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/////////////////////////////////////////////////////////////////////////////
// File: gnLocation.cpp
// Purpose: Standard Location for Feature
// Description: Feature location
// Changes:
// Version: libGenome 0.5.1
// Author: Aaron Darling
// Modified by:
// Copyright: (c) Aaron Darling
// Licenses: See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnLocation.h"
#include "libGenome/gnDebug.h"
using namespace std;
namespace genome {
gnLocation::gnLocation()
{
Clear();
}
gnLocation::gnLocation( const gnLocation& s)
{
SetBounds( s.m_start, s.m_startLength, s.m_end, s.m_endLength );
m_type = s.m_type;
}
gnLocation::gnLocation( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, const gnSeqI endLength, gnLocationType type, string contigName)
{
SetBounds( start, startLength, end, endLength );
m_type = type;
m_name = contigName;
}
gnLocation::gnLocation( const gnSeqI start, const gnSeqI end, const gnLocationType type, string contigName )
{
SetBounds( start, 0, end, 0 );
m_type = type;
m_name = contigName;
}
gnLocation* gnLocation::Clone() const
{
return new gnLocation(*this);
}
void gnLocation::Clear()
{
m_start = 0;
m_end = 0;
m_startLength = 0;
m_endLength = 0;
m_type = LT_Nothing;
}
void gnLocation::GetBounds( gnSeqI &s, gnSeqI &sl, gnSeqI &e, gnSeqI &el ) const
{
s = m_start;
sl = m_startLength;
e = m_end;
el = m_endLength;
}
void gnLocation::SetBounds( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, const gnSeqI endLength)
{
SetStart(start, startLength);
SetEnd(end, endLength);
}
void gnLocation::SetBounds( const gnSeqI start, const gnSeqI end)
{
m_start = start;
m_end = end;
}
boolean gnLocation::CropTo( const gnLocation &l )
{
gnSeqI tmp;
gnSeqI start = l.GetStart();
gnSeqI end = l.GetEnd();
if(m_start < start){
tmp = start < m_end ? start : m_end;
m_startLength += tmp - m_start;
m_start = tmp;
}
if(m_end < end){
tmp = end > m_start ? end : m_start;
m_endLength += m_end - tmp;
m_end = tmp;
}
if( (l.GetFirst() > GetFirst()) )
{
if( l.GetFirst() <= m_end )
m_startLength = m_start - l.GetFirst();
else if( l.GetFirst() <= GetLast() )
{
m_end = l.GetFirst();
m_start = l.GetFirst() + 1;
m_startLength = 0;
}
else
Clear();
}
if( l.GetLast() < GetLast() )
{
if( l.GetLast() >= m_start )
m_endLength = l.GetLast() - m_end;
else if( l.GetLast() >= GetFirst() )
{
m_start = l.GetLast();
m_end = l.GetLast() - 1;
m_endLength = 0;
}
else
Clear();
}
if(m_start == m_end)
return false;
return true;
}
boolean gnLocation::CropStart( const gnSeqI start ){
gnSeqI tmp;
if(m_start < start){
tmp = start < m_end ? start : m_end;
m_startLength += tmp - m_start;
m_start = tmp;
}
if(m_start == m_end)
return false;
return true;
}
boolean gnLocation::CropEnd( const gnSeqI end ){
gnSeqI tmp;
if(m_end > end){
tmp = end > m_start ? end : m_start;
m_endLength += m_end - tmp;
m_end = tmp;
}
if(m_start == m_end)
return false;
return true;
}
// Intersects
boolean gnLocation::Intersects( const gnLocation &l, const intersectRestriction ir ) const{
if( ir == determinedRegions )
{
if( (l.GetStart() <= m_end) && (l.GetEnd() >= m_start) )
return true;
}
else if( ir == undeterminedRegions )
{
if( (l.GetFirst() <= m_start) && (l.GetLast() >= GetFirst()) )
return true;
if( (l.GetFirst() <= GetLast()) && (l.GetLast() >= m_end) )
return true;
}
else if( ir == allRegions )
{
if( (l.GetFirst() <= GetLast()) && (l.GetLast() >= GetFirst()) )
return true;
}
return false;
}
boolean gnLocation::Contains( const gnLocation &l, const intersectRestriction ir ) const{
if(ir == determinedRegions)
return m_start <= l.GetStart() && l.GetEnd() <= m_end;
else if(ir == undeterminedRegions)
return (GetFirst() <= l.GetFirst() && l.GetLast() < m_start) ||
(m_end < l.GetFirst() && l.GetLast() <= GetLast());
return GetFirst() <= l.GetFirst() && l.GetLast() <= GetLast();
}
// Move
boolean gnLocation::MovePositive( const gnSeqI diff )
{
if(m_start > GNSEQI_END - diff || m_end > GNSEQI_END - diff)
return false;
m_start += diff;
m_end += diff;
return true;
}
boolean gnLocation::MoveNegative( const gnSeqI diff )
{
if(m_start < diff || m_end < diff)
return false;
m_start -= diff;
m_end -= diff;
return true;
}
boolean gnLocation::MoveTo( const int direction, const gnSeqI diff )
{
if( direction > 0 )
return MovePositive( diff );
return MoveNegative( diff );
}
gnLocation gnLocation::GetUnion( const gnLocation &l ) const
{
ErrorMsg("gnLocation::getUnion -- not implemented\n");
return l;
}
// Intersects
gnLocation gnLocation::GetIntersection( const gnLocation &l, const intersectRestriction ir ) const{
gnLocation inter_loc;
if( ir == determinedRegions )
{
if( (l.GetStart() <= m_end) && (l.GetEnd() >= m_start) ){
inter_loc.m_start = l.m_start > m_start ? l.m_start : m_start;
inter_loc.m_end = l.m_end < m_end ? l.m_end : m_end;
}
}
else if( ir == undeterminedRegions )
{
ErrorMsg("Not implemented!");
}
else if( ir == allRegions )
{
ErrorMsg("Not implemented!");
}
return inter_loc;
}
} // end namespace genome
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