NCBI C++ ToolKit
win_mask_dup_table.hpp
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1 /* $Id: win_mask_dup_table.hpp 44870 2010-02-23 20:20:11Z morgulis $
2  * ===========================================================================
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5  * National Center for Biotechnology Information
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25  *
26  * Author: Aleksandr Morgulis
27  *
28  * File Description:
29  * Declaration of CheckDuplicates function.
30  *
31  */
32 
33 #ifndef C_WIN_MASK_DUP_TABLE_HPP
34 #define C_WIN_MASK_DUP_TABLE_HPP
35 
36 #include <string>
37 #include <vector>
38 #include <set>
39 
41 #include <objmgr/scope.hpp>
43 #include <objmgr/bioseq_ci.hpp>
44 #include <objmgr/seq_vector.hpp>
45 #include <objmgr/util/sequence.hpp>
47 
48 // #include "win_mask_config.hpp"
49 
51 
52 /**
53  **\brief Check for possibly duplicate sequences in the input.
54  **
55  ** input contains the list of input file names. The files should be in
56  ** the fasta format. The function checks the input sequences for
57  ** duplication and reports possible duplicates to the standard error.
58  **
59  **\param input list of input file names
60  **\param infmt input format
61  **\param ids set of ids to check
62  **\param exclude_ids set of ids to ignore
63  **
64  **/
65 void CheckDuplicates( const vector< string > & input,
66  const string & infmt,
67  const CWinMaskUtil::CIdSet * ids,
68  const CWinMaskUtil::CIdSet * exclude_ids );
69 
71 
72 #endif
Base class for sets of seq_id representations used with -ids and -exclude-ids options.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
static int input()
The Object manager core.
void CheckDuplicates(const vector< string > &input, const string &infmt, const CWinMaskUtil::CIdSet *ids, const CWinMaskUtil::CIdSet *exclude_ids)
Check for possibly duplicate sequences in the input.
Modified on Mon May 20 05:03:56 2024 by modify_doxy.py rev. 669887