NCBI C++ ToolKit
mask_writer_fasta.hpp
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1 /* $Id: mask_writer_fasta.hpp 94083 2021-06-23 15:52:03Z fongah2 $
2  * ===========================================================================
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25  *
26  * Author: Aleksandr Morgulis
27  *
28  * File Description:
29  * Header file for CMaskWriterFasta class.
30  *
31  */
32 
33 #ifndef CMASK_WRITER_FASTA_H
34 #define CMASK_WRITER_FASTA_H
35 
37 
39 
40 /**
41  **\brief Output filter to write masked data in fasta format.
42  **
43  ** In the output the sequence ids are preserved. The masked
44  ** portions of sequences are printed in lower case letters.
45  **
46  **/
48 {
49 public:
50 
51  /**
52  **\brief Object constructor.
53  **
54  **\param arg_os the output stream used to initialize the
55  ** base class instance.
56  **
57  **/
58  CMaskWriterFasta( CNcbiOstream & arg_os, bool hard_masking = false)
59  : CMaskWriter( arg_os ), m_HardMasking(hard_masking) {}
60 
61  /**
62  **\brief Object destructor.
63  **
64  **/
65  virtual ~CMaskWriterFasta() {}
66 
67  /**
68  **\brief Output masked sequence data.
69  **
70  **\param bsh the bioseq handle
71  **\param mask the resulting list of masked intervals
72  **\param parsed_id bioseq id was parsed by CMaskReader.
73  **
74  **/
75  virtual void Print( objects::CBioseq_Handle& bsh,
76  const TMaskList & mask,
77  bool parsed_id = false );
78 private:
80 };
81 
83 
84 #endif
ncbi::TMaskedQueryRegions mask
Output filter to write masked data in fasta format.
virtual ~CMaskWriterFasta()
Object destructor.
CMaskWriterFasta(CNcbiOstream &arg_os, bool hard_masking=false)
Object constructor.
A base class for winmasker output writers.
Definition: mask_writer.hpp:52
virtual void Print(objects::CBioseq_Handle &bsh, const TMaskList &mask, bool parsed_id=false)=0
Output masked sequence data.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
IO_PREFIX::ostream CNcbiOstream
Portable alias for ostream.
Definition: ncbistre.hpp:149
#define NCBI_XOBJREAD_EXPORT
Definition: ncbi_export.h:1315
Modified on Wed Apr 17 13:10:04 2024 by modify_doxy.py rev. 669887