Search Toolkit Book for SAlignmentFile
#include <objtools/readers/alnread.hpp>
Collaboration diagram for SAlignmentFile:
Public Types | |
| using | TLineInfo = SLineInfo |
Public Member Functions | |
| size_t | NumDeflines () const |
| size_t | NumSequences () const |
Public Attributes | |
| vector< TLineInfo > | mIds |
| vector< string > | mSequences |
| vector< TLineInfo > | mDeflines |
| int | num_sequences |
| int | num_organisms |
| int | num_deflines |
| int | num_segments |
| char ** | ids |
| char ** | sequences |
| char ** | organisms |
| char ** | deflines |
| char | align_format_found |
Detailed Description
Definition at line 132 of file alnread.hpp.
Member Typedef Documentation
◆ TLineInfo
| using SAlignmentFile::TLineInfo = SLineInfo |
Definition at line 142 of file alnread.hpp.
Member Function Documentation
◆ NumDeflines()
|
inline |
Definition at line 136 of file alnread.hpp.
References mDeflines.
Referenced by CAlnReader::x_VerifyAlignmentInfo().
◆ NumSequences()
|
inline |
Definition at line 139 of file alnread.hpp.
References mSequences.
Referenced by CAlnReader::x_VerifyAlignmentInfo().
Member Data Documentation
◆ align_format_found
| char SAlignmentFile::align_format_found |
Definition at line 123 of file alnread.h.
Referenced by s_ConvertDataToOutput().
◆ deflines
| char** SAlignmentFile::deflines |
Definition at line 122 of file alnread.h.
Referenced by AlignmentFileFree(), AlignmentFileNew(), and s_ConvertDataToOutput().
◆ ids
| char** SAlignmentFile::ids |
Definition at line 119 of file alnread.h.
Referenced by AlignmentFileFree(), AlignmentFileNew(), and s_ConvertDataToOutput().
◆ mDeflines
| vector<TLineInfo> SAlignmentFile::mDeflines |
Definition at line 146 of file alnread.hpp.
Referenced by NumDeflines(), CAlnReader::x_VerifyAlignmentInfo(), and CAlnScanner::xExportAlignmentData().
◆ mIds
| vector<TLineInfo> SAlignmentFile::mIds |
Definition at line 144 of file alnread.hpp.
Referenced by CAlnReader::x_VerifyAlignmentInfo(), and CAlnScanner::xExportAlignmentData().
◆ mSequences
| vector<string> SAlignmentFile::mSequences |
Definition at line 145 of file alnread.hpp.
Referenced by NumSequences(), CAlnReader::x_VerifyAlignmentInfo(), and CAlnScanner::xExportAlignmentData().
◆ num_deflines
| int SAlignmentFile::num_deflines |
Definition at line 117 of file alnread.h.
Referenced by AlignmentFileFree(), AlignmentFileNew(), and s_ConvertDataToOutput().
◆ num_organisms
| int SAlignmentFile::num_organisms |
Definition at line 116 of file alnread.h.
Referenced by AlignmentFileFree(), AlignmentFileNew(), and s_ConvertDataToOutput().
◆ num_segments
| int SAlignmentFile::num_segments |
Definition at line 118 of file alnread.h.
Referenced by AlignmentFileNew(), and s_ConvertDataToOutput().
◆ num_sequences
| int SAlignmentFile::num_sequences |
Definition at line 115 of file alnread.h.
Referenced by AlignmentFileFree(), AlignmentFileNew(), and s_ConvertDataToOutput().
◆ organisms
| char** SAlignmentFile::organisms |
Definition at line 121 of file alnread.h.
Referenced by AlignmentFileFree(), AlignmentFileNew(), and s_ConvertDataToOutput().
◆ sequences
| char** SAlignmentFile::sequences |
Definition at line 120 of file alnread.h.
Referenced by AlignmentFileFree(), AlignmentFileNew(), and s_ConvertDataToOutput().
The documentation for this struct was generated from the following files:
- include/objtools/readers/alnread.hpp
- include/util/creaders/alnread.h
