1 #ifndef GUI_OBJUTILS___SPARSE_FUNCTIONS__HPP
2 #define GUI_OBJUTILS___SPARSE_FUNCTIONS__HPP
79 const objects::CSeq_id& master_id,
80 vector<SAlignedSeq*>& aln_seqs);
85 const objects::CSeq_id& master_id,
86 vector<SAlignedSeq*>& aln_seqs);
91 vector<SAlignedSeq*>& aln_seqs);
97 vector<SAlignedSeq*>& aln_seqs);
109 const objects::CSeq_id& master_id,
124 vector<SAlignedSeq*>& aln_seqs,
125 objects::CScope& scope);
131 vector<SAlignedSeq*>& aln_seqs,
132 objects::CScope& scope);
140 const objects::CSeq_id& id_2,
CSparseAlignment - an alignment based on CSparse_seg and CAlingRangeCollection classes rather than on...
Template class for iteration on objects of class C (non-medifiable version)
Include a standard set of the NCBI C++ Toolkit most basic headers.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
#define NCBI_GUIOBJUTILS_EXPORT
Defines to provide correct exporting from DLLs in Windows.
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
objects::CAlnVec * BuildDenseAlignment(const objects::CSeq_id &master_id, vector< SAlignedSeq * > &aln_seqs, objects::CScope &scope)
Build a Dense Alignment.
bool ConvertToPairwise(const objects::CSeq_align &align, const objects::CSeq_id &master_id, vector< SAlignedSeq * > &aln_seqs)
Converters.
void GetAlignColl(const objects::CSparse_align &sparse_align, const objects::CSeq_id &master_id, SAlignTools::TAlignColl &coll)
Converter CSparse_align -> TODO redesign API.
CSparseAlignment * BuildSparseAlignment(const objects::CSeq_id &master_id, vector< SAlignedSeq * > &aln_seqs, objects::CScope &scope)
Builder functions.
void ExtractSeqAligns(const T &obj, vector< CConstRef< objects::CSeq_align > > &aligns)
This is the place where elements of the new Alignment Library will be collected.
CRef< objects::CSparse_align > CreateSparseAlign(const objects::CSeq_id &id_1, const objects::CSeq_id &id_2, const SAlignTools::TAlignColl &coll)
Reverse Converters.
SAlignedSeq * CreateAlignRow(const objects::CSparse_align &align, bool master_first)
Helper functions used by Converters.
This is a building block for a Builder represents a Sequence aligned to an Anchor (pairwise alignment...