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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/update__seq__input_8hpp_source.html below:

NCBI C++ ToolKit: include/gui/packages/pkg_sequence_edit/update_seq_input.hpp Source File

1 #ifndef _GUI_PACKAGES_SEQUPDATE_INPUT_HPP_ 2 #define _GUI_PACKAGES_SEQUPDATE_INPUT_HPP_ 55  CUpdateSeq_Input

(

const

objects::CBioseq_Handle& old_bsh,

const

objects::CBioseq_Handle& upd_bsh);

58  const

objects::CBioseq_Handle&

GetOldBioseq

(

void

)

const

{

return

m_OldSeq; }

60  const

objects::CBioseq_Handle&

GetUpdateBioseq

(

void

)

const

{

return

m_UpdSeq; }

62  void SetAlignment

(

const

objects::CSeq_align* align) { m_Align.Reset(align); }

66  bool

SetUpdateBioseq(

const

objects::CBioseq_Handle& bsh);

69  bool

ReadUpdateSequenceFromClipboard(objects::ILineErrorListener* msg_listener);

71  bool

ReadSingleUpdateSequence(objects::ILineErrorListener* msg_listener);

73  bool

ReadSingleAccession(

void

);

75  bool

HaveIdenticalResidues(

void

)

const

;

77  bool

IsReadyForUpdate(

void

)

const

;

79  bool

UpdateSeqHasFeatures(

void

)

const

;

80  bool

OldSeqHasFeatures(

void

)

const

;

81  bool

OldSeqHasProteinFeats()

const

;

85  void

CalculateAlignmentForUnitTest(

void

);

90  static void

s_ConvertDeltaToRawEntry(objects::CSeq_entry& entry);

91  static void

s_ConvertDeltaToRawBioseq(objects::CBioseq& bseq);

94  static bool

s_IsGoodLiteral(

const

objects::CSeq_literal& lit);

95  static bool

s_IsDeltaWithNoGaps(

const

objects::CBioseq& bseq);

97  static bool

s_IsDeltaWithFarPointers(

const

objects::CBioseq& bseq);

100  static void

s_FixCollidingIDs_Entry(objects::CSeq_entry& entry,

const

objects::CBioseq::TId& seq_ids);

102  unsigned int

CountBioseqs();

104  void

ResetUpdateSequence();

107  bool

x_ReadFromStream(

CNcbiIstream

& istr, objects::ILineErrorListener* msg_listener);

108  bool

x_ReadUpdateSeq_Fasta(

CNcbiIstream

& istr, objects::ILineErrorListener* msg_listener);

110  bool

x_ReadAccession(

const string

& acc_id);

113  void

x_FixCollidingIDs_Entry(objects::CSeq_entry& entry);

114  void

x_FixCollidingIDs_Bioseq(objects::CBioseq& bioseq);

Sets up the old and the update sequences, and generates the alignment between them.

bool SetOldBioseqAndScope(const objects::CBioseq_Handle &bsh)

bool SetOldBioseqAndScope(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse)

void SetAlignment(const objects::CSeq_align *align)

objects::CBioseq_Handle m_UpdSeq

CConstRef< objects::CSeq_align > GetAlignment(void) const

objects::CBioseq_Handle GetNCOldBioseq(void) const

CRef< objects::CScope > m_Scope

objects::CBioseq_Handle m_OldSeq

CUpdateSeq_Input(const objects::CBioseq_Handle &old_bsh, const objects::CBioseq_Handle &upd_bsh)

const objects::CBioseq_Handle & GetUpdateBioseq(void) const

CConstRef< objects::CSeq_align > m_Align

const objects::CBioseq_Handle & GetOldBioseq(void) const

IWorkbench is the central interface in the application framework.

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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_GUIPKG_SEQUENCE_EDIT_EXPORT

Defines to provide correct exporting from DLLs in Windows.

Defines NCBI C++ exception handling.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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