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/////////////////////////////////////////////////////////////////
// Sequence.h
//
// Class for reading/manipulating single sequence character data.
/////////////////////////////////////////////////////////////////
#ifndef SEQUENCE_H
#define SEQUENCE_H
#include <string>
#include <fstream>
#include <iostream>
#include <cctype>
#include <cstdlib>
#include "SafeVector.h"
#include "FileBuffer.h"
/////////////////////////////////////////////////////////////////
// Sequence
//
// Class for storing sequence information.
/////////////////////////////////////////////////////////////////
class Sequence {
bool isValid; // a boolean indicating whether the sequence data is valid or not
string header; // string containing the comment line of the FASTA file
SafeVector<char> *data; // pointer to character data
int length; // length of the sequence
int sequenceLabel; // integer sequence label, typically to indicate the ordering of sequences
// in a Multi-FASTA file
int inputLabel; // position of sequence in original input
/////////////////////////////////////////////////////////////////
// Sequence::Sequence()
//
// Default constructor. Does nothing.
/////////////////////////////////////////////////////////////////
Sequence () : isValid (false), header (""), data (NULL), length (0), sequenceLabel (0), inputLabel (0) {}
public:
/////////////////////////////////////////////////////////////////
// Sequence::Sequence()
//
// Constructor. Reads the sequence from a FileBuffer.
/////////////////////////////////////////////////////////////////
Sequence (FileBuffer &infile, bool stripGaps = false) : isValid (false), header ("~"), data (NULL), length(0), sequenceLabel (0), inputLabel (0) {
// read until the first non-blank line
while (!infile.eof()){
infile.GetLine (header);
if (header.length() != 0) break;
}
// check to make sure that it is a correct header line
if (header[0] == '>'){
// if so, remove the leading ">"
header = header.substr (1);
// remove any leading or trailing white space in the header comment
while (header.length() > 0 && isspace (header[0])) header = header.substr (1);
while (header.length() > 0 && isspace (header[header.length() - 1])) header = header.substr(0, header.length() - 1);
// get ready to read the data[] array; note that data[0] is always '@'
char ch;
data = new SafeVector<char>; assert (data);
data->push_back ('@');
// get a character from the file
while (infile.Get(ch)){
// if we've reached a new comment line, put the character back and stop
if (ch == '>'){ infile.UnGet(); break; }
// skip whitespace
if (isspace (ch)) continue;
// substitute gap character
if (ch == '.') ch = '-';
if (stripGaps && ch == '-') continue;
// check for known characters
if (!((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z') || ch == '*' || ch == '-')){
cerr << "ERROR: Unknown character encountered: " << ch << endl;
exit (1);
}
// everything's ok so far, so just store this character.
data->push_back(ch);
++length;
}
// sequence must contain data in order to be valid
isValid = length > 0;
if (!isValid){
delete data;
data = NULL;
}
}
}
/////////////////////////////////////////////////////////////////
// Sequence::Sequence()
//
// Constructor. Builds a sequence from existing data. Note
// that the data must use one-based indexing where data[0] should
// be set to '@'.
/////////////////////////////////////////////////////////////////
Sequence (SafeVector<char> *data, string header, int length, int sequenceLabel, int inputLabel) :
isValid (data != NULL), header(header), data(data), length (length), sequenceLabel (sequenceLabel), inputLabel (inputLabel) {
assert (data);
assert ((*data)[0] == '@');
}
/////////////////////////////////////////////////////////////////
// Sequence::Sequence()
//
// Destructor. Release allocated memory.
/////////////////////////////////////////////////////////////////
~Sequence (){
if (data){
assert (isValid);
delete data;
data = NULL;
isValid = false;
}
}
/////////////////////////////////////////////////////////////////
// Sequence::GetHeader()
//
// Return the string comment associated with this sequence.
/////////////////////////////////////////////////////////////////
string GetHeader () const {
return header;
}
/////////////////////////////////////////////////////////////////
// Sequence::GetName()
//
// Return the first word of the string comment associated with this sequence.
/////////////////////////////////////////////////////////////////
string GetName () const {
char name[1024];
sscanf (header.c_str(), "%s", name);
return string(name);
}
/////////////////////////////////////////////////////////////////
// Sequence::GetDataPtr()
//
// Return the iterator to data associated with this sequence.
/////////////////////////////////////////////////////////////////
SafeVector<char>::iterator GetDataPtr(){
assert (isValid);
assert (data);
return data->begin();
}
/////////////////////////////////////////////////////////////////
// Sequence::GetPosition()
//
// Return the character at position i. Recall that the character
// data is stored with one-based indexing.
/////////////////////////////////////////////////////////////////
char GetPosition (int i) const {
assert (isValid);
assert (data);
assert (i >= 1 && i <= length);
return (*data)[i];
}
/////////////////////////////////////////////////////////////////
// Sequence::SetLabel()
//
// Sets the sequence label to i.
/////////////////////////////////////////////////////////////////
void SetLabel (int i){
assert (isValid);
sequenceLabel = i;
inputLabel = i;
}
/////////////////////////////////////////////////////////////////
// Sequence::SetSortLabel()
//
// Sets the sequence sorting label to i.
/////////////////////////////////////////////////////////////////
void SetSortLabel (int i){
assert (isValid);
sequenceLabel = i;
}
/////////////////////////////////////////////////////////////////
// Sequence::GetLabel()
//
// Retrieves the input label.
/////////////////////////////////////////////////////////////////
int GetLabel () const {
assert (isValid);
return inputLabel;
}
/////////////////////////////////////////////////////////////////
// Sequence::GetSortLabel()
//
// Retrieves the sorting label.
/////////////////////////////////////////////////////////////////
int GetSortLabel () const {
assert (isValid);
return sequenceLabel;
}
/////////////////////////////////////////////////////////////////
// Sequence::Fail()
//
// Checks to see if the sequence successfully loaded.
/////////////////////////////////////////////////////////////////
bool Fail () const {
return !isValid;
}
/////////////////////////////////////////////////////////////////
// Sequence::Length()
//
// Returns the length of the sequence.
/////////////////////////////////////////////////////////////////
int GetLength () const {
assert (isValid);
assert (data);
return length;
}
/////////////////////////////////////////////////////////////////
// Sequence::WriteMFA()
//
// Writes the sequence to outfile in MFA format. Uses numColumns
// columns per line. If useIndex is set to false, then the
// header is printed as normal, but if useIndex is true, then
// ">S###" is printed where ### represents the sequence label.
/////////////////////////////////////////////////////////////////
void WriteMFA (ostream &outfile, int numColumns, bool useIndex = false) const {
assert (isValid);
assert (data);
assert (!outfile.fail());
// print out heading
if (useIndex)
outfile << ">S" << GetLabel() << endl;
else
outfile << ">" << header << endl;
// print out character data
int ct = 1;
for (; ct <= length; ct++){
outfile << (*data)[ct];
if (ct % numColumns == 0) outfile << endl;
}
if ((ct-1) % numColumns != 0) outfile << endl;
}
/////////////////////////////////////////////////////////////////
// Sequence::Clone()
//
// Returns a new deep copy of the seqeuence.
/////////////////////////////////////////////////////////////////
Sequence *Clone () const {
Sequence *ret = new Sequence();
assert (ret);
ret->isValid = isValid;
ret->header = header;
ret->data = new SafeVector<char>; assert (ret->data);
*(ret->data) = *data;
ret->length = length;
ret->sequenceLabel = sequenceLabel;
ret->inputLabel = inputLabel;
return ret;
}
/////////////////////////////////////////////////////////////////
// Sequence::GetRange()
//
// Returns a new sequence object consisting of a range of
// characters from the current seuquence.
/////////////////////////////////////////////////////////////////
Sequence *GetRange (int start, int end) const {
Sequence *ret = new Sequence();
assert (ret);
assert (start >= 1 && start <= length);
assert (end >= 1 && end <= length);
assert (start <= end);
ret->isValid = isValid;
ret->header = header;
ret->data = new SafeVector<char>; assert (ret->data);
ret->data->push_back ('@');
for (int i = start; i <= end; i++)
ret->data->push_back ((*data)[i]);
ret->length = end - start + 1;
ret->sequenceLabel = sequenceLabel;
ret->inputLabel = inputLabel;
return ret;
}
/////////////////////////////////////////////////////////////////
// Sequence::AddGaps()
//
// Given an SafeVector<char> containing the skeleton for an
// alignment and the identity of the current character, this
// routine will create a new sequence with all necesssary gaps added.
// For instance,
// alignment = "XXXBBYYYBBYYXX"
// id = 'X'
// will perform the transformation
// "ATGCAGTCA" --> "ATGCC---GT--CA"
// (XXXBBYYYBBYYXX)
/////////////////////////////////////////////////////////////////
Sequence *AddGaps (SafeVector<char> *alignment, char id){
Sequence *ret = new Sequence();
assert (ret);
ret->isValid = isValid;
ret->header = header;
ret->data = new SafeVector<char>; assert (ret->data);
ret->length = (int) alignment->size();
ret->sequenceLabel = sequenceLabel;
ret->inputLabel = inputLabel;
ret->data->push_back ('@');
SafeVector<char>::iterator dataIter = data->begin() + 1;
for (SafeVector<char>::iterator iter = alignment->begin(); iter != alignment->end(); ++iter){
if (*iter == 'B' || *iter == id){
ret->data->push_back (*dataIter);
++dataIter;
}
else
ret->data->push_back ('-');
}
return ret;
}
/////////////////////////////////////////////////////////////////
// Sequence::GetString()
//
// Returns the sequence as a string with gaps removed.
/////////////////////////////////////////////////////////////////
string GetString (){
string s = "";
for (int i = 1; i <= length; i++){
if ((*data)[i] != '-') s += (*data)[i];
}
return s;
}
/////////////////////////////////////////////////////////////////
// Sequence::GetMapping()
//
// Returns a SafeVector<int> containing the indices of every
// character in the sequence. For instance, if the data is
// "ATGCC---GT--CA", the method returns {1,2,3,4,5,9,10,13,14}.
/////////////////////////////////////////////////////////////////
SafeVector<int> *GetMapping () const {
SafeVector<int> *ret = new SafeVector<int>(1, 0);
for (int i = 1; i <= length; i++){
if ((*data)[i] != '-') ret->push_back (i);
}
return ret;
}
/////////////////////////////////////////////////////////////////
// Sequence::Highlight()
//
// Changes all positions with score >= cutoff to upper case and
// all positions with score < cutoff to lower case.
/////////////////////////////////////////////////////////////////
void Highlight (const SafeVector<float> &scores, const float cutoff){
for (int i = 1; i <= length; i++){
if (scores[i-1] >= cutoff)
(*data)[i] = toupper ((*data)[i]);
else
(*data)[i] = tolower ((*data)[i]);
}
}
};
#endif
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