void CSeqVector_CI::GetSeqData(string& buffer, TSeqPos count)
{
buffer.erase();
TSeqPos pos = GetPos();
_ASSERT(pos <= x_GetSize());
count = min(count, x_GetSize() - pos);
if ( !count ) {
return;
}
if ( m_TSE && !CanGetRange(pos, pos+count) ) {
NCBI_THROW_FMT(CSeqVectorException, eDataError,
"CSeqVector_CI::GetSeqData: "
"cannot get seq-data in range: "
<<pos<<"-"<<pos+count);
}
buffer.reserve(count);
while ( count ) {
TCache_I cache = m_Cache;
TCache_I cache_end = m_CacheEnd;
TSeqPos chunk_count = min(count, TSeqPos(cache_end - cache));
_ASSERT(chunk_count > 0);
TCache_I chunk_end = cache + chunk_count;
buffer.append(cache, chunk_end);
count -= chunk_count;
//if ( count == 0 ) break;
if ( chunk_end == cache_end ) {
x_NextCacheSeg();
}
else {
m_Cache = chunk_end;
}
}
}
void CSeqVector_CI::x_CheckForward(void)
{
TSeqPos scanned = m_ScannedEnd - m_ScannedStart;
TSeqPos more = x_GetSize() - m_ScannedEnd;
TSeqPos check = min(min(scanned, more), kMaxPreloadBases);
if ( check > 0 ) {
CanGetRange(m_ScannedEnd, m_ScannedEnd+check);
}
}
void CSeqVector_CI::x_CheckBackward(void)
{
TSeqPos scanned = m_ScannedEnd - m_ScannedStart;
TSeqPos more = m_ScannedStart;
TSeqPos check = min(min(scanned, more), kMaxPreloadBases);
if ( check > 0 ) {
CanGetRange(m_ScannedStart-check, m_ScannedStart);
}
}
void CSeqVector::GetPackedSeqData(string& dst_str,
TSeqPos src_pos,
TSeqPos src_end)
{
dst_str.erase();
src_end = min(src_end, size());
if ( src_pos >= src_end ) {
return;
}
if ( m_TSE && !CanGetRange(src_pos, src_end) ) {
NCBI_THROW_FMT(CSeqVectorException, eDataError,
"CSeqVector::GetPackedSeqData: "
"cannot get seq-data in range: "
<<src_pos<<"-"<<src_end);
}
TCoding dst_coding = GetCoding();
switch ( dst_coding ) {
case CSeq_data::e_Iupacna:
case CSeq_data::e_Ncbi8na:
case CSeq_data::e_Iupacaa:
case CSeq_data::e_Ncbieaa:
case CSeq_data::e_Ncbi8aa:
case CSeq_data::e_Ncbistdaa:
x_GetPacked8SeqData(dst_str, src_pos, src_end);
break;
case CSeq_data::e_Ncbi4na:
x_GetPacked4naSeqData(dst_str, src_pos, src_end);
break;
case CSeq_data::e_Ncbi2na:
x_GetPacked2naSeqData(dst_str, src_pos, src_end);
break;
default:
NCBI_THROW_FMT(CSeqVectorException, eCodingError,
"Can not pack data using the selected coding: "<<
GetCoding());
}
}
