string WordStringReader::getNextWord()
{
if( isSingleWord() )
{
m_readPos = m_text.length();
return m_text;
}
size_t uNextSpacePosition = m_text.find(' ', m_readPos+1);
if( uNextSpacePosition == string::npos && m_readPos != m_text.length() )
{
size_t count = m_text.length() - m_readPos - 1;
size_t start = m_readPos;
m_readPos = m_text.length();
return m_text.substr(start+1, count);
}
if( uNextSpacePosition != string::npos )
{
size_t start = isFirstRead() ? m_readPos : m_readPos + 1;
size_t count = uNextSpacePosition - start;
m_readPos = uNextSpacePosition;
return m_text.substr(start, count);
}
return "";
}
string WordStringReader::getRemainder()
{
if( m_readPos >= m_text.length() )
return "";
size_t startPos = isFirstRead() ? m_readPos : m_readPos + 1;
return m_text.substr(startPos);
}
/// @deprecated - This is incorrect!
ReadType getReadType(LibraryType lib) const
{
if (!shouldHaveMate() || isFirstRead())
// This isn't valid! F3 isn't always first,
// and an unpaired read isn't always F3
return READ_TYPE_F3;
switch (lib)
{
case LIBRARY_TYPE_RR:
return READ_TYPE_F5_P2;
case LIBRARY_TYPE_RRBC:
return READ_TYPE_F5_BC;
default:
return READ_TYPE_R3; // LIBRARY_TYPE_MP
}
}