#include <ncbi_pch.hpp>#include <corelib/ncbistr.hpp>#include <objtools/readers/reader_error_codes.hpp>#include <objtools/readers/message_listener.hpp>#include "aln_errors.hpp"
Include dependency graph for aln_errors.cpp:
Go to the source code of this file.
Go to the SVN repository for this file.
Functions | |
| ADD_ENUM_VALUE ("Mods", eReader_Mods) | |
| ADD_ENUM_VALUE ("Alignment", eReader_Alignment) | |
| ADD_ENUM_VALUE ("BadDataChars", eAlnSubcode_BadDataChars) | |
| ADD_ENUM_VALUE ("UnterminatedCommand", eAlnSubcode_UnterminatedCommand) | |
| ADD_ENUM_VALUE ("UnterminatedBlock", eAlnSubcode_UnterminatedBlock) | |
| ADD_ENUM_VALUE ("UnexpectedSeqId", eAlnSubcode_UnexpectedSeqId) | |
| ADD_ENUM_VALUE ("BadDataCount", eAlnSubcode_BadDataCount) | |
| ADD_ENUM_VALUE ("BadSequenceCount", eAlnSubcode_BadSequenceCount) | |
| ADD_ENUM_VALUE ("IllegalDataLine", eAlnSubcode_IllegalDataLine) | |
| ADD_ENUM_VALUE ("MissingDataLine", eAlnSubcode_MissingDataLine) | |
| ADD_ENUM_VALUE ("IllegalSequenceId", eAlnSubcode_IllegalSequenceId) | |
| ADD_ENUM_VALUE ("IllegalDefinitionLine", eAlnSubcode_IllegalDefinitionLine) | |
| ADD_ENUM_VALUE ("InsufficientDeflineInfo", eAlnSubcode_InsufficientDeflineInfo) | |
| ADD_ENUM_VALUE ("UnsupportedFileFormat", eAlnSubcode_UnsupportedFileFormat) | |
| ADD_ENUM_VALUE ("UnterminatedComment", eAlnSubcode_UnterminatedComment) | |
| ADD_ENUM_VALUE ("UnusedLine", eAlnSubcode_UnusedLine) | |
| ADD_ENUM_VALUE ("InconsistentMolType", eAlnSubcode_InconsistentMolType) | |
| ADD_ENUM_VALUE ("IllegalDataDescription", eAlnSubcode_IllegalDataDescription) | |
| ADD_ENUM_VALUE ("FileDoesNotExist", eAlnSubcode_FileDoesNotExist) | |
| ADD_ENUM_VALUE ("FileTooShort", eAlnSubcode_FileTooShort) | |
| ADD_ENUM_VALUE ("UnexpectedCommand", eAlnSubcode_UnexpectedCommand) | |
| ADD_ENUM_VALUE ("UnexpectedCommandArgs", eAlnSubcode_UnexpectedCommandArgs) | |
| ADD_ENUM_VALUE ("Unrecognized", eModSubcode_Unrecognized) | |
| ADD_ENUM_VALUE ("InvalidValue", eModSubcode_InvalidValue) | |
| ADD_ENUM_VALUE ("Duplicate", eModSubcode_Duplicate) | |
| ADD_ENUM_VALUE ("ConflictingValues", eModSubcode_ConflictingValues) | |
| ADD_ENUM_VALUE ("Deprecated", eModSubcode_Deprecated) | |
| ADD_ENUM_VALUE ("ProteinModOnNucseq", eModSubcode_ProteinModOnNucseq) | |
| END_ENUM_INFO string | ErrorPrintf (const char *format,...) |
| string | BadCharCountPrintf (int expectedCount, int actualCount) |
Variables | |
| thread_local unique_ptr< CAlnErrorReporter > | theErrorReporter |
| END_ENUM_INFO | |
Function Documentation
◆ ADD_ENUM_VALUE() [1/28]
| ADD_ENUM_VALUE | ( | "Alignment" | , |
| eReader_Alignment | |||
| ) |
◆ ADD_ENUM_VALUE() [2/28]
| ADD_ENUM_VALUE | ( | "BadDataChars" | , |
| eAlnSubcode_BadDataChars | |||
| ) |
◆ ADD_ENUM_VALUE() [3/28]
| ADD_ENUM_VALUE | ( | "BadDataCount" | , |
| eAlnSubcode_BadDataCount | |||
| ) |
◆ ADD_ENUM_VALUE() [4/28]
| ADD_ENUM_VALUE | ( | "BadSequenceCount" | , |
| eAlnSubcode_BadSequenceCount | |||
| ) |
◆ ADD_ENUM_VALUE() [5/28]
| ADD_ENUM_VALUE | ( | "ConflictingValues" | , |
| eModSubcode_ConflictingValues | |||
| ) |
◆ ADD_ENUM_VALUE() [6/28]
| ADD_ENUM_VALUE | ( | "Deprecated" | , |
| eModSubcode_Deprecated | |||
| ) |
◆ ADD_ENUM_VALUE() [7/28]
| ADD_ENUM_VALUE | ( | "Duplicate" | , |
| eModSubcode_Duplicate | |||
| ) |
◆ ADD_ENUM_VALUE() [8/28]
| ADD_ENUM_VALUE | ( | "FileDoesNotExist" | , |
| eAlnSubcode_FileDoesNotExist | |||
| ) |
◆ ADD_ENUM_VALUE() [9/28]
| ADD_ENUM_VALUE | ( | "FileTooShort" | , |
| eAlnSubcode_FileTooShort | |||
| ) |
◆ ADD_ENUM_VALUE() [10/28]
| ADD_ENUM_VALUE | ( | "IllegalDataDescription" | , |
| eAlnSubcode_IllegalDataDescription | |||
| ) |
◆ ADD_ENUM_VALUE() [11/28]
| ADD_ENUM_VALUE | ( | "IllegalDataLine" | , |
| eAlnSubcode_IllegalDataLine | |||
| ) |
◆ ADD_ENUM_VALUE() [12/28]
| ADD_ENUM_VALUE | ( | "IllegalDefinitionLine" | , |
| eAlnSubcode_IllegalDefinitionLine | |||
| ) |
◆ ADD_ENUM_VALUE() [13/28]
| ADD_ENUM_VALUE | ( | "IllegalSequenceId" | , |
| eAlnSubcode_IllegalSequenceId | |||
| ) |
◆ ADD_ENUM_VALUE() [14/28]
| ADD_ENUM_VALUE | ( | "InconsistentMolType" | , |
| eAlnSubcode_InconsistentMolType | |||
| ) |
◆ ADD_ENUM_VALUE() [15/28]
| ADD_ENUM_VALUE | ( | "InsufficientDeflineInfo" | , |
| eAlnSubcode_InsufficientDeflineInfo | |||
| ) |
◆ ADD_ENUM_VALUE() [16/28]
| ADD_ENUM_VALUE | ( | "InvalidValue" | , |
| eModSubcode_InvalidValue | |||
| ) |
◆ ADD_ENUM_VALUE() [17/28]
| ADD_ENUM_VALUE | ( | "MissingDataLine" | , |
| eAlnSubcode_MissingDataLine | |||
| ) |
◆ ADD_ENUM_VALUE() [18/28]
| ADD_ENUM_VALUE | ( | "Mods" | , |
| eReader_Mods | |||
| ) |
◆ ADD_ENUM_VALUE() [19/28]
| ADD_ENUM_VALUE | ( | "ProteinModOnNucseq" | , |
| eModSubcode_ProteinModOnNucseq | |||
| ) |
◆ ADD_ENUM_VALUE() [20/28]
| ADD_ENUM_VALUE | ( | "UnexpectedCommand" | , |
| eAlnSubcode_UnexpectedCommand | |||
| ) |
◆ ADD_ENUM_VALUE() [21/28]
| ADD_ENUM_VALUE | ( | "UnexpectedCommandArgs" | , |
| eAlnSubcode_UnexpectedCommandArgs | |||
| ) |
◆ ADD_ENUM_VALUE() [22/28]
| ADD_ENUM_VALUE | ( | "UnexpectedSeqId" | , |
| eAlnSubcode_UnexpectedSeqId | |||
| ) |
◆ ADD_ENUM_VALUE() [23/28]
| ADD_ENUM_VALUE | ( | "Unrecognized" | , |
| eModSubcode_Unrecognized | |||
| ) |
◆ ADD_ENUM_VALUE() [24/28]
| ADD_ENUM_VALUE | ( | "UnsupportedFileFormat" | , |
| eAlnSubcode_UnsupportedFileFormat | |||
| ) |
◆ ADD_ENUM_VALUE() [25/28]
| ADD_ENUM_VALUE | ( | "UnterminatedBlock" | , |
| eAlnSubcode_UnterminatedBlock | |||
| ) |
◆ ADD_ENUM_VALUE() [26/28]
| ADD_ENUM_VALUE | ( | "UnterminatedCommand" | , |
| eAlnSubcode_UnterminatedCommand | |||
| ) |
◆ ADD_ENUM_VALUE() [27/28]
| ADD_ENUM_VALUE | ( | "UnterminatedComment" | , |
| eAlnSubcode_UnterminatedComment | |||
| ) |
◆ ADD_ENUM_VALUE() [28/28]
| ADD_ENUM_VALUE | ( | "UnusedLine" | , |
| eAlnSubcode_UnusedLine | |||
| ) |
◆ BadCharCountPrintf()
Definition at line 108 of file aln_errors.cpp.
References ErrorPrintf().
Referenced by CAlnScannerClustal::sProcessClustalDataLine(), CAlnScannerFastaGap::xImportAlignmentData(), CAlnScannerPhylip::xImportAlignmentData(), and CAlnScannerNexus::xProcessMatrix().
◆ ErrorPrintf()
| END_ENUM_INFO string ErrorPrintf | ( | const char * | format, |
| ... | |||
| ) |
Definition at line 99 of file aln_errors.cpp.
References format, and NStr::FormatVarargs().
Referenced by BadCharCountPrintf(), AlnUtil::CheckId(), CAlnScannerClustal::sProcessClustalDataLine(), sTerminateBlock(), CAlnReader::x_VerifyAlignmentInfo(), CAlnScannerNexus::xBeginBlock(), CAlnScannerFastaGap::xImportAlignmentData(), CAlnScannerPhylip::xImportAlignmentData(), CAlnScannerSequin::xImportAlignmentData(), CAlnScannerNexus::xProcessDimensions(), CAlnScannerNexus::xProcessMatrix(), CAlnScannerPhylip::xVerifyAlignmentData(), CAlnScanner::xVerifySingleSequenceData(), and CAlnScannerMultAlign::xVerifySingleSequenceData().
Variable Documentation
◆ END_ENUM_INFO
| END_ENUM_INFO |
Initial value:
{
ADD_ENUM_VALUE("Mods", eReader_Mods)
Definition at line 52 of file aln_errors.cpp.
◆ theErrorReporter
| thread_local unique_ptr<CAlnErrorReporter> theErrorReporter |
Definition at line 42 of file aln_errors.cpp.
Referenced by ReadAlignmentFile(), CAlnReader::x_ParseAndValidateSeqIds(), CAlnReader::x_VerifyAlignmentInfo(), CAlnScannerNexus::xProcessNCBIBlockCommand(), and CAlnScannerNexus::xUnexpectedEndBlock().
