19 #ifndef OST_SEQ_ALIGNMENT_HANDLE_HH
20 #define OST_SEQ_ALIGNMENT_HANDLE_HH
31 namespace ost {
namespace seq {
36 class AlignedColumnIterator;
63 int GetPos(
int seq_index,
int residue_index)
const;
68 int GetResidueIndex(
int seq_index,
int pos)
const;
72 char GetOneLetterCode(
int seq_index,
int pos)
const;
85 void RemoveSequence(
int seq_index);
87 String ToString(
int width=80)
const;
90 int GetLength()
const;
101 int FindSequenceIndex(
const String& name)
const;
110 const String& chain_name);
115 void SetSequenceName(
int seq_index,
const String& name);
117 void SetSequenceOffset(
int seq_index,
int offset);
118 int GetSequenceOffset(
int seq_index);
131 AlignedRegion MakeRegion(
int start,
int n,
int master=-1)
const;
134 int GetCount()
const;
149 void Cut(
int start,
int end);
157 void ShiftRegion(
int start,
int end,
int amount,
int master=-1);
164 bool IsValid()
const {
return impl_.get()!=0; }
171 Real GetCoverage(
int seq_index)
const;
174 const String& GetSequenceRole(
int seq_index);
176 void SetSequenceRole(
int seq_index,
const String& role);
178 void CheckValidity()
const;
#define DLLEXPORT_OST_SEQ
boost::shared_ptr< SequenceListImpl > SequenceListImplPtr
AlignmentHandle DLLEXPORT_OST_SEQ AlignmentFromSequenceList(const SequenceList &seq_list)
convert alignment from sequence list
pointer_it< T > end(const std::vector< T > &values)
bool DLLEXPORT_OST_GEOM operator==(const Line2 &l1, const Line2 &l2)
list of immutable sequences.
DLLEXPORT_OST_IMG_BASE bool operator!=(const ImageHandle &lhs, const ConstImageHandle &rhs)
represents a region in a sequence alignment
std::vector< AlignmentHandle > AlignmentList
std::vector< SequenceImplPtr > SequenceList
pointer_it< T > begin(const std::vector< T > &values)
Provides access to a column in a aligned region or a sequence alignment.
AlignedColumnIterator iterator
std::pair< EntityView, EntityView > EntityViewPair
AlignmentHandle DLLEXPORT_OST_SEQ CreateAlignment()
representation of a multiple sequence alignemnt consisting of two or more sequences ...