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NCBI C++ ToolKit: include/objtools/align_format/showalign.hpp Source File

(

objects::CSeq_id&

) : m_Id(&id) {}

*m_Id < *other.

;

objects::CSeq_id& ()

{

*m_Id; }

eSequenceRetrieval = (1 << 2),

eMergeAlign = (1 << 3),

eShowMiddleLine = (1 << 4),

eShowIdentity = (1 << 7),

eShowBlastInfo = (1 << 8),

eShowBlastStyleId = (1 << 9),

eNewTargetWindow = (1 << 10),

eShowCdsFeature = (1 << 11),

eShowGeneFeature = (1 << 12),

eMasterAnchored = (1 << 13),

eColorDifferentBases = (1 << 14),

eTranslateNucToNucAlignment = (1 << 15),

eShowBl2seqLink = (1 << 16),

eDynamicFeature = (1 << 17),

eShowNoDeflineInfo = (1 << 18),

eHyperLinkSlaveSeqid = (1 << 19),

eHyperLinkMasterSeqid = (1 << 20),

eDisplayTreeView = (1 << 21),

eShowInfoOnMouseOverSeqid = (1 << 22),

eShowSortControls = (1 << 23),

eShowGeneInfo = (1 << 24),

eShowCheckBox = (1 << 25),

eShowEndGaps = (1 << 26),

eShowGapOnlyLines = (1 << 27),

eShowRawScoreOnly = (1 << 28),

eShowTranslationForLocalSeq = (1 << 29),

eShowAlignStatsForMultiAlignView = (1 << 30),

eShowSequencePropertyLabel = (1 << 31)

m_TranslatedFrameForLocalSeq = frame;

eDisplayResourcesLinks = (1 << 0),

eDisplayDownloadLink = (1 << 1)

objects::CScope & scope,

list < FeatureInfo * >* external_feature =

,

& mv_build_name)

m_MapViewerBuildName = mv_build_name;

DisplayPairwiseSeqalign(

&

,unordered_set <string> selectedIDs);

m_NumAlignToShow = num;

m_MasterGeneticCode =

;

m_SlaveGeneticCode =

;

m_currAlignSeqListIndex = alignSeqListIndex;

m_PreComputedResID = preComputedResID;

PrepareBlastUngappedSeqalign(

objects::CSeq_align_set & alnset);

PrepareBlastUngappedSeqalignEx(

objects::CSeq_align_set & alnset);

PrepareBlastUngappedSeqalignEx2(objects::CSeq_align_set & alnset);

m_DomainInfo = domain;

m_SeqPropertyLabel.reset(SequencePropertyLabel, ownership);

m_ResultPositionIndex = index;

vector<objects::CAlnMap::TSignedRange>

;

list<CRef<objects::CSeq_id> >

;

x_PrintDefLine(

objects::CBioseq_Handle& bsp_handle,

* aln_vec_info);

x_OutputSeq(

& sequence,

objects::CSeq_id&

,

start,

,

frame,

,

color_mismatch,

custom_genetic_code,

objects::CScope & scope,

objects::CSeqFeatData::E_Choice choice,

,

list<objects::ENa_strand>& feat_seq_strand,

fill_feat_range)

;

x_FillInserts(

, objects::CAlnMap::TSignedRange& aln_range,

aln_start, list < string >& inserts,

& insert_pos_string,

x_DoFills(

, objects::CAlnMap::TSignedRange& aln_range,

aln_start,

list < string > &inserts)

;

x_GetSegs(

)

;

x_FillIdentityInfo(

& sequence_standard,

& sequence,

&

,

&

,

& middle_line);

aln_from,

aln_to,

aln_stop,

pattern_char,

pattern_id,

& alternative_feat_str,

genetic_code)

;

objects::CAlnMap::TSeqPosList& insert_aln_start,

objects::CAlnMap::TSeqPosList& insert_seq_start,

objects::CAlnMap::TSeqPosList& insert_length,

x_GetGeneLinkUrl(

gene_id);

x_GetQueryFeatureList(

row_num,

aln_stop,

vector<TSAlnFeatureInfoList>& features)

;

x_FillSeqid(

&

,

)

;

x_GetLinkout(

objects::CSeq_id &

);

& master_feat_str,

x_DisplayRowData(

*alnRoInfo);

x_DisplayRowDataSet(

*alnRoInfo,

aln_start, vector<int> &prev_stop);

x_ProcessRowDataSet(

*alnRoInfo,

aln_start, vector<int> &prev_stop);

* aln_vec_info,

showSortControls);

x_PrepareIdentityInfo(

* aln_vec_info);

x_PrepareDynamicFeatureInfo(

* aln_vec_info);

x_FormatSingleAlign(

* aln_vec_info);

x_FormatAlignSortInfo();

x_FormatAlnBlastInfo(

* aln_vec_info);

x_FormatIdentityInfo(

alignInfo,

* aln_vec_info);

x_FormatDynamicFeaturesInfo(

alignInfo,

* aln_vec_info);

x_FormatOneDynamicFeature(

viewerURL,

x_PreProcessSeqAlign(objects::CSeq_align_set &actual_aln_list);

x_CalcUrlLinksParams(

objects::CSeq_align& align,

idString,

toolUrl);

x_InitAlignParams(objects::CSeq_align_set &actual_aln_list);

x_PreProcessSingleAlign(objects::CSeq_align_set::Tdata::const_iterator currSeqAlignIter,

objects::CSeq_align_set &actual_aln_list,

x_FormatAlnHSPLinks(

&alignInfo);

objects::CBioseq_Handle& bsp_handle,

list<string> &use_this_seqid,

numLinkoutReads);

x_FormatDefLinesHeader(

objects::CBioseq_Handle& bsp_handle,

* aln_vec_info);

x_InitDefLinesHeader(

objects::CBioseq_Handle& bsp_handle,

* aln_vec_info);

x_MapDefLine(

*alnDispParams,

isFisrt,

linkout,

hideDefline,

seqLength);

x_GetDomainInfo(

row_num,

aln_stop,

vector<TSAlnFeatureInfoList>& retval)

;

x_AddTranslationForLocalSeq(vector<TSAlnFeatureInfoList>& retval,

vector<string>& sequence)

;

User-defined methods of the data storage class.

#define BLAST_DEFAULT_MATRIX

Example:

DisplayOption

option for alignment display

void x_DisplayAlnvecInfoHead(CNcbiOstream &out, SAlnInfo *aln_vec_info)

void SetLineLen(size_t len)

number of bases or amino acids per line

list< string > m_HSPLinksList

TranslatedFrameForLocalSeq

CDisplaySeqalign(const CDisplaySeqalign &other)

Prohibit copy constructor.

list< CRef< DomainInfo > > * m_DomainInfo

void SetLinkoutDB(ILinkoutDB *l, const string &mv_build_name)

Set the linkout implementation.

objects::CGetFeature * m_DynamicFeature

list< FeatureInfo * > * m_QueryFeature

external feature such as phiblast

SeqLocColorOption

colors for seqloc display

void SetQueryNumber(int number)

for linking to mapviewer

CNcbiIfstream * m_ConfigFile

string m_CurrAlnID_Lbl

gi(if exists) that is used for html formatting otherwise id without db part

int m_currAlignHsp

Current HSP number for single alignmnet.

AlignType

Alignment display type, specific for showing blast-related info.

void SetSeqLocColor(SeqLocColorOption option=eBlack)

color for seqloc display such as masked region

SeqLocColorOption m_SeqLocColor

ILinkoutDB * m_LinkoutDB

Reference to LinkoutDB implementation. Not owned by this class.

void SetMasterDomain(list< CRef< DomainInfo > > *domain)

void SetMiddleLineStyle(MiddleLineStyle option=eBar)

set middle line style

TSubjectMaskMap m_SubjectMasks

Map of subject masks.

void SetSeqLocChar(SeqLocCharOption option=eX)

character style for seqloc display such as masked region

list< string > m_CustomLinksList

void SetAlignOption(int option)

Set functions.

string m_CurrAlnID_DbLbl

gi(if exists) that is used for html formatting otherwise id with db part like ti:xxxxxxx or GNOMON:XX...

void SetRid(string rid)

set blast request id

void SetPreComputedResID(string preComputedResID)

Sets CDD precomputed results ID.

int m_ResultPositionIndex

result position index for multiple query case

map< string, struct SAlnLinksParams > m_AlnLinksParams

void SetTranslatedFrameForLocalSeq(TranslatedFrameForLocalSeq frame)

SAlnDispParams * x_FillAlnDispParams(const objects::CBioseq_Handle &bsp_handle)

void x_DisplayIdentityInfo(SAlnRowInfo *alnRoInfo, CNcbiOstream &out)

Display identities,positives,frames etc.

CRef< objects::CObjectManager > m_FeatObj

void SetDbType(bool is_na)

database type.

SeqLocCharOption m_SeqLocChar

void SetCddRid(string cdd_rid)

CDD rid for constructing linkout.

bool m_UseLongSeqIds

print long sequence ids (with gi and accession with database source)

objects::CScope & m_Scope

void SetAlignSeqListIndex(int alignSeqListIndex)

Set subject seq index.

void SetResultPositionIndex(int index)

AutoPtr< const vector< string > > m_SeqPropertyLabel

void SetQueryAnchoredIndex(int queryAnchoredSetIndex)

Sets index of Query anchored alignment set to display or download.

list< CRef< SAlnSeqlocInfo > > TSAlnSeqlocInfoList

List of SAlnSeqlocInfo structures.

string m_MapViewerBuildName

mapviewer build name associated with the sequences in the BLAST database out of which the results are...

CAlignFormatUtil::SLinkoutInfo m_LinkoutInfo

int m_cur_align

Gene info reader object, reads Gene info entries from files.

void SetDbName(string name)

set blast database name

void SetSequencePropertyLabel(const vector< string > *SequencePropertyLabel, EOwnership ownership=eNoOwnership)

CDisplaySeqalign(const objects::CSeq_align_set &seqalign, objects::CScope &scope, list< CRef< CSeqLocInfo > > *mask_seqloc=NULL, list< FeatureInfo * > *external_feature=NULL, const char *matrix_name="BLOSUM62")

Constructors.

int m_QueryAnchoredSetIndex

string x_PrintDynamicFeatures(void)

SAlignTemplates * m_AlignTemplates

void SetCgiContext(CCgiContext &ctx)

string m_AlignedRegionsUrl

string m_PreComputedResID

CDD precomputed results ID.

void SetAlignType(AlignType type)

Needed only if you want to display positives and strand.

void SetBlastType(string type)

internal blast type

void SetEntrezTerm(string term)

for constructing structure linkout

list< CRef< SAlnFeatureInfo > > TSAlnFeatureInfoList

string m_CurrAlnAccession

accession that is displayed

CConstRef< objects::CSeq_align_set > m_SeqalignSetRef

reference to seqalign set

list< CRef< SInsertInformation > > TSInsertInformationList

int m_currAlignSeqListIndex

Current subject seq index in descriptions table.

SeqLocCharOption

character used to display seqloc, such as masked sequence

static TGi x_GetGiForSeqIdList(const list< CRef< objects::CSeq_id > > &ids)

list< string > m_LinkoutList

MiddleLineStyle m_MidLineStyle

void SetMasterGeneticCode(int code)

Set genetic code for master sequence.

CDisplaySeqalign & operator=(const CDisplaySeqalign &rhs)

Prohibit assignment operator.

TranslatedFrameForLocalSeq m_TranslatedFrameForLocalSeq

list< CRef< CSeqLocInfo > > * m_Seqloc

display character option for list of seqloc

void SetSlaveGeneticCode(int code)

Set Genetic cod for slaves.

void SetNumAlignToShow(int num)

Display top num seqalign Note this only limit the number of seqalign regardless of the seqids.

MiddleLineStyle

Middle line style option.

CRef< objects::CScope > m_featScope

SAlnDispParams * x_FillAlnDispParams(const CRef< objects::CBlast_def_line > &iter, const objects::CBioseq_Handle &bsp_handle, list< string > &use_this_seqid, TGi firstGi, int numLinkoutReads)

int m_NumBlastDefLines

Number of subject sequence deflines.

void UseLongSequenceIds(void)

Sets usage of long sequence ids (database|accession)

void SetAlignTemplates(SAlignTemplates *alignTemplates)

map< SSeqIdKey, TMaskedQueryRegions > TSubjectMaskMap

Definition of std::map of objects::CSeq_ids to masks.

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

main entry point for tests

SStrictId_Tax::TId TTaxId

Taxon id type.

@ eNoOwnership

No ownership is assumed.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

enum ENcbiOwnership EOwnership

Ownership relations between objects.

#define NCBI_ALIGN_FORMAT_EXPORT

Process information in the NCBI Registry, including working with configuration files.

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

Structure that holds information needed for creation seqID URL in descriptions and alignments.

structure for showing domains on the master sequence

bool is_subject_start_valid

CConstRef< objects::CSeq_loc > subject_seqloc

bool is_subject_stop_valid

CConstRef< objects::CSeq_loc > seqloc

structure for store feature display info

CConstRef< objects::CSeq_loc > seqloc

string alignRowTmpl

Template for displayin actual pairwise alignment - BLAST_ALIGN_ROWS.

string alnTitlesTmpl

Template for displaying multiple defline titles.

string alignFeatureLinkTmpl

Template for displaying align features link -ALN_FEATURES_LINK.

string alignInfoFrameTmpl

Template for displaying frame data ALIGN_PARAMS_FRAME, part of BLAST_ALIGN_PARAMS.

string alnSeqInfoTmpl

Template for displaying sequnce link in defline.

string alignQueryAnchTempl

Template for displaying one set of query anchored alignment - BLAST_QUERY_ANCH_NAV.

string alnTitlesLinkTmpl

Template for displaying link for more defline titles.

string alignInfoMethodTmpl

Template for displaying frame data ALIGN_PARAMS_METHOD, part of BLAST_ALIGN_PARAMS.

string alignFeatureTmpl

Template for displaying align features -ALN_FEATURES.

string sortInfoTmpl

Template for displaying Sort by header - SORT_ALIGNS_SEQ.

string alnDefLineTmpl

Template for displaying one defline ALN_DEFLINE_ROW.

string alignInfoTmpl

Template for displaying singe align params - BLAST_ALIGN_PARAMS_NUC,BLAST_ALIGN_PARAMS_PROT.

string alignHeaderTmpl

Template for displaying header,deflines and gene info - BLAST_ALIGN_HEADER.

string alignRowTmplLast

Template for displayin actual last pairwise alignment - BLAST_ALIGN_ROWS_LST.

string label

sequence label

CRef< objects::CSeq_id > seqID

seqID used in defline

string linkoutStr

string containing all linkout urls

CAlignFormatUtil::SSeqURLInfo * seqUrlInfo

list< CRef< objects::CSeq_id > > ids

TGi gi

gi used in defline

string title

sequnce title

string id_url

entrz, mapview etc id url

string dumpGnlUrl

download sequnce url

store feature information

CRange< TSignedSeqPos > aln_range

CRef< FeatureInfo > feature

list< TSeqPos > feature_start

store alnvec and score info

CRange< TSeqPos > actual_range

CRef< objects::CAlnVec > alnvec

vector< objects::SFeatInfo * > feat_list

objects::SFeatInfo * feat5

list< string > use_this_seqid

objects::SFeatInfo * feat3

Info used to contstruct seq url obtained from processing the whole seq align for particular subject s...

string segs

seq align segments in the format seg1start-seg1end,seg2start-seg2end,

bool flip

opposite starnds indicator

CRange< TSeqPos > * subjRange

subject sequnce range

SAlnLinksParams()

Constructor.

vector< string > align_stats

vector< objects::CAlnMap::TSignedRange > rowRng

vector< objects::CAlnMap::TSeqPosList > insertLength

bool show_seq_property_label

vector< double > percent_ident

vector< objects::CAlnMap::TSeqPosList > seqStarts

vector< string > seq_property_label

vector< TSAlnSeqlocInfoList > masked_regions

objects::CAlnMap::TSignedRange currRange

vector< objects::CAlnMap::TSeqPosList > insertAlnStart

vector< TSAlnFeatureInfoList > bioseqFeature

vector< objects::CAlnMap::TSeqPosList > insertStart

vector< string > sequence

vector< string > seqidArray

vector< objects::CAlnMap::TSeqPosList > seqStops

int max_seq_property_label

vector< int > align_length

CRef< CSeqLocInfo > seqloc

CRange< TSignedSeqPos > aln_range

internal insert information aln_start.

Auxiliary type to embed a CConstRef<objects::CSeq_id> in STL containers that require operator< to be ...

SSeqIdKey(const objects::CSeq_id &id)

Constructor.

CConstRef< objects::CSeq_id > m_Id

The wrapped object.

bool operator<(const SSeqIdKey &other) const

Operator< to comply with STL container requirements.

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