void AddSpotId(string& short_id, const CBamAlignIterator* iter) {
string seq = iter->GetShortSequence();
if ( iter->IsSetStrand() && IsReverse(iter->GetStrand()) ) {
seq = Reverse(seq);
}
SShortSeqInfo& info = m_ShortSeqs[short_id];
if ( info.spot1.empty() ) {
info.spot1 = seq;
short_id += ".1";
return;
}
if ( info.spot1 == seq ) {
short_id += ".1";
return;
}
if ( info.spot2.empty() ) {
++m_ResolveCount;
info.spot2 = seq;
short_id += ".2";
return;
}
if ( info.spot2 == seq ) {
short_id += ".2";
return;
}
short_id += ".?";
}
void CSeqVector_CI::SetStrand(ENa_strand strand)
{
if ( IsReverse(m_Strand) == IsReverse(strand) ) {
m_Strand = strand;
return;
}
TSeqPos pos = GetPos();
m_Strand = strand;
x_ResetBackup();
if ( x_CacheSize() ) {
x_ResetCache();
if ( m_Seg ) {
m_Seg = CSeqMap_CI();
x_SetPos(pos);
}
}
}
// return true if there is zero-length gap before current position
// it might happen only if current position is at the beginning of buffer
bool CSeqVector_CI::HasZeroGapBefore(void)
{
if ( x_CacheOffset() != 0 ) {
return false;
}
TSeqPos pos = GetPos();
if ( IsReverse(m_Strand) ) {
pos = x_GetSize() - pos;
}
return m_SeqMap->HasZeroGapAt(pos, m_Scope.GetScopeOrNull());
}
//---------------------------------------------------------------------
void BaseTween::ForceToEnd(float _time)
{
m_currentTime = _time - GetFullDuration();
m_step = m_repeatCount*2 + 1;
m_flags.ChangeMask(eIsIteratingStep, false);
if(IsReverse(m_repeatCount*2))
{
ForceStartValues();
}
else
{
ForceEndValues();
}
}
//---------------------------------------------------------------------
void BaseTween::ForceToStart()
{
m_currentTime = -m_delay;
m_step = -1;
m_flags.ChangeMask(eIsIteratingStep, false);
if(IsReverse(0))
{
ForceEndValues();
}
else
{
ForceStartValues();
}
}
// Corresponds to SortFeatItemListByPos from the C toolkit
int CSeq_feat::CompareNonLocation(const CSeq_feat& f2,
const CSeq_loc& loc1,
const CSeq_loc& loc2) const
{
const CSeqFeatData& data1 = GetData();
const CSeqFeatData& data2 = f2.GetData();
CSeqFeatData::E_Choice type1 = data1.Which();
CSeqFeatData::E_Choice type2 = data2.Which();
// operon first
if ( int diff = s_IsOperon(data2) - s_IsOperon(data1) ) {
return diff;
}
if ( type1 != type2 ) {
// order by feature type
int order1 = GetTypeSortingOrder(type1);
int order2 = GetTypeSortingOrder(type2);
int diff = order1 - order2;
if ( diff != 0 )
return diff;
}
// minus strand last
ENa_strand strand1 = loc1.GetStrand();
ENa_strand strand2 = loc2.GetStrand();
if ( int diff = IsReverse(strand1) - IsReverse(strand2) ) {
return diff;
}
if ( int diff = loc1.CompareSubLoc(loc2, strand1) ) {
return diff;
}
{{ // compare subtypes
CSeqFeatData::ESubtype subtype1 = data1.GetSubtype();
CSeqFeatData::ESubtype subtype2 = data2.GetSubtype();
int diff = subtype1 - subtype2;
if ( diff != 0 )
return diff;
}}
// subtypes are equal, types must be equal too
_ASSERT(type1 == type2);
// type dependent comparison
if ( type1 == CSeqFeatData::e_Cdregion ) {
// compare frames of identical CDS ranges
if ( int diff = s_GetCdregionOrder(data1)-s_GetCdregionOrder(data2) ) {
return diff;
}
}
else if ( type1 == CSeqFeatData::e_Imp ) {
// compare labels of imp features
int diff = NStr::CompareNocase(data1.GetImp().GetKey(),
data2.GetImp().GetKey());
if ( diff != 0 )
return diff;
}
// XXX - should compare parent seq-annots
// XXX 1. parent Seq-annot idx.itemID
// XXX 2. features itemID
return 0; // unknown
}
//---------------------------------------------------------------------
void BaseTween::UpdateStep()
{
while(IsStepValid(m_step))
{
if(!IsIterationStep() && m_currentTime + m_dt <= 0.0f)
{
m_flags.ChangeMask(eIsIteratingStep, true);
-- m_step;
float fDt = 0.0f - m_currentTime;
m_dt -= fDt;
m_currentTime = m_duration;
(IsReverse(m_step)) ? ForceStartValues() : ForceEndValues();
CallCallback(eTweenBackStart);
OnUpdate(m_step, m_step + 1, IsIterationStep(), fDt);
}
else if(!IsIterationStep() && m_currentTime + m_dt >= m_repeatDelay)
{
m_flags.ChangeMask(eIsIteratingStep, true);
++ m_step;
float fDt = m_repeatDelay - m_currentTime;
m_dt -= fDt;
m_currentTime = 0.0f;
(IsReverse(m_step)) ? ForceEndValues() : ForceStartValues();
CallCallback(eTweenStart);
OnUpdate(m_step, m_step - 1, IsIterationStep(), fDt);
}
else if(IsIterationStep() && m_currentTime + m_dt < 0.0f)
{
m_flags.ChangeMask(eIsIteratingStep, false);
-- m_step;
float fDt = 0.0f - m_currentTime;
m_dt -= fDt;
m_currentTime = 0.0f;
OnUpdate(m_step, m_step + 1, IsIterationStep(), fDt);
CallCallback(eTweenBackEnd);
if(m_step < 0 && m_repeatCount >= 0)
{
CallCallback(eTweenBackComplete);
}
else
{
m_currentTime = m_repeatDelay;
}
}
else if(IsIterationStep() && m_currentTime + m_dt > m_duration)
{
m_flags.ChangeMask(eIsIteratingStep, false);
++ m_step;
float fDt = m_duration - m_currentTime;
m_dt -= fDt;
m_currentTime = m_duration;
OnUpdate(m_step, m_step - 1, IsIterationStep(), fDt);
CallCallback(eTweenEnd);
if(m_step > m_repeatCount*2 && m_repeatCount >= 0)
{
CallCallback(eTweenComplete);
}
m_currentTime = 0.0f;
}
else if(IsIterationStep())
{
float fDt = m_dt;
m_dt -= fDt;
m_currentTime += fDt;
OnUpdate(m_step, m_step, IsIterationStep(), fDt);
break;
}
else
{
float fDt = m_dt;
m_dt -= fDt;
m_currentTime += fDt;
break;
}
}
}
bool CSeq_interval::x_IsMinusStrand(void) const
{
return IsSetStrand() && IsReverse(GetStrand());
}
CAnnotCompare::TCompareFlags
CAnnotCompare::CompareFeats(const CSeq_feat& feat1,
const CSeq_loc& loc1,
CScope& scope1,
const CSeq_feat& feat2,
const CSeq_loc& loc2,
CScope& scope2,
vector<ECompareFlags>* complex_flags,
list<string>* comments)
{
TCompareFlags loc_state = 0;
ENa_strand strand1 = sequence::GetStrand(loc1, &scope1);
ENa_strand strand2 = sequence::GetStrand(loc2, &scope2);
if (!SameOrientation(strand1, strand2)) {
loc_state |= eLocation_Missing;
} else {
sequence::ECompare comp_val = sequence::Compare(loc1, loc2, &scope1);
switch (comp_val) {
case sequence::eSame:
loc_state |= eLocation_Same;
break;
case sequence::eOverlap:
loc_state |= eLocation_Complex;
break;
case sequence::eContains:
case sequence::eContained:
{{
CSeq_loc_CI loc1_iter(loc1);
size_t loc1_exons = 0;
for ( ; loc1_iter; ++loc1_iter, ++loc1_exons) {
}
CSeq_loc_CI loc2_iter(loc2);
size_t loc2_exons = 0;
for ( ; loc2_iter; ++loc2_iter, ++loc2_exons) {
}
bool rev = IsReverse(strand1);
TSeqRange range1 = loc1.GetTotalRange();
TSeqRange range2 = loc2.GetTotalRange();
if (loc1_exons == loc2_exons) {
bool agreement_3prime;
bool agreement_5prime;
if (!rev) {
agreement_5prime =
range1.GetFrom() == range2.GetFrom();
agreement_3prime =
range1.GetTo() == range2.GetTo();
} else {
agreement_3prime =
range1.GetFrom() == range2.GetFrom();
agreement_5prime =
range1.GetTo() == range2.GetTo();
}
loc1_iter.Rewind();
loc2_iter.Rewind();
bool agreement_internal = true;
for (unsigned int i = 0;
i < loc1_exons;
++i, ++loc1_iter, ++loc2_iter) {
if ((i != 0 || rev)
&& (i != loc1_exons - 1 || !rev)) {
if (loc1_iter.GetRange().GetFrom()
!= loc2_iter.GetRange().GetFrom()) {
agreement_internal = false;
break;
}
}
if ((i != 0 || !rev)
&& (i != loc1_exons - 1 || rev)) {
if (loc1_iter.GetRange().GetTo()
!= loc2_iter.GetRange().GetTo()) {
agreement_internal = false;
break;
}
}
}
if (!agreement_internal) {
loc_state |= eLocation_Complex;
} else if (agreement_5prime && !agreement_3prime) {
loc_state |= eLocation_3PrimeExtension;
} else if (agreement_3prime && !agreement_5prime) {
loc_state |= eLocation_5PrimeExtension;
} else {
// both 3' and 5' disagreement
loc_state |= eLocation_Complex;
}
} else {
loc1_iter.Rewind();
loc2_iter.Rewind();
while (loc1_iter && loc2_iter) {
if (loc1_iter.GetRange() == loc2_iter.GetRange()) {
++loc1_iter;
++loc2_iter;
} else {
if (loc1_exons > loc2_exons) {
++loc1_iter;
} else {
++loc2_iter;
}
}
}
if ((loc1_exons > loc2_exons && !loc2_iter) ||
(loc2_exons > loc1_exons && !loc1_iter)) {
loc_state |= eLocation_MissingExon;
} else {
loc_state |= eLocation_Complex;
}
}
}}
break;
default:
case sequence::eNoOverlap:
loc_state |= eLocation_Missing;
break;
}
}
///
/// now, do a very simple sequence comparison
///
CSeqVector v1(loc1, scope1);
CSeqVector v2(loc2, scope2);
CSeqVector_CI v1_iter = v1.begin();
CSeqVector_CI v2_iter = v2.begin();
TCompareFlags seq_state = 0;
for (size_t count = 0;
v1_iter != v1.end() && v2_iter != v2.end();
++v1_iter, ++v2_iter, ++count) {
if (*v1_iter != *v2_iter) {
seq_state |= eSequence_DifferentSeq;
break;
}
}
if (v1_iter != v1.end() || v2_iter != v2.end()) {
seq_state |= eSequence_DifferentSeq;
}
if (seq_state) {
loc_state |= seq_state;
} else {
loc_state |= eSequence_SameSeq;
}
///
/// also compare products
///
if (feat1.IsSetProduct() && feat2.IsSetProduct()) {
CSeqVector v1(feat1.GetProduct(), scope1);
CSeqVector v2(feat2.GetProduct(), scope2);
CSeqVector_CI v1_iter = v1.begin();
CSeqVector_CI v2_iter = v2.begin();
for ( ; v1_iter != v1.end() && v2_iter != v2.end(); ++v1_iter, ++v2_iter) {
if (*v1_iter != *v2_iter) {
loc_state |= eSequence_DifferentProduct;
break;
}
}
if ((loc_state & eSequence_DifferentProduct) == 0) {
loc_state |= eSequence_SameProduct;
}
} else if (feat1.IsSetProduct() != feat2.IsSetProduct()) {
loc_state |= eSequence_DifferentProduct;
}
return loc_state;
}
//--------------------------------------------------------------------------------
void Timeline::OnUpdate (int _step, int _lastStep, bool _isIterationStep, float _dt)
{
if(!_isIterationStep && _step > _lastStep)
{
TWEEN_ASSERT(_dt >= 0, "Delta should be positive");
float currentDelta = IsReverse(_lastStep) ? (-_dt - 1.0f) : (_dt + 1.0f);
UpdateChildren(currentDelta);
return;
}
if(!_isIterationStep && _step < _lastStep)
{
TWEEN_ASSERT(_dt <= 0, "Delta should be negative");
float currentDelta = IsReverse(_lastStep) ? (-_dt - 1.0f) : (_dt + 1.0f);
UpdateChildren(currentDelta, true);
return;
}
TWEEN_ASSERT(_isIterationStep, "Not an iteration step and last step equal to step should not happen");
if(_step > _lastStep)
{
if(IsReverse(_step))
{
ForceEndValues();
}
else
{
ForceStartValues();
}
UpdateChildren(_dt);
}
else if( _step < _lastStep)
{
if(IsReverse(_step))
{
ForceStartValues();
}
else
{
ForceEndValues();
}
UpdateChildren(_dt, true);
}
else
{
float currentDelta = IsReverse(_step) ? -_dt : _dt;
if(_dt >= 0.0f)
{
UpdateChildren(currentDelta);
}
else
{
UpdateChildren(currentDelta, true);
}
}
}