+++ /dev/null
-/*
- * 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(){}
-/***********************************************************************/
-
projects / mothur.git / blobdiff