Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnmap_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/alnmgr/alnmap.hpp Source File

fNotAlignedToSeqOnAnchor = 0x0002,

fInsert = fSeq | fNotAlignedToSeqOnAnchor,

fUnalignedOnRight = 0x0004,

fUnalignedOnLeft = 0x0008,

fNoSeqOnRight = 0x0010,

fNoSeqOnLeft = 0x0020,

fUnalignedOnRightOnAnchor = 0x0200,

fUnalignedOnLeftOnAnchor = 0x0400,

fIgnoreUnaligned = 0x0001,

fInsertSameAsSeq = 0x0002,

fDeletionSameAsGap = 0x0004,

fIgnoreAnchor = fInsertSameAsSeq | fDeletionSameAsGap,

fChunkSameAsSeg = 0x0010,

fSkipUnalignedGaps = 0x0020,

fSkipDeletions = 0x0040,

fSkipAllGaps = fSkipUnalignedGaps | fSkipDeletions,

fSkipInserts = 0x0080,

fSeqOnly = fSkipAllGaps | fSkipInserts,

fInsertsOnly = fSkipAllGaps | fSkipAlnSeq,

fAlnSegsOnly = fSkipInserts | fSkipUnalignedGaps,

fDoNotTruncateSegs = 0x0200,

fAddUnalignedChunks = 0x0400

CreateAlignFromRange(

vector<TNumrow>& selected_rows,

ESegmentTrimFlag seg_flag = eSegment_Trim);

TNumseg GetNumSegs(

)

;

GetNumRows(

)

;

IsPositiveStrand(TNumrow

)

;

IsNegativeStrand(TNumrow

)

;

StrandSign (TNumrow

)

;

GetWidth (TNumrow

)

;

TSignedRange GetSeqAlnRange(TNumrow

)

;

GetSeqRange (TNumrow

)

;

TSignedRange GetRange (TNumrow

, TNumseg seg,

= 0)

;

TSegTypeFlags GetSegType(TNumrow

, TNumseg seg,

= 0)

;

TSegTypeFlags GetTypeAtAlnPos(TNumrow

,

aln_pos)

;

IsTypeInsert(TSegTypeFlags

);

GetAlnStart(TNumseg seg)

;

GetAlnStop (TNumseg seg)

;

GetAlnStop (

)

;

IsSetAnchor(

)

;

TNumrow GetAnchor (

)

;

SetAnchor (TNumrow anchor);

UnsetAnchor(

);

TNumseg GetSeg (

aln_pos)

;

TNumseg GetRawSeg (TNumrow

,

seq_pos,

ESearchDirection dir =

,

try_reverse_dir =

)

;

ESearchDirection dir =

,

try_reverse_dir =

)

;

ESearchDirection dir =

,

try_reverse_dir =

)

;

ESearchDirection dir =

,

try_reverse_dir =

)

;

GetResidueIndexMap (TNumrow row0,

vector<TSignedSeqPos>&

,

x_GetChunks (CAlnChunkVec * vec,

TGetChunkFlags

)

;

TGetChunkFlags

= fAlnSegsOnly)

;

TGetChunkFlags

= fAlnSegsOnly)

;

{ m_TypeFlags =

;

*

; }

(

)

{

m_SeqRange.GetFrom() < 0; }

: m_AlnSeg(seg), m_Offset(

) { }

x_Init (

);

x_CreateAlnStarts (

);

try_reverse_dir)

;

CsvTable(

delim =

);

PrintSeqPos(

pos)

;

m_NumRows(ds.GetDim()),

m_NumSegs(ds.GetNumseg()),

m_Starts(ds.GetStarts()),

m_Lens(ds.GetLens()),

m_Strands(ds.GetStrands()),

m_Scores(ds.GetScores()),

m_Widths(ds.GetWidths()),

m_NumRows(ds.GetDim()),

m_NumSegs(ds.GetNumseg()),

m_Starts(ds.GetStarts()),

m_Lens(ds.GetLens()),

m_Strands(ds.GetStrands()),

m_Scores(ds.GetScores()),

m_Widths(ds.GetWidths()),

((start > -1) ?

const CAlnMap::TNumrow m_NumRows

const string & GetId(CAlnMap::TNumrow row) const

Fasta style Ids.

CAlnChunkVec(const CAlnMap &aln_map, TNumrow row)

vector< TNumseg > m_StartSegs

vector< TNumseg > m_StopSegs

TNumchunk size(void) const

const TSignedRange & GetRange(void) const

const TSignedRange & GetAlnRange(void) const

TSegTypeFlags GetType(void) const

TSignedRange & SetRange(void)

TSegTypeFlags m_TypeFlags

TSignedRange & SetAlnRange(void)

CAlnChunk & SetType(TSegTypeFlags type_flags)

TNumseg GetAlnSeg(void) const

int GetOffset(void) const

CNumSegWithOffset(TNumseg seg, int offset=0)

TSignedSeqPos GetStop(TNumrow row, TNumseg seg, int offset=0) const

void x_GetChunks(CAlnChunkVec *vec, TNumrow row, TNumseg left_seg, TNumseg right_seg, TGetChunkFlags flags) const

TRawSegTypes * m_RawSegTypes

TSeqPos GetSeqLen(TNumrow row, TNumseg seg, int offset=0) const

const CDense_seg::TScores & m_Scores

bool IsSetAnchor(void) const

list< TSeqPos > TSeqPosList

int GetWidth(TNumrow row) const

CRef< CAlnChunkVec > GetSeqChunks(TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

const TNumseg & x_GetSeqLeftSeg(TNumrow row) const

const CDense_seg::TStarts & m_Starts

TSegTypeFlags GetSegType(TNumrow row, TNumseg seg, int offset=0) const

CNumSegWithOffset x_GetSegFromRawSeg(TNumseg seg) const

TSeqPos x_GetLen(TNumrow row, TNumseg seg) const

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

const CSeq_id & GetSeqId(TNumrow row) const

bool IsPositiveStrand(TNumrow row) const

const CDense_seg::TIds & m_Ids

TSegTypeFlags GetTypeAtAlnPos(TNumrow row, TSeqPos aln_pos) const

TNumseg GetSeg(TSeqPos aln_pos) const

TNumseg x_GetRawSegFromSeg(TNumseg seg) const

vector< CNumSegWithOffset > m_NumSegWithOffsets

TRawSegTypes & x_GetRawSegTypes() const

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TDim GetNumRows(void) const

bool IsNegativeStrand(TNumrow row) const

CRange< TSignedSeqPos > TSignedRange

void SetAnchor(TNumrow anchor)

TSignedRange GetSeqAlnRange(TNumrow row) const

CDense_seg::TStarts m_AlnStarts

vector< TNumseg > m_AlnSegIdx

void x_CreateAlnStarts(void)

vector< TNumseg > m_SeqLeftSegs

const CDense_seg::TStrands & m_Strands

CConstRef< CDense_seg > m_DS

const TNumseg & x_GetSeqRightSeg(TNumrow row) const

TSegTypeFlags x_GetRawSegType(TNumrow row, TNumseg seg, int hint_idx=-1) const

vector< TNumseg > m_SeqRightSegs

TRange GetSeqRange(TNumrow row) const

CAlnMap & operator=(const CAlnMap &value)

CRef< CAlnChunkVec > GetAlnChunks(TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

unsigned int TSegTypeFlags

TNumrow GetAnchor(void) const

CAlnMap(const CAlnMap &value)

TSeqPos GetAlnStart(void) const

TSignedSeqPos x_GetRawStop(TNumrow row, TNumseg seg) const

TSeqPos GetLen(TNumseg seg, int offset=0) const

CDense_seg::TNumseg TNumseg

const CDense_seg::TWidths & m_Widths

const CDense_seg & GetDenseg(void) const

TSeqPos GetAlnStop(void) const

TSeqPos GetSeqStop(TNumrow row) const

TSignedRange GetRange(TNumrow row, TNumseg seg, int offset=0) const

int StrandSign(TNumrow row) const

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

TNumseg GetNumSegs(void) const

TSeqPos GetSeqStart(TNumrow row) const

void x_SetRawSegTypes(TNumrow row) const

CAlnMap(const CDense_seg &ds)

static bool IsTypeInsert(TSegTypeFlags type)

TSignedSeqPos x_GetRawStart(TNumrow row, TNumseg seg) const

vector< TSegTypeFlags > TRawSegTypes

const CDense_seg::TLens & m_Lens

Alignment explorer interface.

ESearchDirection

Position search options.

std::ofstream out("events_result.xml")

main entry point for tests

static const struct type types[]

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

#define NCBI_XALNMGR_EXPORT

vector< ENa_strand > TStrands

vector< TSignedSeqPos > TStarts

vector< CRef< CSeq_id > > TIds

vector< CRef< CScore > > TScores

const GenericPointer< typename T::ValueType > T2 value

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

static Int4 GetSeqLen(const DataBlk &entry)

#define row(bind, expected)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4