+++ /dev/null
-/*
- * bellerophon.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 7/9/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "bellerophon.h"
-#include "eachgapdist.h"
-#include "ignoregaps.h"
-#include "onegapdist.h"
-
-
-/***************************************************************************************************************/
-
-Bellerophon::Bellerophon(string name, bool filterSeqs, bool c, int win, int inc, int p, string o) : Chimera() {
- try {
- fastafile = name;
- correction = c;
- outputDir = o;
- window = win;
- increment = inc;
- processors = p;
-
- //read in sequences
- seqs = readSeqs(fastafile);
- numSeqs = seqs.size();
- if (numSeqs == 0) { m->mothurOut("Error in reading you sequences."); m->mothurOutEndLine(); exit(1); }
-
- //do soft filter
- if (filterSeqs) {
- createFilter(seqs, 0.5);
- for (int i = 0; i < seqs.size(); i++) { runFilter(seqs[i]); }
- }
-
- distCalculator = new eachGapDist();
-
- //set default window to 25% of sequence length
- string seq0 = seqs[0]->getAligned();
- if (window == 0) { window = seq0.length() / 4; }
- else if (window > (seq0.length() / 2)) {
- m->mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); m->mothurOutEndLine();
- window = (seq0.length() / 2);
- }
-
- if (increment > (seqs[0]->getAlignLength() - (2*window))) {
- if (increment != 10) {
-
- m->mothurOut("You have selected a increment that is too large. I will use the default."); m->mothurOutEndLine();
- increment = 10;
- if (increment > (seqs[0]->getAlignLength() - (2*window))) { increment = 0; }
-
- }else{ increment = 0; }
- }
-
- if (increment == 0) { iters = 1; }
- else { iters = ((seqs[0]->getAlignLength() - (2*window)) / increment); }
-
- //initialize pref
- pref.resize(iters);
- for (int i = 0; i < iters; i++) {
- Preference temp;
- for (int j = 0; j < numSeqs; j++) {
- pref[i].push_back(temp);
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "Bellerophon");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-int Bellerophon::print(ostream& out, ostream& outAcc, string s) {
- try {
- int above1 = 0;
-
- //sorted "best" preference scores for all seqs
- vector<Preference> best = getBestPref();
-
- if (m->control_pressed) { return numSeqs; }
-
- out << "Name\tScore\tLeft\tRight\t" << endl;
- //output prefenence structure to .chimeras file
- for (int i = 0; i < best.size(); i++) {
-
- if (m->control_pressed) { return numSeqs; }
-
- out << best[i].name << '\t' << setprecision(3) << best[i].score << '\t' << best[i].leftParent << '\t' << best[i].rightParent << endl;
-
- //calc # of seqs with preference above 1.0
- if (best[i].score > 1.0) {
- above1++;
- outAcc << best[i].name << endl;
- m->mothurOut(best[i].name + " is a suspected chimera at breakpoint " + toString(best[i].midpoint)); m->mothurOutEndLine();
- m->mothurOut("It's score is " + toString(best[i].score) + " with suspected left parent " + best[i].leftParent + " and right parent " + best[i].rightParent); m->mothurOutEndLine();
- }
- }
-
- //output results to screen
- m->mothurOutEndLine();
- m->mothurOut("Sequence with preference score above 1.0: " + toString(above1)); m->mothurOutEndLine();
- int spot;
- spot = best.size()-1;
- m->mothurOut("Minimum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.975;
- m->mothurOut("2.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.75;
- m->mothurOut("25%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.50;
- m->mothurOut("Median: \t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.25;
- m->mothurOut("75%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.025;
- m->mothurOut("97.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = 0;
- m->mothurOut("Maximum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
-
- return numSeqs;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "print");
- exit(1);
- }
-}
-#ifdef USE_MPI
-//***************************************************************************************************************
-int Bellerophon::print(MPI_File& out, MPI_File& outAcc, string s) {
- try {
-
- int pid;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- string outString = "";
-
- //sorted "best" preference scores for all seqs
- vector<Preference> best = getBestPref();
-
- int above1 = 0;
- int ninetyfive = best.size() * 0.05;
- float cutoffScore = best[ninetyfive].score;
-
- if (m->control_pressed) { return numSeqs; }
-
- outString = "Name\tScore\tLeft\tRight\n";
- MPI_Status status;
- int olength = outString.length();
- char* buf5 = new char[olength];
- memcpy(buf5, outString.c_str(), olength);
-
- MPI_File_write_shared(out, buf5, olength, MPI_CHAR, &status);
-
- delete buf5;
-
- //output prefenence structure to .chimeras file
- for (int i = 0; i < best.size(); i++) {
-
- if (m->control_pressed) { return numSeqs; }
-
- outString = best[i].name + "\t" + toString(best[i].score) + "\t" + best[i].leftParent + "\t" + best[i].rightParent + "\n";
-
- MPI_Status status;
- int length = outString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outString.c_str(), length);
-
- MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
-
- delete buf2;
-
- //calc # of seqs with preference above 95%tile
- if (best[i].score >= cutoffScore) {
- above1++;
- string outAccString = "";
- outAccString += best[i].name + "\n";
-
- MPI_Status statusAcc;
- length = outAccString.length();
- char* buf = new char[length];
- memcpy(buf, outAccString.c_str(), length);
-
- MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
-
- delete buf;
-
- cout << best[i].name << " is a suspected chimera at breakpoint " << toString(best[i].midpoint) << endl;
- cout << "It's score is " << toString(best[i].score) << " with suspected left parent " << best[i].leftParent << " and right parent " << best[i].rightParent << endl;
- }
- }
-
- //output results to screen
- m->mothurOutEndLine();
- m->mothurOut("Sequence with preference score above " + toString(cutoffScore) + ": " + toString(above1)); m->mothurOutEndLine();
- int spot;
- spot = best.size()-1;
- m->mothurOut("Minimum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.975;
- m->mothurOut("2.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.75;
- m->mothurOut("25%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.50;
- m->mothurOut("Median: \t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.25;
- m->mothurOut("75%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = best.size() * 0.025;
- m->mothurOut("97.5%-tile:\t" + toString(best[spot].score)); m->mothurOutEndLine();
- spot = 0;
- m->mothurOut("Maximum:\t" + toString(best[spot].score)); m->mothurOutEndLine();
-
- }
-
- return numSeqs;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "print");
- exit(1);
- }
-}
-#endif
-//********************************************************************************************************************
-//sorts highest score to lowest
-inline bool comparePref(Preference left, Preference right){
- return (left.score > right.score);
-}
-//***************************************************************************************************************
-int Bellerophon::getChimeras() {
- try {
-
- //create breaking points
- vector<int> midpoints; midpoints.resize(iters, window);
- for (int i = 1; i < iters; i++) { midpoints[i] = midpoints[i-1] + increment; }
-
- #ifdef USE_MPI
- int pid, numSeqsPerProcessor;
-
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- numSeqsPerProcessor = iters / processors;
-
- //each process hits this only once
- unsigned long long startPos = pid * numSeqsPerProcessor;
- if(pid == processors - 1){
- numSeqsPerProcessor = iters - pid * numSeqsPerProcessor;
- }
- lines.push_back(linePair(startPos, numSeqsPerProcessor));
-
- //fill pref with scores
- driverChimeras(midpoints, lines[0]);
-
- if (m->control_pressed) { return 0; }
-
- //each process must send its parts back to pid 0
- if (pid == 0) {
-
- //receive results
- for (int j = 1; j < processors; j++) {
-
- vector<string> MPIBestSend;
- for (int i = 0; i < numSeqs; i++) {
-
- if (m->control_pressed) { return 0; }
-
- MPI_Status status;
- //receive string
- int length;
- MPI_Recv(&length, 1, MPI_INT, j, 2001, MPI_COMM_WORLD, &status);
-
- char* buf = new char[length];
- MPI_Recv(&buf[0], length, MPI_CHAR, j, 2001, MPI_COMM_WORLD, &status);
-
- string temp = buf;
- if (temp.length() > length) { temp = temp.substr(0, length); }
- delete buf;
-
- MPIBestSend.push_back(temp);
- }
-
- fillPref(j, MPIBestSend);
-
- if (m->control_pressed) { return 0; }
- }
-
- }else {
- //takes best window for each sequence and turns Preference to string that can be parsed by pid 0.
- //played with this a bit, but it may be better to try user-defined datatypes with set string lengths??
- vector<string> MPIBestSend = getBestWindow(lines[0]);
- pref.clear();
-
- //send your result to parent
- for (int i = 0; i < numSeqs; i++) {
-
- if (m->control_pressed) { return 0; }
-
- int bestLength = MPIBestSend[i].length();
- char* buf = new char[bestLength];
- memcpy(buf, MPIBestSend[i].c_str(), bestLength);
-
- MPI_Send(&bestLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD);
- MPI_Send(buf, bestLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD);
- delete buf;
- }
-
- MPIBestSend.clear();
- }
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- #else
-
- //divide breakpoints between processors
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if(processors == 1){
- lines.push_back(linePair(0, iters));
-
- //fill pref with scores
- driverChimeras(midpoints, lines[0]);
-
- }else{
-
- int numSeqsPerProcessor = iters / processors;
-
- for (int i = 0; i < processors; i++) {
- unsigned long long startPos = i * numSeqsPerProcessor;
- if(i == processors - 1){
- numSeqsPerProcessor = iters - i * numSeqsPerProcessor;
- }
- lines.push_back(linePair(startPos, numSeqsPerProcessor));
- }
-
- createProcesses(midpoints);
- }
- #else
- lines.push_back(linePair(0, iters));
-
- ///fill pref with scores
- driverChimeras(midpoints, lines[0]);
- #endif
-
- #endif
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "getChimeras");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-int Bellerophon::createProcesses(vector<int> mid) {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int process = 0;
- int exitCommand = 1;
- vector<int> processIDS;
-
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
-
- if (pid > 0) {
- processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
- process++;
- }else if (pid == 0){
- exitCommand = driverChimeras(mid, lines[process]);
- string tempOut = outputDir + toString(getpid()) + ".temp";
- writePrefs(tempOut, lines[process]);
- exit(0);
- }else {
- m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
- }
- }
-
- //force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- //get info that other processes created
- for (int i = 0; i < processIDS.size(); i++) {
- string tempIn = outputDir + toString(processIDS[i]) + ".temp";
- readPrefs(tempIn);
- }
-
- return exitCommand;
-#endif
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "createProcesses");
- exit(1);
- }
-}
-//***************************************************************************************************************
-int Bellerophon::driverChimeras(vector<int> midpoints, linePair line) {
- try {
-
- for (int h = line.start; h < (line.start + line.num); h++) {
- count = h;
- int midpoint = midpoints[h];
-
- //initialize pref[count]
- for (int i = 0; i < numSeqs; i++ ) {
- pref[count][i].name = seqs[i]->getName();
- pref[count][i].midpoint = midpoint;
- }
-
- if (m->control_pressed) { return 0; }
-
- //create 2 vectors of sequences, 1 for left side and one for right side
- vector<Sequence> left; vector<Sequence> right;
-
- for (int i = 0; i < seqs.size(); i++) {
-
- if (m->control_pressed) { return 0; }
-
- //cout << "midpoint = " << midpoint << "\twindow = " << window << endl;
- //cout << "whole = " << seqs[i]->getAligned().length() << endl;
- //save left side
- string seqLeft = seqs[i]->getAligned().substr(midpoint-window, window);
- Sequence tempLeft;
- tempLeft.setName(seqs[i]->getName());
- tempLeft.setAligned(seqLeft);
- left.push_back(tempLeft);
- //cout << "left = " << tempLeft.getAligned().length() << endl;
- //save right side
- string seqRight = seqs[i]->getAligned().substr(midpoint, window);
- Sequence tempRight;
- tempRight.setName(seqs[i]->getName());
- tempRight.setAligned(seqRight);
- right.push_back(tempRight);
- //cout << "right = " << seqRight.length() << endl;
- }
-
- //this should be parallelized
- //perference = sum of (| distance of my left to sequence j's left - distance of my right to sequence j's right | )
- //create a matrix containing the distance from left to left and right to right
- //calculate distances
- SparseMatrix* SparseLeft = new SparseMatrix();
- SparseMatrix* SparseRight = new SparseMatrix();
-
- createSparseMatrix(0, left.size(), SparseLeft, left);
-
- if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
-
- createSparseMatrix(0, right.size(), SparseRight, right);
-
- if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
-
- left.clear(); right.clear();
- vector<SeqMap> distMapRight;
- vector<SeqMap> distMapLeft;
-
- // Create a data structure to quickly access the distance information.
- //this is from thallingers reimplementation on get.oturep
- // It consists of a vector of distance maps, where each map contains
- // all distances of a certain sequence. Vector and maps are accessed
- // via the index of a sequence in the distance matrix
- distMapRight = vector<SeqMap>(numSeqs);
- distMapLeft = vector<SeqMap>(numSeqs);
- //cout << "left" << endl << endl;
- for (MatData currentCell = SparseLeft->begin(); currentCell != SparseLeft->end(); currentCell++) {
- distMapLeft[currentCell->row][currentCell->column] = currentCell->dist;
- if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
- //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
- }
- //cout << "right" << endl << endl;
- for (MatData currentCell = SparseRight->begin(); currentCell != SparseRight->end(); currentCell++) {
- distMapRight[currentCell->row][currentCell->column] = currentCell->dist;
- if (m->control_pressed) { delete SparseLeft; delete SparseRight; return 0; }
- //cout << " i = " << currentCell->row << " j = " << currentCell->column << " dist = " << currentCell->dist << endl;
- }
-
- delete SparseLeft;
- delete SparseRight;
-
- //fill preference structure
- generatePreferences(distMapLeft, distMapRight, midpoint);
-
- if (m->control_pressed) { return 0; }
-
- //report progress
- if((h+1) % 10 == 0){ cout << "Processing sliding window: " << toString(h+1) << "\n"; m->mothurOutJustToLog("Processing sliding window: " + toString(h+1) + "\n") ; }
-
- }
-
- //report progress
- if((line.start + line.num) % 10 != 0){ cout << "Processing sliding window: " << toString(line.start + line.num) << "\n"; m->mothurOutJustToLog("Processing sliding window: " + toString(line.start + line.num) + "\n") ; }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "driverChimeras");
- exit(1);
- }
-}
-
-/***************************************************************************************************************/
-int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* sparse, vector<Sequence> s){
- try {
-
- for(int i=startSeq; i<endSeq; i++){
-
- for(int j=0;j<i;j++){
-
- if (m->control_pressed) { return 0; }
-
- distCalculator->calcDist(s[i], s[j]);
- float dist = distCalculator->getDist();
-
- PCell temp(i, j, dist);
- sparse->addCell(temp);
-
- }
- }
-
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "createSparseMatrix");
- exit(1);
- }
-}
-/***************************************************************************************************************/
-int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
- try {
-
- SeqMap::iterator itR;
- SeqMap::iterator itL;
-
- for (int i = 0; i < left.size(); i++) {
-
- SeqMap currentLeft = left[i]; //example i = 3; currentLeft is a map of 0 to the distance of sequence 3 to sequence 0,
- // 1 to the distance of sequence 3 to sequence 1,
- // 2 to the distance of sequence 3 to sequence 2.
- SeqMap currentRight = right[i]; // same as left but with distances on the right side.
-
- for (int j = 0; j < i; j++) {
-
- if (m->control_pressed) { return 0; }
-
- itL = currentLeft.find(j);
- itR = currentRight.find(j);
-//cout << " i = " << i << " j = " << j << " distLeft = " << itL->second << endl;
-//cout << " i = " << i << " j = " << j << " distright = " << itR->second << endl;
-
- //if you can find this entry update the preferences
- if ((itL != currentLeft.end()) && (itR != currentRight.end())) {
-
- if (!correction) {
- pref[count][i].score += abs((itL->second - itR->second));
- pref[count][j].score += abs((itL->second - itR->second));
-//cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
-//cout << "abs = " << abs((itL->second - itR->second)) << endl;
-//cout << i << " score = " << pref[i].score[1] << endl;
-//cout << j << " score = " << pref[j].score[1] << endl;
- }else {
- pref[count][i].score += abs((sqrt(itL->second) - sqrt(itR->second)));
- pref[count][j].score += abs((sqrt(itL->second) - sqrt(itR->second)));
-//cout << "left " << i << " " << j << " = " << itL->second << " right " << i << " " << j << " = " << itR->second << endl;
-//cout << "abs = " << abs((sqrt(itL->second) - sqrt(itR->second))) << endl;
-//cout << i << " score = " << pref[i].score[1] << endl;
-//cout << j << " score = " << pref[j].score[1] << endl;
- }
-//cout << "pref[" << i << "].closestLeft[1] = " << pref[i].closestLeft[1] << " parent = " << pref[i].leftParent[1] << endl;
- //are you the closest left sequence
- if (itL->second < pref[count][i].closestLeft) {
-
- pref[count][i].closestLeft = itL->second;
- pref[count][i].leftParent = seqs[j]->getName();
-//cout << "updating closest left to " << pref[i].leftParent[1] << endl;
- }
-//cout << "pref[" << j << "].closestLeft[1] = " << pref[j].closestLeft[1] << " parent = " << pref[j].leftParent[1] << endl;
- if (itL->second < pref[count][j].closestLeft) {
- pref[count][j].closestLeft = itL->second;
- pref[count][j].leftParent = seqs[i]->getName();
-//cout << "updating closest left to " << pref[j].leftParent[1] << endl;
- }
-
- //are you the closest right sequence
- if (itR->second < pref[count][i].closestRight) {
- pref[count][i].closestRight = itR->second;
- pref[count][i].rightParent = seqs[j]->getName();
- }
- if (itR->second < pref[count][j].closestRight) {
- pref[count][j].closestRight = itR->second;
- pref[count][j].rightParent = seqs[i]->getName();
- }
-
- }
- }
-
- }
-
-
- return 1;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "generatePreferences");
- exit(1);
- }
-}
-/**************************************************************************************************/
-vector<Preference> Bellerophon::getBestPref() {
- try {
-
- vector<Preference> best;
-
- //for each sequence
- for (int i = 0; i < numSeqs; i++) {
-
- //set best pref score to first one
- Preference temp = pref[0][i];
-
- if (m->control_pressed) { return best; }
-
- //for each window
- for (int j = 1; j < pref.size(); j++) {
-
- //is this a better score
- if (pref[j][i].score > temp.score) { temp = pref[j][i]; }
- }
-
- best.push_back(temp);
- }
-
- //rank preference score to eachother
- float dme = 0.0;
- float expectedPercent = 1 / (float) (best.size());
-
- for (int i = 0; i < best.size(); i++) { dme += best[i].score; }
-
- for (int i = 0; i < best.size(); i++) {
-
- if (m->control_pressed) { return best; }
-
- //gives the actual percentage of the dme this seq adds
- best[i].score = best[i].score / dme;
-
- //how much higher or lower is this than expected
- best[i].score = best[i].score / expectedPercent;
-
- }
-
- //sort Preferences highest to lowest
- sort(best.begin(), best.end(), comparePref);
-
- return best;
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "getBestPref");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int Bellerophon::writePrefs(string file, linePair tempLine) {
- try {
-
- ofstream outTemp;
- m->openOutputFile(file, outTemp);
-
- //lets you know what part of the pref matrix you are writing
- outTemp << tempLine.start << '\t' << tempLine.num << endl;
-
- for (int i = tempLine.start; i < (tempLine.start + tempLine.num); i++) {
-
- for (int j = 0; j < numSeqs; j++) {
-
- if (m->control_pressed) { outTemp.close(); m->mothurRemove(file); return 0; }
-
- outTemp << pref[i][j].name << '\t' << pref[i][j].leftParent << '\t' << pref[i][j].rightParent << '\t';
- outTemp << pref[i][j].score << '\t' << pref[i][j].closestLeft << '\t' << pref[i][j].closestRight << '\t' << pref[i][j].midpoint << endl;
- }
- }
-
- outTemp.close();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "writePrefs");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int Bellerophon::readPrefs(string file) {
- try {
-
- ifstream inTemp;
- m->openInputFile(file, inTemp);
-
- int start, num;
-
- //lets you know what part of the pref matrix you are writing
- inTemp >> start >> num; m->gobble(inTemp);
-
- for (int i = start; i < num; i++) {
-
- for (int j = 0; j < numSeqs; j++) {
-
- if (m->control_pressed) { inTemp.close(); m->mothurRemove(file); return 0; }
-
- inTemp >> pref[i][j].name >> pref[i][j].leftParent >> pref[i][j].rightParent;
- inTemp >> pref[i][j].score >> pref[i][j].closestLeft >> pref[i][j].closestRight >> pref[i][j].midpoint;
- m->gobble(inTemp);
- }
- }
-
- inTemp.close();
-
- m->mothurRemove(file);
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "writePrefs");
- exit(1);
- }
-}
-/**************************************************************************************************/
-vector<string> Bellerophon::getBestWindow(linePair line) {
- try {
-
- vector<string> best;
-
- //for each sequence
- for (int i = 0; i < numSeqs; i++) {
-
- //set best pref score to first one
- Preference temp = pref[line.start][i];
-
- if (m->control_pressed) { return best; }
-
- //for each window
- for (int j = (line.start+1); j < (line.start+line.num); j++) {
-
- //is this a better score
- if (pref[j][i].score > temp.score) { temp = pref[j][i]; }
- }
-
- string tempString = temp.name + '\t' + temp.leftParent + '\t' + temp.rightParent + '\t' + toString(temp.score);
- best.push_back(tempString);
- }
-
- return best;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "getBestWindow");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int Bellerophon::fillPref(int process, vector<string>& best) {
- try {
- //figure out where you start so you can put the best scores there
- int numSeqsPerProcessor = iters / processors;
- int start = process * numSeqsPerProcessor;
-
- for (int i = 0; i < best.size(); i++) {
-
- if (m->control_pressed) { return 0; }
-
- istringstream iss (best[i],istringstream::in);
-
- string tempScore;
- iss >> pref[start][i].name >> pref[start][i].leftParent >> pref[start][i].rightParent >> tempScore;
- convert(tempScore, pref[start][i].score);
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Bellerophon", "fillPref");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
projects / mothur.git / blobdiff