X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitmatrix.cpp;fp=splitmatrix.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=dabcd0469461f25a79ac707cf0e785c19974cc1e;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
deleted file mode 100644
index dabcd04..0000000
--- a/splitmatrix.cpp
+++ /dev/null
@@ -1,907 +0,0 @@
-/*
- *  splitmatrix.cpp
- *  Mothur
- *
- *  Created by westcott on 5/19/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "splitmatrix.h"
-#include "phylotree.h"
-#include "distancecommand.h"
-#include "seqsummarycommand.h"
-
-/***********************************************************************/
-
-SplitMatrix::SplitMatrix(string distfile, string name, string tax, float c, string t, bool l){
-	m = MothurOut::getInstance();
-	distFile = distfile;
-	cutoff = c;
-	namefile = name;
-	method = t;
-	taxFile = tax;
-	large = l;
-}
-/***********************************************************************/
-
-SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float cu, string t, int p, string output){
-	m = MothurOut::getInstance();
-	fastafile = ffile;
-	namefile = name;
-	taxFile = tax;
-	cutoff = c;  //tax level cutoff
-	distCutoff = cu; //for fasta method if you are creating distance matrix you need a cutoff for that
-	method = t;
-	processors = p;
-	outputDir = output;
-}
-
-/***********************************************************************/
-
-int SplitMatrix::split(){
-	try {
-        
-		if (method == "distance") {  
-			splitDistance();
-		}else if ((method == "classify") || (method == "fasta")) {
-			splitClassify();
-		}else {
-			m->mothurOut("Unknown splitting method, aborting split."); m->mothurOutEndLine();
-			map<string, string> temp;
-			temp[distFile] = namefile;
-			dists.push_back(temp);
-		}
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "split");
-		exit(1);
-	}
-}
-/***********************************************************************/
-int SplitMatrix::splitDistance(){
-	try {
-        
-		if (large)	{ splitDistanceLarge(); }
-		else		{ splitDistanceRAM();	}
-		
-		return 0;
-			
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "splitDistance");
-		exit(1);
-	}
-}
-
-/***********************************************************************/
-int SplitMatrix::splitClassify(){
-	try {
-		cutoff = int(cutoff);
-				
-		map<string, int> seqGroup;
-		map<string, int>::iterator it;
-		map<string, int>::iterator it2;
-		
-		int numGroups = 0;
-		
-		//build tree from users taxonomy file
-		PhyloTree* phylo = new PhyloTree();
-		
-		ifstream in;
-		m->openInputFile(taxFile, in);
-			
-		//read in users taxonomy file and add sequences to tree
-		string seqname, tax;
-		while(!in.eof()){
-			in >> seqname >> tax; m->gobble(in);
-			phylo->addSeqToTree(seqname, tax);
-		}
-		in.close();
-		
-		phylo->assignHeirarchyIDs(0);
-
-		//make sure the cutoff is not greater than maxlevel
-		if (cutoff > phylo->getMaxLevel()) { m->mothurOut("splitcutoff is greater than the longest taxonomy, using " + toString(phylo->getMaxLevel())); m->mothurOutEndLine(); cutoff = phylo->getMaxLevel(); }
-	
-		//for each node in tree
-		for (int i = 0; i < phylo->getNumNodes(); i++) {
-		
-			//is this node within the cutoff
-			TaxNode taxon = phylo->get(i);
-	
-			if (taxon.level == cutoff) {//if yes, then create group containing this nodes sequences
-				if (taxon.accessions.size() > 1) { //if this taxon just has one seq its a singleton
-					for (int j = 0; j < taxon.accessions.size(); j++) {
-						seqGroup[taxon.accessions[j]] = numGroups;
-					}
-					numGroups++;
-				}
-			}
-		}
-	
-		delete phylo;
-		
-		if (method == "classify") {
-			splitDistanceFileByTax(seqGroup, numGroups);
-		}else {
-			createDistanceFilesFromTax(seqGroup, numGroups);
-		}
-		
-		return 0;
-			
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "splitClassify");
-		exit(1);
-	}
-}
-/***********************************************************************/
-int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numGroups){
-	try {
-		map<string, int> copyGroups = seqGroup;
-		map<string, int>::iterator it;
-		set<string> names;
-				
-		for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
-			m->mothurRemove((fastafile + "." + toString(i) + ".temp"));
-		}
-			
-		ifstream in;
-		m->openInputFile(fastafile, in);
-	
-		//parse fastafile
-		ofstream outFile;
-		while (!in.eof()) {
-			Sequence query(in); m->gobble(in);
-			if (query.getName() != "") {
-		
-				it = seqGroup.find(query.getName());
-				
-				//save names in case no namefile is given
-				if (namefile == "") {  names.insert(query.getName()); }
-			
-				if (it != seqGroup.end()) { //not singleton 
-					m->openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile);
-					query.printSequence(outFile); 
-					outFile.close();
-					
-					copyGroups.erase(query.getName());
-				}
-			}
-		}
-		in.close();
-		
-		//warn about sequence in groups that are not in fasta file
-		for(it = copyGroups.begin(); it != copyGroups.end(); it++) {
-			m->mothurOut("ERROR: " + it->first + " is missing from your fastafile. This could happen if your taxonomy file is not unique and your fastafile is, or it could indicate and error."); m->mothurOutEndLine();
-			exit(1);
-		}
-		
-		copyGroups.clear();
-		
-		//process each distance file
-		for (int i = 0; i < numGroups; i++) { 
-			
-			string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
-			if (outputDir != "") { options += ", outputdir=" + outputDir; }
-			
-			Command* command = new DistanceCommand(options);
-			
-			command->execute();
-			delete command;
-			
-			m->mothurRemove((fastafile + "." + toString(i) + ".temp"));
-			
-			//remove old names files just in case
-			m->mothurRemove((namefile + "." + toString(i) + ".temp"));
-		}
-			
-		singleton = namefile + ".extra.temp";
-		ofstream remainingNames;
-		m->openOutputFile(singleton, remainingNames);
-		
-		bool wroteExtra = false;
-
-		ifstream bigNameFile;
-		m->openInputFile(namefile, bigNameFile);
-		
-		string name, nameList;
-		while(!bigNameFile.eof()){
-			bigNameFile >> name >> nameList;  m->gobble(bigNameFile);
-			
-			//did this sequence get assigned a group
-			it = seqGroup.find(name);
-			
-			if (it != seqGroup.end()) {  
-				m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
-				outFile << name << '\t' << nameList << endl;
-				outFile.close();
-			}else{
-				wroteExtra = true;
-				remainingNames << name << '\t' << nameList << endl;
-			}
-		}
-		bigNameFile.close();
-		
-		for(int i=0;i<numGroups;i++){
-			string tempNameFile = namefile + "." + toString(i) + ".temp";
-			if (outputDir == "") { outputDir = m->hasPath(fastafile); }
-			string tempDistFile = outputDir + m->getRootName(m->getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
-
-			//if there are valid distances
-			ifstream fileHandle;
-			fileHandle.open(tempDistFile.c_str());
-			if(fileHandle) 	{	
-				m->gobble(fileHandle);
-				if (!fileHandle.eof()) {  //check for blank file - this could occur if all dists in group are above cutoff
-					map<string, string> temp;
-					temp[tempDistFile] = tempNameFile;
-					dists.push_back(temp);
-				}else {
-					ifstream in;
-					m->openInputFile(tempNameFile, in);
-				
-					while(!in.eof()) { 
-						in >> name >> nameList;  m->gobble(in);
-						wroteExtra = true;
-						remainingNames << name << '\t' << nameList << endl;
-					}
-					in.close();
-					m->mothurRemove(tempNameFile);
-				}
-			}
-			fileHandle.close();
-		}
-		
-		remainingNames.close();
-		if (!wroteExtra) { 
-			m->mothurRemove(singleton);
-			singleton = "none";
-		}
-
-		if (m->control_pressed)	 {  for (int i = 0; i < dists.size(); i++) { m->mothurRemove((dists[i].begin()->first)); m->mothurRemove((dists[i].begin()->second)); } dists.clear(); }
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "createDistanceFilesFromTax");
-		exit(1);
-	}
-}
-/***********************************************************************/
-int SplitMatrix::splitDistanceFileByTax(map<string, int>& seqGroup, int numGroups){
-	try {
-		map<string, int>::iterator it;
-		map<string, int>::iterator it2;
-		
-		ifstream dFile;
-		m->openInputFile(distFile, dFile);
-		ofstream outFile;
-		
-		for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
-			m->mothurRemove((distFile + "." + toString(i) + ".temp"));
-		}
-		
-		//for buffering the io to improve speed
-		 //allow for 10 dists to be stored, then output.
-		vector<string> outputs;  outputs.resize(numGroups, "");
-		vector<int> numOutputs;	 numOutputs.resize(numGroups, 0);	
-		
-		//you can have a group made, but their may be no distances in the file for this group if the taxonomy file and distance file don't match
-		//this can occur if we have converted the phylip to column, since we reduce the size at that step by using the cutoff value
-		vector<bool> validDistances;   validDistances.resize(numGroups, false); 
-		
-		//for each distance
-		while(dFile){
-			string seqA, seqB;
-			float dist;
-			
-			if (m->control_pressed) { dFile.close(); for (int i = 0; i < numGroups; i++) { m->mothurRemove((distFile + "." + toString(i) + ".temp"));	} }
-			
-			dFile >> seqA >> seqB >> dist;  m->gobble(dFile);
-			
-			//if both sequences are in the same group then they are within the cutoff
-			it = seqGroup.find(seqA);
-			it2 = seqGroup.find(seqB);
-			
-			if ((it != seqGroup.end()) && (it2 != seqGroup.end())) { //they are both not singletons 
-				if (it->second == it2->second) { //they are from the same group so add the distance
-					if (numOutputs[it->second] > 30) {
-						m->openOutputFileAppend((distFile + "." + toString(it->second) + ".temp"), outFile);
-						outFile << outputs[it->second] << seqA << '\t' << seqB << '\t' << dist << endl;
-						outFile.close();
-						outputs[it->second] = "";
-						numOutputs[it->second] = 0;
-						validDistances[it->second] = true;
-					}else{
-						outputs[it->second] += seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
-						numOutputs[it->second]++;
-					}
-				}
-			}
-		}
-		dFile.close();
-	
-		for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
-			m->mothurRemove((namefile + "." + toString(i) + ".temp"));
-			
-			//write out any remaining buffers
-			if (numOutputs[i] > 0) {
-				m->openOutputFileAppend((distFile + "." + toString(i) + ".temp"), outFile);
-				outFile << outputs[i];
-				outFile.close();
-				outputs[i] = "";
-				numOutputs[i] = 0;
-				validDistances[i] = true;
-			}
-		}
-		
-		ifstream bigNameFile;
-		m->openInputFile(namefile, bigNameFile);
-		
-		singleton = namefile + ".extra.temp";
-		ofstream remainingNames;
-		m->openOutputFile(singleton, remainingNames);
-		
-		bool wroteExtra = false;
-						
-		string name, nameList;
-		while(!bigNameFile.eof()){
-			bigNameFile >> name >> nameList;  m->gobble(bigNameFile);
-			
-			//did this sequence get assigned a group
-			it = seqGroup.find(name);
-			
-			if (it != seqGroup.end()) {  
-				m->openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
-				outFile << name << '\t' << nameList << endl;
-				outFile.close();
-			}else{
-				wroteExtra = true;
-				remainingNames << name << '\t' << nameList << endl;
-			}
-		}
-		bigNameFile.close();
-				
-		for(int i=0;i<numGroups;i++){
-			string tempNameFile = namefile + "." + toString(i) + ".temp";
-			string tempDistFile = distFile + "." + toString(i) + ".temp";
-
-			//if there are valid distances
-			if (validDistances[i]) {
-				map<string, string> temp;
-				temp[tempDistFile] = tempNameFile;
-				dists.push_back(temp);
-			}else{
-				ifstream in;
-				m->openInputFile(tempNameFile, in);
-				
-				while(!in.eof()) { 
-					in >> name >> nameList;  m->gobble(in);
-					wroteExtra = true;
-					remainingNames << name << '\t' << nameList << endl;
-				}
-				in.close();
-				m->mothurRemove(tempNameFile);
-			}
-		}
-		
-		remainingNames.close();
-		
-		if (!wroteExtra) { 
-			m->mothurRemove(singleton);
-			singleton = "none";
-		}
-
-		if (m->control_pressed)	 {  
-			for (int i = 0; i < dists.size(); i++) { 
-				m->mothurRemove((dists[i].begin()->first));
-				m->mothurRemove((dists[i].begin()->second));
-			}
-			dists.clear();
-		}
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "splitDistanceFileByTax");
-		exit(1);
-	}
-}
-/***********************************************************************/
-int SplitMatrix::splitDistanceLarge(){
-	try {
-		vector<set<string> > groups;
-		
-		//for buffering the io to improve speed
-		 //allow for 30 dists to be stored, then output.
-		vector<string> outputs;
-		vector<int> numOutputs;
-		vector<bool> wroteOutPut;
-		
-		int numGroups = 0;
-
-		ofstream outFile;
-		ifstream dFile;
-		m->openInputFile(distFile, dFile);
-	
-		while(dFile){
-			string seqA, seqB;
-			float dist;
-
-			dFile >> seqA >> seqB >> dist;
-			
-			if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){	if(groups[i].size() > 0){  m->mothurRemove((distFile + "." + toString(i) + ".temp")); }  } return 0; }
-					
-			if(dist < cutoff){
-				//cout << "in cutoff: " << dist << endl;
-				int groupIDA = -1;
-				int groupIDB = -1;
-				int groupID = -1;
-				
-				for(int i=0;i<numGroups;i++){
-					set<string>::iterator aIt = groups[i].find(seqA);
-					set<string>::iterator bIt = groups[i].find(seqB);
-					
-					if(groupIDA == -1 && aIt != groups[i].end()){//seqA is not already assigned to a group and is in group[i], so assign seqB to group[i]
-						groups[i].insert(seqB);
-						groupIDA = i;
-						groupID = groupIDA;
-
-						//cout << "in aIt: " << groupID << endl;
-	//					break;
-					}
-					else if(groupIDB == -1 && bIt != groups[i].end()){//seqB is not already assigned to a group and is in group[i], so assign seqA to group[i]
-						groups[i].insert(seqA);
-						groupIDB = i;
-						groupID = groupIDB;
-
-					//	cout << "in bIt: " << groupID << endl;
-	//					break;
-					}
-				
-					if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
-						if(groupIDA < groupIDB){
-						//	cout << "A: " << groupIDA << "\t" << groupIDB << endl;
-							groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
-							groups[groupIDB].clear(); 
-							groupID = groupIDA;
-						}
-						else{
-						//	cout << "B: " << groupIDA << "\t" << groupIDB << endl;
-							groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
-							groups[groupIDA].clear();  
-							groupID = groupIDB;
-						}
-						break;
-					}
-				}
-				
-	//windows is gonna gag on the reuse of outFile, will need to make it local...
-				
-				if(groupIDA == -1 && groupIDB == -1){ //we need a new group
-					set<string> newGroup;
-					newGroup.insert(seqA);
-					newGroup.insert(seqB);
-					groups.push_back(newGroup);
-									
-					string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
-					outputs.push_back(tempOut);
-					numOutputs.push_back(1);
-					wroteOutPut.push_back(false);
-					
-					numGroups++;
-				}
-				else{
-					string fileName = distFile + "." + toString(groupID) + ".temp";
-											
-					//have we reached the max buffer size
-					if (numOutputs[groupID] > 60) { //write out sequence
-						outFile.open(fileName.c_str(), ios::app);
-						outFile << outputs[groupID] << seqA << '\t' << seqB << '\t' << dist << endl;
-						outFile.close();
-						
-						outputs[groupID] = "";
-						numOutputs[groupID] = 0;
-						wroteOutPut[groupID] = true;
-					}else {
-						outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
-						numOutputs[groupID]++;
-					}
-					
-					if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
-						string row, column, distance;
-						if(groupIDA<groupIDB){
-							
-							//merge memory
-							numOutputs[groupID] += numOutputs[groupIDB];
-							outputs[groupID] += outputs[groupIDB];
-							
-							outputs[groupIDB] = "";
-							numOutputs[groupIDB] = 0;
-							
-							//if groupB is written to file it is above buffer size so read and write to new merged file
-							if (wroteOutPut[groupIDB]) {
-								string fileName2 = distFile + "." + toString(groupIDB) + ".temp";
-								ifstream fileB(fileName2.c_str(), ios::ate);
-								
-								outFile.open(fileName.c_str(), ios::app);
-								
-								long size;
-								char* memblock;
-
-								size = fileB.tellg();
-				
-								fileB.seekg (0, ios::beg);
-								
-								int numRead = size / 1024;
-								int lastRead = size % 1024;
-
-								for (int i = 0; i < numRead; i++) {
-				
-									memblock = new char [1024];
-								
-									fileB.read (memblock, 1024);
-									
-									string temp = memblock;
-									outFile << temp.substr(0, 1024);
-									
-									delete memblock;
-								}
-								
-								memblock = new char [lastRead];
-								
-								fileB.read (memblock, lastRead);
-								
-								//not sure why but it will read more than lastRead char...??
-								string temp = memblock;
-								outFile << temp.substr(0, lastRead);
-								delete memblock;
-								
-								fileB.close();
-								m->mothurRemove(fileName2);
-								
-								//write out the merged memory
-								if (numOutputs[groupID] > 60) {
-									outFile << outputs[groupID];
-									outputs[groupID] = "";
-									numOutputs[groupID] = 0;
-								}
-								
-								outFile.close();
-								
-								wroteOutPut[groupID] = true;
-								wroteOutPut[groupIDB] = false;
-							}else{ } //just merge b's memory with a's memory 
-						}
-						else{
-							numOutputs[groupID] += numOutputs[groupIDA];
-							outputs[groupID] += outputs[groupIDA];
-							
-							outputs[groupIDA] = "";
-							numOutputs[groupIDA] = 0;
-							
-							if (wroteOutPut[groupIDA]) {
-								string fileName2 = distFile + "." + toString(groupIDA) + ".temp";
-								ifstream fileB(fileName2.c_str(), ios::ate);
-								
-								outFile.open(fileName.c_str(), ios::app);
-								
-								long size;
-								char* memblock;
-
-								size = fileB.tellg();
-															
-								fileB.seekg (0, ios::beg);
-								
-								int numRead = size / 1024;
-								int lastRead = size % 1024;
-
-								for (int i = 0; i < numRead; i++) {
-				
-									memblock = new char [1024];
-								
-									fileB.read (memblock, 1024);
-									string temp = memblock;
-									outFile << temp.substr(0, 1024);
-									
-									delete memblock;
-								}
-								
-								memblock = new char [lastRead];
-								
-								fileB.read (memblock, lastRead);
-								
-								//not sure why but it will read more than lastRead char...??
-								string temp = memblock;
-								outFile << temp.substr(0, lastRead);
-									
-								delete memblock;
-								
-								fileB.close();
-								m->mothurRemove(fileName2);
-								
-								//write out the merged memory
-								if (numOutputs[groupID] > 60) {
-									outFile << outputs[groupID];
-									outputs[groupID] = "";
-									numOutputs[groupID] = 0;
-								}
-								
-								outFile.close();
-								
-								wroteOutPut[groupID] = true;
-								wroteOutPut[groupIDA] = false;
-							}else { } //just merge memory
-						}					
-					}
-				}
-			}
-			m->gobble(dFile);
-		}
-		dFile.close();
-		
-		for (int i = 0; i < numGroups; i++) {
-			if (numOutputs[i] > 0) {
-				string fileName = distFile + "." + toString(i) + ".temp";
-				outFile.open(fileName.c_str(), ios::app);
-				outFile << outputs[i];
-				outFile.close();
-			}
-		}
-
-		splitNames(groups);
-				
-		return 0;			
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "splitDistanceLarge");
-		exit(1);
-	}
-}
-//********************************************************************************************************************
-int SplitMatrix::splitNames(vector<set<string> >& groups){
-	try {
-		int numGroups = groups.size();
-	
-		ifstream bigNameFile(namefile.c_str());
-		if(!bigNameFile){
-			cerr << "Error: We can't open the name file\n";
-			exit(1);
-		}
-		
-		map<string, string> nameMap;
-		string name, nameList;
-		while(bigNameFile){
-			bigNameFile >> name >> nameList;
-			nameMap[name] = nameList;
-			m->gobble(bigNameFile);
-		}
-		bigNameFile.close();
-			
-		for(int i=0;i<numGroups;i++){  //parse names file to match distance files
-			int numSeqsInGroup = groups[i].size();
-			
-			if(numSeqsInGroup > 0){
-				string fileName = namefile + "." + toString(i) + ".temp";
-				ofstream smallNameFile(fileName.c_str(), ios::ate);
-				
-				for(set<string>::iterator gIt=groups[i].begin();gIt!=groups[i].end();gIt++){
-					map<string,string>::iterator nIt = nameMap.find(*gIt);
-					if (nIt != nameMap.end()) {
-						smallNameFile << nIt->first << '\t' << nIt->second << endl;
-						nameMap.erase(nIt);
-					}else{
-						m->mothurOut((*gIt) + " is in your distance file and not in your namefile.  Please correct."); m->mothurOutEndLine(); exit(1);
-					}
-				}
-				smallNameFile.close();
-			}
-		}
-		
-		//names of singletons
-		if (nameMap.size() != 0) {
-			singleton = namefile + ".extra.temp";
-			ofstream remainingNames(singleton.c_str(), ios::ate);
-			for(map<string,string>::iterator nIt=nameMap.begin();nIt!=nameMap.end();nIt++){
-				remainingNames << nIt->first << '\t' << nIt->second << endl;
-			}
-			remainingNames.close();
-		}else { singleton = "none"; }
-			
-		for(int i=0;i<numGroups;i++){
-			if(groups[i].size() > 0){
-				string tempNameFile = namefile + "." + toString(i) + ".temp";
-				string tempDistFile = distFile + "." + toString(i) + ".temp";
-				
-				map<string, string> temp;
-				temp[tempDistFile] = tempNameFile;
-				dists.push_back(temp);
-			}
-		}
-		
-		if (m->control_pressed)	 {  
-			for (int i = 0; i < dists.size(); i++) { 
-				m->mothurRemove((dists[i].begin()->first));
-				m->mothurRemove((dists[i].begin()->second));
-			}
-			dists.clear();
-		}
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "splitNames");
-		exit(1);
-	}
-}
-//********************************************************************************************************************
-int SplitMatrix::splitDistanceRAM(){
-	try {
-		vector<set<string> > groups;
-		vector<string> outputs;
-		
-		int numGroups = 0;
-
-		ifstream dFile;
-		m->openInputFile(distFile, dFile);
-
-		while(dFile){
-			string seqA, seqB;
-			float dist;
-
-			dFile >> seqA >> seqB >> dist;
-			
-			if (m->control_pressed) {   dFile.close();  for(int i=0;i<numGroups;i++){	if(groups[i].size() > 0){  m->mothurRemove((distFile + "." + toString(i) + ".temp")); }  } return 0; }
-					
-			if(dist < cutoff){
-				//cout << "in cutoff: " << dist << endl;
-				int groupIDA = -1;
-				int groupIDB = -1;
-				int groupID = -1;
-				
-				for(int i=0;i<numGroups;i++){
-					set<string>::iterator aIt = groups[i].find(seqA);
-					set<string>::iterator bIt = groups[i].find(seqB);
-					
-					if(groupIDA == -1 && aIt != groups[i].end()){//seqA is not already assigned to a group and is in group[i], so assign seqB to group[i]
-						groups[i].insert(seqB);
-						groupIDA = i;
-						groupID = groupIDA;
-
-						//cout << "in aIt: " << groupID << endl;
-	//					break;
-					}
-					else if(groupIDB == -1 && bIt != groups[i].end()){//seqB is not already assigned to a group and is in group[i], so assign seqA to group[i]
-						groups[i].insert(seqA);
-						groupIDB = i;
-						groupID = groupIDB;
-
-					//	cout << "in bIt: " << groupID << endl;
-	//					break;
-					}
-				
-					if(groupIDA != -1 && groupIDB != -1){//both ifs above have been executed, so we need to decide who to assign them to
-						if(groupIDA < groupIDB){
-						//	cout << "A: " << groupIDA << "\t" << groupIDB << endl;
-							groups[groupIDA].insert(groups[groupIDB].begin(), groups[groupIDB].end()); //merge two groups into groupIDA
-							groups[groupIDB].clear(); 
-							groupID = groupIDA;
-						}
-						else{
-						//	cout << "B: " << groupIDA << "\t" << groupIDB << endl;
-							groups[groupIDB].insert(groups[groupIDA].begin(), groups[groupIDA].end()); //merge two groups into groupIDB
-							groups[groupIDA].clear();  
-							groupID = groupIDB;
-						}
-						break;
-					}
-				}
-				
-	//windows is gonna gag on the reuse of outFile, will need to make it local...
-				
-				if(groupIDA == -1 && groupIDB == -1){ //we need a new group
-					set<string> newGroup;
-					newGroup.insert(seqA);
-					newGroup.insert(seqB);
-					groups.push_back(newGroup);
-									
-					string tempOut = seqA + '\t' + seqB + '\t' + toString(dist) + '\n';
-					outputs.push_back(tempOut);
-					numGroups++;
-				}
-				else{
-											
-					outputs[groupID] +=  seqA + '\t' + seqB + '\t' + toString(dist)  + '\n';
-					
-					if(groupIDA != -1 && groupIDB != -1){ //merge distance files of two groups you merged above
-						string row, column, distance;
-						if(groupIDA<groupIDB){
-							//merge memory
-							outputs[groupID] += outputs[groupIDB];
-							outputs[groupIDB] = "";
-						}else{
-							outputs[groupID] += outputs[groupIDA];
-							outputs[groupIDA] = "";
-						}					
-					}
-				}
-			}
-			m->gobble(dFile);
-		}
-		dFile.close();
-		
-		for (int i = 0; i < numGroups; i++) {
-			if (outputs[i] != "") {
-				ofstream outFile;
-				string fileName = distFile + "." + toString(i) + ".temp";
-				outFile.open(fileName.c_str(), ios::ate);
-				outFile << outputs[i];
-				outFile.close();
-			}
-		}
-
-		splitNames(groups);
-				
-		return 0;			
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "splitDistanceRAM");
-		exit(1);
-	}
-}
-//********************************************************************************************************************
-//sorts biggest to smallest
-inline bool compareFileSizes(map<string, string> left, map<string, string> right){
-	
-	FILE * pFile;
-	long leftsize = 0;
-		
-	//get num bytes in file
-	string filename = left.begin()->first;
-	pFile = fopen (filename.c_str(),"rb");
-	string error = "Error opening " + filename;
-	if (pFile==NULL) perror (error.c_str());
-	else{
-		fseek (pFile, 0, SEEK_END);
-		leftsize=ftell (pFile);
-		fclose (pFile);
-	}
-
-	FILE * pFile2;
-	long rightsize = 0;
-		
-	//get num bytes in file
-	filename = right.begin()->first;
-	pFile2 = fopen (filename.c_str(),"rb");
-	error = "Error opening " + filename;
-	if (pFile2==NULL) perror (error.c_str());
-	else{
-		fseek (pFile2, 0, SEEK_END);
-		rightsize=ftell (pFile2);
-		fclose (pFile2);
-	}
-
-	return (leftsize > rightsize);	
-} 
-/***********************************************************************/
-//returns map of distance files -> namefile sorted by distance file size
-vector< map< string, string> > SplitMatrix::getDistanceFiles(){
-	try {	
-		
-		sort(dists.begin(), dists.end(), compareFileSizes);
-		
-		return dists;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SplitMatrix", "getDistanceFiles");
-		exit(1);
-	}
-}
-/***********************************************************************/
-SplitMatrix::~SplitMatrix(){}
-/***********************************************************************/
-