NCBI C++ ToolKit
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Search Toolkit Book for CDisplaySeqalign::SAlnRowInfo
#include <objtools/align_format/showalign.hpp>
Public Attributes | |
vector< string > | sequence |
vector< objects::CAlnMap::TSeqPosList > | seqStarts |
vector< objects::CAlnMap::TSeqPosList > | seqStops |
vector< objects::CAlnMap::TSeqPosList > | insertStart |
vector< objects::CAlnMap::TSeqPosList > | insertAlnStart |
vector< objects::CAlnMap::TSeqPosList > | insertLength |
vector< string > | seqidArray |
string | middleLine |
vector< objects::CAlnMap::TSignedRange > | rowRng |
vector< int > | frame |
vector< TTaxId > | taxid |
vector< TSAlnFeatureInfoList > | bioseqFeature |
vector< TSAlnSeqlocInfoList > | masked_regions |
size_t | maxIdLen |
size_t | maxStartLen |
int | max_feature_num |
bool | colorMismatch |
int | rowNum |
vector< int > | match |
vector< int > | align_length |
vector< double > | percent_ident |
vector< string > | align_stats |
int | max_align_stats_len |
vector< string > | seq_property_label |
int | max_seq_property_label |
bool | show_align_stats |
bool | show_seq_property_label |
int | currPrintSegment |
int | currActualLineLen |
objects::CAlnMap::TSignedRange | currRange |
Additional Inherited Members | |
Public Types inherited from CObject | |
enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
Control filling of newly allocated memory. More... | |
typedef CObjectCounterLocker | TLockerType |
Default locker type for CRef. More... | |
typedef atomic< Uint8 > | TCounter |
Counter type is CAtomiCounter. More... | |
typedef Uint8 | TCount |
Alias for value type of counter. More... | |
Public Member Functions inherited from CObject | |
CObject (void) | |
Constructor. More... | |
CObject (const CObject &src) | |
Copy constructor. More... | |
virtual | ~CObject (void) |
Destructor. More... | |
CObject & | operator= (const CObject &src) THROWS_NONE |
Assignment operator. More... | |
bool | CanBeDeleted (void) const THROWS_NONE |
Check if object can be deleted. More... | |
bool | IsAllocatedInPool (void) const THROWS_NONE |
Check if object is allocated in memory pool (not system heap) More... | |
bool | Referenced (void) const THROWS_NONE |
Check if object is referenced. More... | |
bool | ReferencedOnlyOnce (void) const THROWS_NONE |
Check if object is referenced only once. More... | |
void | AddReference (void) const |
Add reference to object. More... | |
void | RemoveReference (void) const |
Remove reference to object. More... | |
void | ReleaseReference (void) const |
Remove reference without deleting object. More... | |
virtual void | DoNotDeleteThisObject (void) |
Mark this object as not allocated in heap – do not delete this object. More... | |
virtual void | DoDeleteThisObject (void) |
Mark this object as allocated in heap – object can be deleted. More... | |
void * | operator new (size_t size) |
Define new operator for memory allocation. More... | |
void * | operator new[] (size_t size) |
Define new[] operator for 'array' memory allocation. More... | |
void | operator delete (void *ptr) |
Define delete operator for memory deallocation. More... | |
void | operator delete[] (void *ptr) |
Define delete[] operator for memory deallocation. More... | |
void * | operator new (size_t size, void *place) |
Define new operator. More... | |
void | operator delete (void *ptr, void *place) |
Define delete operator. More... | |
void * | operator new (size_t size, CObjectMemoryPool *place) |
Define new operator using memory pool. More... | |
void | operator delete (void *ptr, CObjectMemoryPool *place) |
Define delete operator. More... | |
virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
Define method for dumping debug information. More... | |
Public Member Functions inherited from CDebugDumpable | |
CDebugDumpable (void) | |
virtual | ~CDebugDumpable (void) |
void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
void | DumpToConsole (void) const |
Static Public Member Functions inherited from CObject | |
static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
Define method to throw null pointer exception. More... | |
static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
static EAllocFillMode | GetAllocFillMode (void) |
static void | SetAllocFillMode (EAllocFillMode mode) |
static void | SetAllocFillMode (const string &value) |
Set mode from configuration parameter value. More... | |
Static Public Member Functions inherited from CDebugDumpable | |
static void | EnableDebugDump (bool on) |
Static Public Attributes inherited from CObject | |
static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
Define possible object states. More... | |
static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
Heap signature was found. More... | |
static const TCount | eCounterBitsPlaceMask |
Mask for 'in heap' state flags. More... | |
static const int | eCounterStep = 1 << 2 |
Skip over the "in heap" bits. More... | |
static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
static const TCount | eCounterStateMask |
Valid object, and object in heap. More... | |
Protected Member Functions inherited from CObject | |
virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
Definition at line 508 of file showalign.hpp.
vector<int> CDisplaySeqalign::SAlnRowInfo::align_length |
Definition at line 528 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_PrepareRowData().
vector<string> CDisplaySeqalign::SAlnRowInfo::align_stats |
Definition at line 530 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), and CDisplaySeqalign::x_PrepareRowData().
vector<TSAlnFeatureInfoList> CDisplaySeqalign::SAlnRowInfo::bioseqFeature |
Definition at line 520 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_PrintFeatures().
bool CDisplaySeqalign::SAlnRowInfo::colorMismatch |
Definition at line 525 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrepareIdentityInfo(), and CDisplaySeqalign::x_PrepareRowData().
int CDisplaySeqalign::SAlnRowInfo::currActualLineLen |
Definition at line 538 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayMiddLine(), CDisplaySeqalign::x_DisplayRowData(), CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrintFeatures(), and CDisplaySeqalign::x_ProcessRowDataSet().
int CDisplaySeqalign::SAlnRowInfo::currPrintSegment |
Definition at line 537 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplayMiddLine(), CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrintFeatures(), and CDisplaySeqalign::x_ProcessRowDataSet().
objects::CAlnMap::TSignedRange CDisplaySeqalign::SAlnRowInfo::currRange |
Definition at line 539 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_PrintFeatures(), and CDisplaySeqalign::x_ProcessRowDataSet().
vector<int> CDisplaySeqalign::SAlnRowInfo::frame |
Definition at line 518 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_DisplaySingleAlignParams(), CDisplaySeqalign::x_FormatIdentityInfo(), and CDisplaySeqalign::x_PrepareRowData().
vector<objects::CAlnMap::TSeqPosList> CDisplaySeqalign::SAlnRowInfo::insertAlnStart |
Definition at line 513 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), and CDisplaySeqalign::x_PrepareRowData().
vector<objects::CAlnMap::TSeqPosList> CDisplaySeqalign::SAlnRowInfo::insertLength |
Definition at line 514 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), and CDisplaySeqalign::x_PrepareRowData().
vector<objects::CAlnMap::TSeqPosList> CDisplaySeqalign::SAlnRowInfo::insertStart |
Definition at line 512 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), and CDisplaySeqalign::x_PrepareRowData().
vector<TSAlnSeqlocInfoList> CDisplaySeqalign::SAlnRowInfo::masked_regions |
Definition at line 521 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayMiddLine(), CDisplaySeqalign::x_DisplaySequenceLine(), and CDisplaySeqalign::x_PrepareRowData().
vector<int> CDisplaySeqalign::SAlnRowInfo::match |
Definition at line 527 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_PrepareRowData().
int CDisplaySeqalign::SAlnRowInfo::max_align_stats_len |
Definition at line 531 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_PrintFeatures().
int CDisplaySeqalign::SAlnRowInfo::max_feature_num |
Definition at line 524 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_PrepareRowData().
int CDisplaySeqalign::SAlnRowInfo::max_seq_property_label |
Definition at line 533 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_PrintFeatures().
size_t CDisplaySeqalign::SAlnRowInfo::maxIdLen |
Definition at line 522 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplayMiddLine(), CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_PrintFeatures().
size_t CDisplaySeqalign::SAlnRowInfo::maxStartLen |
Definition at line 523 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplayMiddLine(), CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_PrintFeatures().
string CDisplaySeqalign::SAlnRowInfo::middleLine |
Definition at line 516 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayMiddLine(), CDisplaySeqalign::x_PrepareIdentityInfo(), and CDisplaySeqalign::x_PrepareRowData().
vector<double> CDisplaySeqalign::SAlnRowInfo::percent_ident |
Definition at line 529 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_PrepareRowData().
int CDisplaySeqalign::SAlnRowInfo::rowNum |
Definition at line 526 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayRowData(), CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_ProcessRowDataSet().
vector<objects::CAlnMap::TSignedRange> CDisplaySeqalign::SAlnRowInfo::rowRng |
Definition at line 517 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_ProcessRowDataSet().
vector<string> CDisplaySeqalign::SAlnRowInfo::seq_property_label |
Definition at line 532 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), and CDisplaySeqalign::x_PrepareRowData().
vector<string> CDisplaySeqalign::SAlnRowInfo::seqidArray |
vector<objects::CAlnMap::TSeqPosList> CDisplaySeqalign::SAlnRowInfo::seqStarts |
Definition at line 510 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_ProcessRowDataSet().
vector<objects::CAlnMap::TSeqPosList> CDisplaySeqalign::SAlnRowInfo::seqStops |
Definition at line 511 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrepareRowData(), and CDisplaySeqalign::x_ProcessRowDataSet().
vector<string> CDisplaySeqalign::SAlnRowInfo::sequence |
Definition at line 509 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayRowDataSet(), CDisplaySeqalign::x_DisplaySequenceLine(), CDisplaySeqalign::x_PrepareIdentityInfo(), and CDisplaySeqalign::x_PrepareRowData().
bool CDisplaySeqalign::SAlnRowInfo::show_align_stats |
Definition at line 534 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplayRowData(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), and CDisplaySeqalign::x_PrintFeatures().
bool CDisplaySeqalign::SAlnRowInfo::show_seq_property_label |
Definition at line 535 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_DisplayInsertsForQueryAnchored(), CDisplaySeqalign::x_DisplayRowData(), CDisplaySeqalign::x_DisplaySequenceIDForQueryAnchored(), and CDisplaySeqalign::x_PrintFeatures().
vector<TTaxId> CDisplaySeqalign::SAlnRowInfo::taxid |
Definition at line 519 of file showalign.hpp.
Referenced by CDisplaySeqalign::x_HTMLSeqIDLink(), and CDisplaySeqalign::x_PrepareRowData().