bool Aligner::Align(const char* query, const Filter& filter,
Alignment* alignment) const
{
if (!translation_matrix_) return false;
if (reference_length_ == 0) return false;
int query_len = strlen(query);
if (query_len == 0) return false;
int8_t* translated_query = new int8_t[query_len];
TranslateBase(query, query_len, translated_query);
const int8_t score_size = 2;
s_profile* profile = ssw_init(translated_query, query_len, score_matrix_,
score_matrix_size_, score_size);
uint8_t flag = 0;
SetFlag(filter, &flag);
s_align* s_al = ssw_align(profile, translated_reference_, reference_length_,
static_cast<int>(gap_opening_penalty_),
static_cast<int>(gap_extending_penalty_),
flag, filter.score_filter, filter.distance_filter, query_len);
alignment->Clear();
ConvertAlignment(*s_al, query_len, alignment);
alignment->mismatches = CalculateNumberMismatch(&*alignment, translated_reference_, translated_query, query_len);
// Free memory
delete [] translated_query;
align_destroy(s_al);
init_destroy(profile);
return true;
}
// *********************************************************************
// InitFromCategory()
// *********************************************************************
void GdiLabelDrawer::InitFromCategory(CLabelOptions* options)
{
_penFontOutline.CreatePen(PS_SOLID, options->fontOutlineWidth, options->fontOutlineColor);
_penFrameOutline.CreatePen(options->frameOutlineStyle, options->frameOutlineWidth, options->frameOutlineColor);
double haloWidth = fabs(options->fontSize / 16.0 * options->haloSize);
_penHalo.CreatePen(PS_SOLID, (int)haloWidth, options->haloColor);
// we can select brush at once because it's the only one to use
_brushFrameBack.CreateSolidBrush(options->frameBackColor);
_oldBrush = _dc->SelectObject(&_brushFrameBack);
_alignment = ConvertAlignment(options->inboxAlignment);
_dc->SetTextColor(options->fontColor);
}
