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/*
* alignmentdb.cpp
* Mothur
*
* Created by westcott on 11/4/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "alignmentdb.h"
#include "kmerdb.hpp"
#include "suffixdb.hpp"
/**************************************************************************************************/
AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid, bool writeShortcut){ // This assumes that the template database is in fasta format, may
try { // need to alter this in the future?
m = MothurOut::getInstance();
current = CurrentFile::getInstance();
longest = 0;
method = s;
bool needToGenerate = true;
threadID = tid;
Utils util;
long start = time(nullptr);
m->mothurOut("\nReading in the " + fastaFileName + " template sequences...\t"); cout.flush();
//bool aligned = false;
int tempLength = 0;
ifstream fastaFile; util.openInputFile(fastaFileName, fastaFile);
while (!fastaFile.eof()) {
Sequence temp(fastaFile); gobble(fastaFile);
if (m->getControl_pressed()) { templateSequences.clear(); break; }
if (temp.getName() != "") {
templateSequences.push_back(temp);
//save longest base
if (temp.getUnaligned().length() >= longest) { longest = ((int)temp.getUnaligned().length()+1); }
if (tempLength != 0) {
if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->setControl_pressed(true); }
}else { tempLength = (int)temp.getAligned().length(); }
}
}
fastaFile.close();
numSeqs = (int)templateSequences.size();
//all of this is elsewhere already!
m->mothurOut("DONE.\n");
cout.flush();
m->mothurOut("It took " + toString(time(nullptr) - start) + " to read " + toString(templateSequences.size()) + " sequences.\n");
//in case you delete the seqs and then ask for them
emptySequence = Sequence();
emptySequence.setName("no_match");
emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
string kmerDBName;
if(method == "kmer") {
search = new KmerDB(fastaFileName, kmerSize);
kmerDBName = fastaFileName.substr(0,fastaFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
ifstream kmerFileTest(kmerDBName.c_str());
if(kmerFileTest){
string line = util.getline(kmerFileTest);
bool GoodFile = util.checkReleaseVersion(line, current->getVersion()); kmerFileTest.close();
int shortcutTimeStamp = util.getTimeStamp(kmerDBName);
int referenceTimeStamp = util.getTimeStamp(fastaFileName);
//if the shortcut file is older then the reference file, remake shortcut file
if (shortcutTimeStamp < referenceTimeStamp) { GoodFile = false; }
if (GoodFile) { needToGenerate = false; }
}
}
else if(method == "suffix") { search = new SuffixDB(numSeqs); }
else {
method = "kmer";
m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.\n");
search = new KmerDB(fastaFileName, 8);
}
if (!m->getControl_pressed()) {
if (needToGenerate) {
//add sequences to search
for (int i = 0; i < templateSequences.size(); i++) {
search->addSequence(templateSequences[i]);
if (m->getControl_pressed()) { templateSequences.clear(); break; }
}
if (m->getControl_pressed()) { templateSequences.clear(); }
if ((method != "kmer") || ((method == "kmer") && (writeShortcut))) { search->generateDB(); }
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
search->readDB(kmerFileTest);
}
search->setNumSeqs(numSeqs);
}
}
catch(exception& e) {
m->errorOut(e, "AlignmentDB", "AlignmentDB");
exit(1);
}
}
/**************************************************************************************************/
AlignmentDB::AlignmentDB(string s){
try {
m = MothurOut::getInstance();
method = s;
if(method == "suffix") { search = new SuffixDB(); }
else { search = new KmerDB(); }
//in case you delete the seqs and then ask for them
emptySequence = Sequence();
emptySequence.setName("no_match");
emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
}
catch(exception& e) {
m->errorOut(e, "AlignmentDB", "AlignmentDB");
exit(1);
}
}
/**************************************************************************************************/
AlignmentDB::~AlignmentDB() { delete search; }
/**************************************************************************************************/
Sequence AlignmentDB::findClosestSequence(Sequence* seq, float& searchScore) const {
try{
vector<float> scores;
vector<int> spot = search->findClosestSequences(seq, 1, scores);
if (spot.size() != 0) { searchScore = scores[0]; return templateSequences[spot[0]]; }
else { searchScore = 0; return emptySequence; }
}
catch(exception& e) {
m->errorOut(e, "AlignmentDB", "findClosestSequence");
exit(1);
}
}
/**************************************************************************************************/
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