string> taxons;
-		
-		tax = tax.substr(0, tax.length()-1);  //get rid of last ';'
-	
-		//parse taxonomy
-		string individual;
-		while (tax.find_first_of(';') != -1) {
-			individual = tax.substr(0,tax.find_first_of(';'));
-			tax = tax.substr(tax.find_first_of(';')+1, tax.length());
-			taxons.push_back(individual);
-			
-		}
-		//get last one
-		taxons.push_back(tax);
-		
-		return taxons;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "Classify", "parseTax");
-		exit(1);
-	}
-}
-/**************************************************************************************************/
-
+/*
+ *  classify.cpp
+ *  Mothur
+ *
+ *  Created by westcott on 11/3/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "classify.h"
+#include "sequence.hpp"
+#include "kmerdb.hpp"
+#include "suffixdb.hpp"
+#include "blastdb.hpp"
+#include "distancedb.hpp"
+#include "referencedb.h"
+
+/**************************************************************************************************/
+void Classify::generateDatabaseAndNames(string tfile, string tempFile, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch)  {		
+	try {	
+		ReferenceDB* rdb = ReferenceDB::getInstance();
+		
+		if (tfile == "saved") { tfile = rdb->getSavedTaxonomy(); }
+		
+		taxFile = tfile;
+		
+		int numSeqs = 0;
+		
+		if (tempFile == "saved") {
+			int start = time(NULL);
+			m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine();
+			
+			numSeqs = rdb->referenceSeqs.size();
+			templateFile = rdb->getSavedReference();
+			tempFile = rdb->getSavedReference();
+			
+			bool needToGenerate = true;
+			string kmerDBName;
+			if(method == "kmer")			{	
+				database = new KmerDB(tempFile, kmerSize);			
+				
+				kmerDBName = tempFile.substr(0,tempFile.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;	}
+				}
+			}
+			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, "", 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.");
+				m->mothurOutEndLine();
+				database = new KmerDB(tempFile, 8);
+			}
+			
+			if (needToGenerate) {
+				for (int k = 0; k < rdb->referenceSeqs.size(); k++) {
+					Sequence temp(rdb->referenceSeqs[k].getName(), rdb->referenceSeqs[k].getAligned());
+					names.push_back(temp.getName());
+					database->addSequence(temp);	
+				}
+				if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); }
+			}else if ((method == "kmer") && (!needToGenerate)) {	
+				ifstream kmerFileTest(kmerDBName.c_str());
+				database->readKmerDB(kmerFileTest);	
+				
+				for (int k = 0; k < rdb->referenceSeqs.size(); k++) {
+					names.push_back(rdb->referenceSeqs[k].getName());
+				}			
+			}	
+			
+			database->setNumSeqs(numSeqs);
+			
+			m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences and generate the search databases.");m->mothurOutEndLine();  
+			
+		}else {
+			
+			templateFile = tempFile;	
+			
+			int start = time(NULL);
+			
+			m->mothurOut("Generating search database...    "); cout.flush();
+	#ifdef USE_MPI	
+				int pid, processors;
+				vector<unsigned long long> positions;
+				int tag = 2001;
+			
+				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);
+
+				//char* inFileName = new char[tempFile.length()];
+				//memcpy(inFileName, tempFile.c_str(), tempFile.length());
+				
+				char inFileName[1024];
+				strcpy(inFileName, tempFile.c_str());
+
+				MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
+				//delete inFileName;
+
+				if (pid == 0) { //only one process needs to scan file
+					positions = m->setFilePosFasta(tempFile, 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);
+				}
+				
+				//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, "", 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();
+					database = new KmerDB(tempFile, 8);
+				}
+
+				//read file 
+				for(int i=0;i<numSeqs;i++){
+					//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() != "") {
+						if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+						names.push_back(temp.getName());
+						database->addSequence(temp);	
+					}
+				}
+				
+				database->generateDB();
+				MPI_File_close(&inMPI);
+				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+		#else
+			
+			//need to know number of template seqs for suffixdb
+			if (method == "suffix") {
+				ifstream inFASTA;
+				m->openInputFile(tempFile, inFASTA);
+				m->getNumSeqs(inFASTA, numSeqs);
+				inFASTA.close();
+			}
+
+			bool needToGenerate = true;
+			string kmerDBName;
+			if(method == "kmer")			{	
+				database = new KmerDB(tempFile, kmerSize);			
+				
+				kmerDBName = tempFile.substr(0,tempFile.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;	}
+				}
+			}
+			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, "", 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.");
+				m->mothurOutEndLine();
+				database = new KmerDB(tempFile, 8);
+			}
+			
+			if (needToGenerate) {
+				ifstream fastaFile;
+				m->openInputFile(tempFile, fastaFile);
+				
+				while (!fastaFile.eof()) {
+					Sequence temp(fastaFile);
+					m->gobble(fastaFile);
+					
+					if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+					
+					names.push_back(temp.getName());
+								
+					database->addSequence(temp);	
+				}
+				fastaFile.close();
+
+                if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); } 
+				
+			}else if ((method == "kmer") && (!needToGenerate)) {	
+				ifstream kmerFileTest(kmerDBName.c_str());
+				database->readKmerDB(kmerFileTest);	
+			
+				ifstream fastaFile;
+				m->openInputFile(tempFile, fastaFile);
+				
+				while (!fastaFile.eof()) {
+					Sequence temp(fastaFile);
+					m->gobble(fastaFile);
+					
+					if (rdb->save) { rdb->referenceSeqs.push_back(temp); }
+					names.push_back(temp.getName());
+				}
+				fastaFile.close();
+			}
+	#endif	
+            	
+			database->setNumSeqs(names.size());
+			
+			m->mothurOut("DONE."); m->mothurOutEndLine();
+			m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
+		}
+        
+        readTaxonomy(taxFile);
+        
+        //sanity check
+        bool okay = phyloTree->ErrorCheck(names);
+        
+        if (!okay) { m->control_pressed = true; }
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Classify", "generateDatabaseAndNames");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	phyloTree=NULL; flipped=false; }
+/**************************************************************************************************/
+
+int Classify::readTaxonomy(string file) {
+	try {
+		
+		phyloTree = new PhyloTree();
+		string name, taxInfo;
+		
+		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;
+		int tag = 2001;
+		
+		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);
+		
+		char inFileName[1024];
+		strcpy(inFileName, file.c_str());
+
+		MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
+		//delete inFileName;
+
+		if (pid == 0) {
+			positions = m->setFilePosEachLine(file, num);
+			
+			//send file positions to all processes
+			for(int i = 1; i < processors; i++) { 
+				MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+				MPI_Send(&positions[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+			}
+		}else{
+			MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+			positions.resize(num+1);
+			MPI_Recv(&positions[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+		}
+	
+		//read file 
+		for(int i=0;i<num;i++){
+			//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);
+			iss >> name; m->gobble(iss);
+            iss >> taxInfo;
+            if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
+			if (m->inUsersGroups(name, names)) {
+                taxonomy[name] = taxInfo;
+                phyloTree->addSeqToTree(name, taxInfo);
+            }else {
+                m->mothurOut("[WARNING]: " + name + " is in your taxonomy file and not in your reference file, ignoring.\n");
+            }		
+        }
+		
+		MPI_File_close(&inMPI);
+		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+#else	
+        
+        taxonomy.clear(); 
+        m->readTax(file, taxonomy);
+        
+        //commented out to save time with large templates. 6/12/13
+        //map<string, string> tempTaxonomy;
+        for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {  
+            //if (m->inUsersGroups(itTax->first, names)) {
+                phyloTree->addSeqToTree(itTax->first, itTax->second);
+            if (m->control_pressed) { break; }
+                //tempTaxonomy[itTax->first] = itTax->second;
+           // }else {
+            //    m->mothurOut("[WARNING]: " + itTax->first + " is in your taxonomy file and not in your reference file, ignoring.\n");
+            //}
+        }
+        //taxonomy = tempTaxonomy;
+#endif	
+		phyloTree->assignHeirarchyIDs(0);
+		
+		phyloTree->setUp(file);
+	
+		m->mothurOut("DONE.");
+		m->mothurOutEndLine();	cout.flush();
+		
+		return phyloTree->getNumSeqs();
+	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Classify", "readTaxonomy");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+
+vector<string> Classify::parseTax(string tax) {
+	try {
+		vector<string> taxons;
+		m->splitAtChar(tax, taxons, ';');
+        return taxons;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Classify", "parseTax");
+		exit(1);
+	}
+}
+/**************************************************************************************************/
+
+double Classify::getLogExpSum(vector<double> probabilities, int& maxIndex){
+	try {
+        //	http://jblevins.org/notes/log-sum-exp
+        
+        double maxProb = probabilities[0];
+        maxIndex = 0;
+        
+        int numProbs = (int)probabilities.size();
+        
+        for(int i=1;i<numProbs;i++){
+            if(probabilities[i] >= maxProb){
+                maxProb = probabilities[i];
+                maxIndex = i;
+            }
+        }
+        
+        double probSum = 0.0000;
+        
+        for(int i=0;i<numProbs;i++){
+            probSum += exp(probabilities[i] - maxProb);		
+        }
+        
+        probSum = log(probSum) + maxProb;
+        
+        return probSum;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Classify", "getLogExpSum");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+