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/*
* sequencedb.cpp
* Mothur
*
* Created by Thomas Ryabin on 4/13/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "sequencedb.h"
#include "sequence.hpp"
#include "mothur.h"
#include "calculator.h"
#include "kmer.hpp"
/***********************************************************************/
SequenceDB::SequenceDB() : StorageDatabase(){};
/***********************************************************************/
//the clear function free's the memory
SequenceDB::~SequenceDB() { data.clear(); }
/***********************************************************************/
SequenceDB::SequenceDB(int newSize) : StorageDatabase() { data.resize(newSize, Sequence()); }
/***********************************************************************/
//kmerDB[0] = vector<int> maxKmers long, contains kmer counts
SequenceDB::SequenceDB(ifstream& filehandle, int kmerSize, vector< vector< int > >& kmerDB, vector< int >& lengths) {
try{
Utils util; length = 0; samelength = true; lengths.clear(); kmerDB.clear();
int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
int maxKmer = power4s[kmerSize];
Kmer kmer(kmerSize);
while (!filehandle.eof()) {
//input sequence info into sequencedb
Sequence newSequence(filehandle); gobble(filehandle);
if (newSequence.getName() != "") {
if (length == 0) { length = newSequence.getAligned().length(); }
if (length != newSequence.getAligned().length()) { samelength = false; }
data.push_back(newSequence);
vector<int> kmerLocations; kmerLocations.resize(maxKmer+1, 0);
int numKmers = newSequence.getNumBases() - kmerSize + 1;
for(int i=0;i<numKmers;i++){
int kmerNumber = kmer.getKmerNumber(newSequence.getUnaligned(), i);
kmerLocations[kmerNumber]++; //ok, we've seen the kmer now
}
kmerDB.push_back(kmerLocations);
lengths.push_back(newSequence.getNumBases());
}
}
filehandle.close();
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "SequenceDB");
exit(1);
}
}
/***********************************************************************/
SequenceDB::SequenceDB(ifstream& filehandle) : StorageDatabase() {
try{
//read through file
while (!filehandle.eof()) {
//input sequence info into sequencedb
Sequence newSequence(filehandle);
if (newSequence.getName() != "") {
if (length == 0) { length = newSequence.getAligned().length(); }
if (length != newSequence.getAligned().length()) { samelength = false; }
data.push_back(newSequence);
}
//takes care of white space
gobble(filehandle);
}
filehandle.close();
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "SequenceDB");
exit(1);
}
}
/***********************************************************************/
SequenceDB::SequenceDB(const SequenceDB& sdb, unordered_set<string> names) : StorageDatabase() {
try{
int numSeqs = sdb.data.size();
for (int i = 0; i < numSeqs; i++) {
Sequence seqI = sdb.data[i];
if (names.count(seqI.getName()) != 0) {
if (length == 0) { length = seqI.getAligned().length(); }
if (length != seqI.getAligned().length()) { samelength = false; }
data.push_back(seqI);
}
}
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "SequenceDB");
exit(1);
}
}
/***********************************************************************/
SequenceDB::SequenceDB(const SequenceDB& sdb, unordered_set<string> names, int kmerSize, vector< vector< int > >& kmerDB, vector< int >& lengths) : StorageDatabase() {
try{
int numSeqs = sdb.data.size();
Utils util; length = 0; samelength = true; lengths.clear(); kmerDB.clear();
int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
int maxKmer = power4s[kmerSize];
Kmer kmer(kmerSize);
for (int i = 0; i < numSeqs; i++) {
Sequence newSequence = sdb.data[i];
if (names.count(newSequence.getName()) != 0) {
if (length == 0) { length = newSequence.getAligned().length(); }
if (length != newSequence.getAligned().length()) { samelength = false; }
data.push_back(newSequence);
vector<int> kmerLocations; kmerLocations.resize(maxKmer+1, 0);
int numKmers = newSequence.getNumBases() - kmerSize + 1;
for(int i=0;i<numKmers;i++){
int kmerNumber = kmer.getKmerNumber(newSequence.getUnaligned(), i);
kmerLocations[kmerNumber]++; //ok, we've seen the kmer now
}
kmerDB.push_back(kmerLocations);
lengths.push_back(newSequence.getNumBases());
}
}
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "SequenceDB");
exit(1);
}
}
/***********************************************************************/
int SequenceDB::getNumSeqs() {
return data.size();
}
/***********************************************************************/
Sequence SequenceDB::getSeq(int index) {
return data[index];
}
/***********************************************************************/
void SequenceDB::push_back(Sequence newSequence) {
try {
if (length == 0) { length = newSequence.getAligned().length(); }
if (length != newSequence.getAligned().length()) { samelength = false; }
data.push_back(newSequence);
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "push_back");
exit(1);
}
}
/***********************************************************************/
void SequenceDB::print(string outputFileName) {
try {
ofstream out; util.openOutputFile(outputFileName, out);
for (int i = 0; i < data.size(); i++) {
data[i].printSequence(out);
}
out.close();
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "print");
exit(1);
}
}
/***********************************************************************/
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