NCBI C++ ToolKit
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Search Toolkit Book for CAlnScanner
#include "aln_scanner.hpp"
(Private to src/objtools/readers
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Public Types | |
using | TDeflines = vector< TLineInfo > |
Public Member Functions | |
CAlnScanner () | |
virtual | ~CAlnScanner () |
virtual void | ProcessAlignmentFile (CSequenceInfo &, CLineInput &, SAlignmentFile &) |
Protected Types | |
enum class | ESeqIdComparison { eIdentical , eDifferByCase , eDifferentChars , eDifferent } |
using | TLineInfo = SLineInfo |
Protected Member Functions | |
virtual void | xImportAlignmentData (CSequenceInfo &, CLineInput &) |
virtual void | xAdjustSequenceInfo (CSequenceInfo &) |
virtual void | xVerifyAlignmentData (const CSequenceInfo &) |
virtual void | xExportAlignmentData (SAlignmentFile &alignmentInfo) |
virtual void | xVerifySingleSequenceData (const CSequenceInfo &, const TLineInfo &seqId, const vector< TLineInfo > seqData) |
ESeqIdComparison | xGetExistingSeqIdInfo (const string &seqId, TLineInfo &existingInfo) |
bool | xSeqIdIsEqualToInfoAt (const string &seqId, int index) |
Protected Attributes | |
vector< TLineInfo > | mSeqIds |
vector< vector< TLineInfo > > | mSequences |
vector< TLineInfo > | mDeflines |
Definition at line 44 of file aln_scanner.hpp.
using CAlnScanner::TDeflines = vector<TLineInfo> |
Definition at line 51 of file aln_scanner.hpp.
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protected |
Definition at line 48 of file aln_scanner.hpp.
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strongprotected |
Enumerator | |
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eIdentical | |
eDifferByCase | |
eDifferentChars | |
eDifferent |
Definition at line 65 of file aln_scanner.hpp.
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inline |
Definition at line 53 of file aln_scanner.hpp.
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inlinevirtual |
Definition at line 55 of file aln_scanner.hpp.
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virtual |
Definition at line 48 of file aln_scanner.cpp.
References xAdjustSequenceInfo(), xExportAlignmentData(), xImportAlignmentData(), and xVerifyAlignmentData().
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protectedvirtual |
Reimplemented in CAlnScannerSequin, CAlnScannerNexus, and CAlnScannerMultAlign.
Definition at line 75 of file aln_scanner.cpp.
Referenced by ProcessAlignmentFile().
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protectedvirtual |
Definition at line 175 of file aln_scanner.cpp.
References SAlignmentFile::mDeflines, mDeflines, SAlignmentFile::mIds, mSeqIds, SAlignmentFile::mSequences, and mSequences.
Referenced by ProcessAlignmentFile().
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protected |
Definition at line 199 of file aln_scanner.cpp.
References eDifferByCase, eDifferentChars, eIdentical, mSeqIds, and NStr::ToLower().
Referenced by CAlnScannerClustal::sProcessClustalDataLine(), CAlnScannerFastaGap::xImportAlignmentData(), CAlnScannerPhylip::xImportAlignmentData(), and CAlnScannerSequin::xImportAlignmentData().
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protectedvirtual |
Reimplemented in CAlnScannerSequin, CAlnScannerPhylip, CAlnScannerNexus, CAlnScannerMultAlign, CAlnScannerFastaGap, and CAlnScannerClustal.
Definition at line 62 of file aln_scanner.cpp.
References eAlnSubcode_UnsupportedFileFormat.
Referenced by ProcessAlignmentFile().
Definition at line 229 of file aln_scanner.cpp.
References mSeqIds.
Referenced by CAlnScannerMultAlign::xImportAlignmentData(), and CAlnScannerSequin::xImportAlignmentData().
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protectedvirtual |
Reimplemented in CAlnScannerPhylip.
Definition at line 83 of file aln_scanner.cpp.
References i, mSeqIds, mSequences, and xVerifySingleSequenceData().
Referenced by ProcessAlignmentFile(), and CAlnScannerPhylip::xVerifyAlignmentData().
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protectedvirtual |
Reimplemented in CAlnScannerMultAlign.
Definition at line 101 of file aln_scanner.cpp.
References CSequenceInfo::Alphabet(), CSequenceInfo::BeginningGap(), eAlnSubcode_BadDataChars, CSequenceInfo::EndGap(), ErrorPrintf(), HEAD, CSequenceInfo::Match(), SLineInfo::mData, CSequenceInfo::MiddleGap(), CSequenceInfo::Missing(), and TAIL.
Referenced by xVerifyAlignmentData().
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protected |
Definition at line 107 of file aln_scanner.hpp.
Referenced by CAlnScannerNexus::SetDeflines(), xExportAlignmentData(), CAlnScannerFastaGap::xImportAlignmentData(), CAlnScannerPhylip::xImportAlignmentData(), and CAlnScannerNexus::xProcessSequin().
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protected |
Definition at line 105 of file aln_scanner.hpp.
Referenced by CAlnScannerClustal::sProcessClustalDataLine(), xExportAlignmentData(), xGetExistingSeqIdInfo(), CAlnScannerFastaGap::xImportAlignmentData(), CAlnScannerMultAlign::xImportAlignmentData(), CAlnScannerPhylip::xImportAlignmentData(), CAlnScannerSequin::xImportAlignmentData(), CAlnScannerNexus::xProcessMatrix(), xSeqIdIsEqualToInfoAt(), xVerifyAlignmentData(), and CAlnScannerPhylip::xVerifyAlignmentData().
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protected |
Definition at line 106 of file aln_scanner.hpp.
Referenced by CAlnScannerClustal::sProcessClustalDataLine(), xExportAlignmentData(), CAlnScannerClustal::xImportAlignmentData(), CAlnScannerFastaGap::xImportAlignmentData(), CAlnScannerMultAlign::xImportAlignmentData(), CAlnScannerPhylip::xImportAlignmentData(), CAlnScannerSequin::xImportAlignmentData(), CAlnScannerNexus::xProcessMatrix(), xVerifyAlignmentData(), and CAlnScannerPhylip::xVerifyAlignmentData().