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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"
/***********************************************************************/
SequenceDB::SequenceDB() { m = MothurOut::getInstance(); length = 0; samelength = true; }
/***********************************************************************/
//the clear function free's the memory
SequenceDB::~SequenceDB() { clear(); }
/***********************************************************************/
SequenceDB::SequenceDB(int newSize) {
data.resize(newSize, Sequence());
length = 0; samelength = true;
}
/***********************************************************************/
SequenceDB::SequenceDB(ifstream& filehandle) {
try{
length = 0; samelength = true;
//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
m->gobble(filehandle);
}
filehandle.close();
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "SequenceDB");
exit(1);
}
}
/*******************************************************************************/
string SequenceDB::readName(ifstream& in) {
try{
string name = "";
int c;
string temp;
while ((c = in.get()) != EOF) {
//if c is not a line return
if (c != 10) {
name += c;
}else { break; }
}
return name;
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "readName");
exit(1);
}
}
/*******************************************************************************/
string SequenceDB::readSequence(ifstream& in) {
try{
string sequence = "";
string line;
int pos, c;
while (!in.eof()) {
//save position in file in case next line is a new name.
pos = in.tellg();
line = "";
in >> line;
//if you are at a new name
if (line[0] == '>') {
//put file pointer back since you are now at a new name
in.seekg(pos, ios::beg);
c = in.get(); //because you put it back to a newline char
break;
}else { sequence += line; }
}
if (length == 0) { length = sequence.length(); }
if (length != sequence.length()) { samelength = false; }
return sequence;
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "readSequence");
exit(1);
}
}
/***********************************************************************/
int SequenceDB::getNumSeqs() {
return data.size();
}
/***********************************************************************/
void SequenceDB::set(int index, string newUnaligned) {
try {
if (length == 0) { length = newUnaligned.length(); }
if (length != newUnaligned.length()) { samelength = false; }
data[index] = Sequence(data[index].getName(), newUnaligned);
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "set");
exit(1);
}
}
/***********************************************************************/
void SequenceDB::set(int index, Sequence newSeq) {
try {
if (length == 0) { length = newSeq.getAligned().length(); }
if (length != newSeq.getAligned().length()) { samelength = false; }
data[index] = newSeq;
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "set");
exit(1);
}
}
/***********************************************************************/
Sequence SequenceDB::get(int index) {
return data[index];
}
/***********************************************************************/
void SequenceDB::resize(int newSize) {
try {
data.resize(newSize);
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "resize");
exit(1);
}
}
/***********************************************************************/
void SequenceDB::clear() {
try {
data.clear();
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "clear");
exit(1);
}
}
/***********************************************************************/
int SequenceDB::size() {
return data.size();
}
/***********************************************************************/
void SequenceDB::print(ostream& out) {
try {
for(int i = 0; i < data.size(); i++) {
data[i].printSequence(out);
}
}
catch(exception& e) {
m->errorOut(e, "SequenceDB", "print");
exit(1);
}
}
/***********************************************************************/
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);
}
}
/***********************************************************************/
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