void GenBank::appendFromStream(istream & input, VectorSequenceContainer & vsc) const throw (Exception)
{
if (!input) {
throw IOException ("GenBank::read: fail to open file");
}
string temp, name, sequence = ""; // Initialization
// Main loop : for all file lines
while (!input.eof())
{
getline(input, temp, '\n'); // Copy current line in temporary string
if(temp.size() >= 9 && temp.substr(0,9) == "ACCESSION")
{
name = TextTools::removeSurroundingWhiteSpaces(temp.substr(10));
StringTokenizer st(name, " ");
name = st.nextToken();
//cout << name << endl;
}
if(temp.size() >=6 && temp.substr(0,6) == "ORIGIN")
{
sequence = "";
getline(input, temp, '\n'); // Copy current line in temporary string
while(!input.eof() && temp.size() > 2 && temp.substr(0,2) != "//")
{
sequence += TextTools::removeWhiteSpaces(temp.substr(10));
getline(input, temp, '\n'); // Copy current line in temporary string
}
if(name == "") throw Exception("GenBank::read(). Sequence with no ACCESSION number!");
Sequence * seq = new Sequence(name, sequence, vsc.getAlphabet());
vsc.addSequence(* seq);
name = "";
}
}
}
void Mase::appendFromStream(istream & input, VectorSequenceContainer & vsc) const throw (Exception)
{
if (!input) { throw IOException ("Mase::read : fail to open file"); }
// Initialization
Comments seqComments, fileComments;
string temp, name, sequence = "";
bool comments = false;
// Get current general comments is VectorSequenceContainer
fileComments = vsc.getGeneralComments();
// Main loop : for all file lines
while(!input.eof())
{
getline(input, temp, '\n'); // Copy current line in temporary string
// If first character is ;
if(temp[0] == ';')
{
// If second character is also ;
if(temp[1] == ';')
{
// File comments isolation
temp.erase(0,2); // Characters ;; deletion
if(temp != "") fileComments.push_back(temp);
}
else
{
// If a name and a sequence were founded
if((name != "") && (sequence != ""))
{
// New sequence creation, and addition in existing VectorSequenceContainer
vsc.addSequence(Sequence(name, sequence, seqComments, vsc.getAlphabet()), _checkNames);
name = "";
sequence = "";
seqComments.clear();
}
// Sequence commentaries isolation
temp.erase(temp.begin()); // Character ; deletion
if(temp != "") seqComments.push_back(temp);
comments = true;
}
}
else
{
// If sequence commentaries were just isolated
if(comments)
{
// Sequence name isolation
name = temp;
comments = false;
}
else sequence += temp; // Sequence isolation
}
}
// Addition of the last sequence in file
if((name != "") && (sequence != ""))
{
vsc.addSequence(Sequence(name, sequence, seqComments, vsc.getAlphabet()), _checkNames);
}
// Set new general comments in VectorSequenceContainer (old + new comments)
vsc.setGeneralComments(fileComments);
}
