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NCBI C++ ToolKit: src/objtools/align_format/seqalignfilter.cpp Source File

& fname_out_seqaligns,

& fname_gis_to_filter)

& fname_out_seqaligns,

& fname_gis_to_filter,

filtered_aln.

().clear();

(!((*iter)->GetSegs().IsDisc())) {

id_aligned_seq = &((*iter)->GetSeq_id(1));

(seqdb_gis->FindGi(gi)) {

filtered_aln.

().push_back(*iter);

aln_disc->

(**iter);

aln_disc->

().SetDisc(*filtered_sub_aln);

filtered_aln.

().push_back(aln_disc);

list<TGi>& list_gis,

filtered_aln.

().clear();

(!((*iter)->GetSegs().IsDisc())) {

id_aligned_seq = &((*iter)->GetSeq_id(1));

(find(list_gis.begin(), list_gis.end(), gi) != list_gis.end()) {

filtered_aln.

().push_back(*iter);

((*iter)->GetSegs().GetDisc(), list_gis, *filtered_sub_aln);

aln_disc->

(**iter);

aln_disc->

().SetDisc(*filtered_sub_aln);

filtered_aln.

().push_back(aln_disc);

list< CRef<CSeq_id> > seqid_list = db->

(oid);

gis.reserve(seqid_list.size());

gis.push_back((**id).GetGi());

(gis.begin(), gis.end());

filtered_aln.

().clear();

(!((*iter_aln)->GetSegs().IsDisc())) {

id_aligned_seq = &((*iter_aln)->GetSeq_id(1));

gi_aligned_seq = id_aligned_seq->

();

oid_aligned_seq = -1;

db->

(gi_aligned_seq, oid_aligned_seq);

vector<TGi> vec_gis_from_DB;

(oid_aligned_seq > 0)

(!vec_gis_from_DB.empty()) {

((*iter_aln)->GetSegs().GetDisc(), db, *filtered_sub_aln);

aln_disc->Assign(**iter_aln);

aln_disc->SetSegs().SetDisc(*filtered_sub_aln);

filtered_aln.

().push_back(aln_disc);

(out_gi_vec.size() == 0)

(vector<TGi>::const_iterator it_gi_out = out_gi_vec.begin();

it_gi_out != out_gi_vec.end(); it_gi_out++)

success =

;

in_gi, *it_gi_out, success);

out_aln.

().push_back(sa_copy);

vector<TGi> vec_old_extra_gis;

vector<TGi> vec_new_extra_gis;

(in_gi, vec_old_extra_gis, out_gi_vec, main_new_gi, vec_new_extra_gis);

success =

;

main_new_gi, success);

out_aln.

().push_back(sa_copy);

vector<TGi>& vec_old_extra_gis,

vector<TGi>& vec_out_gis,

vector<TGi>& vec_new_extra_gis)

(vec_out_gis.empty())

i_out_gi = 0, i_old_gi = 0, i_new_gi = 0;

(find(vec_out_gis.begin(), vec_out_gis.end(), main_old_gi) != vec_out_gis.end())

main_new_gi = main_old_gi;

main_new_gi = vec_out_gis[0];

num_gis_left = vec_out_gis.size();

(num_gis_left > 0)

vec_new_extra_gis.resize(num_gis_left);

(; i_old_gi < (

)(vec_old_extra_gis.size()); i_old_gi++)

old_gi = vec_old_extra_gis[i_old_gi];

(find(vec_out_gis.begin(), vec_out_gis.end(), old_gi) != vec_out_gis.end())

vec_new_extra_gis[i_new_gi++] = old_gi;

(; i_out_gi < (

)(vec_out_gis.size()); i_out_gi++)

out_gi = vec_out_gis[i_out_gi];

(find(vec_old_extra_gis.begin(), vec_old_extra_gis.end(), out_gi)

== vec_old_extra_gis.end())

vec_new_extra_gis[i_new_gi++] = out_gi;

vec_new_extra_gis.clear();

old_gi,

new_gi,

& success)

gi_changed =

;

((*iter_diag)->IsSetIds() && n_row < (*iter_diag)->GetIds().size())

& id_to_change = *((*iter_diag)->GetIds()[n_row]);

(id_to_change.

() &&

id_to_change.

() == old_gi)

(*iter_diag)->SetIds()[n_row]->

(new_gi);

(denseg.IsSetIds() && n_row < denseg.GetIds().size())

& id_to_change = *(denseg.GetIds()[n_row]);

(id_to_change.

() &&

id_to_change.

() == old_gi)

denseg.SetIds()[n_row]->

(new_gi);

((*iter_std)->IsSetLoc() && n_row < (*iter_std)->GetLoc().size())

& loc_to_change = *((*iter_std)->SetLoc()[n_row]);

* p_id_to_change = loc_to_change.

();

(p_id_to_change->

() &&

p_id_to_change->

() == old_gi)

loc_to_change.

(*id_updated);

success = gi_changed;

vec_extra_gis.clear();

(score_entry->CScore_Base::IsSetId())

(score_entry->GetId().IsStr())

str_id = score_entry->GetId().GetStr();

(str_id ==

)

gi_v = (

) (score_entry->GetValue().GetInt());

vec_extra_gis.push_back(gi);

(

i_gi = 0; i_gi < (

)(vec_extra_gis.size()); i_gi++)

CSeq_align::TScore::iterator iter_score = score_entries.begin();

(iter_score != score_entries.end())

erase_entry =

;

(score_entry->IsSetId())

(score_entry->GetId().IsStr())

str_id = score_entry->GetId().GetStr();

erase_entry = (str_id ==

);

iter_score = score_entries.erase(iter_score);

score_entry->SetId().SetStr(

);

sa->

().push_back(score_entry);

& fname_gis)

seqdb =

(fname_db,

seqdb_gis->GetGiList(vec_gis);

(vec_gis.begin(), vec_gis.end());

(vector<TGi>::iterator it = vec_gis.begin(); it != vec_gis.end(); it++)

list_gis.push_back(*it);

seqdb_gis->GetGiList(vec_gis);

(vec_gis.begin(), vec_gis.end());

(!subjid.

(*newSeqID)) {

(denseg.IsSetIds() && denseg.GetIds().size() == 2)

denseg.SetIds()[1] = newSeqID;

vector< CRef<CSeq_id> > seqids;

list< CRef<CSeq_id> > seqid_list = filteredDB->

(oid);

seqids.reserve(seqid_list.size());

(subjid.

() && (**id).IsGi()) {

seqids.push_back(*

);

(!subjid.

() && !(**id).IsGi()) {

seqids.push_back(*

);

(!seqids.empty()) {

newSubjectID = seqids[0];

vector <string> useThisSeqs;

(

= 0;

< seqids.size();

++) {

(seqids[0]->IsGi()) {

useThisSeqs.push_back(

+ textSeqID);

useThisSeqs.push_back(

+ textSeqID);

userObject->

().SetStr(

);

userObject->

(

, useThisSeqs);

sa_copy->

().push_back(userObject);

vector<int>& oid_vec)

success =

;

(previous_id.

() || !subjid->

(*previous_id))

(oid_vec[

] > 0) {

(!filtered_aln.

()) {

previous_id = subjid;

(success && !filtered_aln.

()) {

new_aln->

().push_back(filtered_aln);

tax_ids.

(leaf_ids.begin(), leaf_ids.end());

(user_tax_ids.

() > tax_ids.

()) {

(user_tax_ids.

(*itr) != user_tax_ids.

()) {

(tax_ids.

(*itr) != tax_ids.

()) {

list< CRef< CBlast_def_line > >& bdlSet = bdlRef->

();

vector <string> useThisSeqs;

list<string> use_this_seq;

(use_this_seq.size() > 0) {

(sa_copy.

()) {

useThisSeqs.push_back(

+ textSeqID);

useThisSeqs.push_back(

+ textSeqID);

userObject->

().SetStr(

);

userObject->

(

, useThisSeqs);

sa_copy->

().push_back(userObject);

success =

;

(previous_id.

() || !subjid->

(*previous_id))

(!filtered_aln.

()) {

previous_id = subjid;

(success && !filtered_aln.

()) {

new_aln->

().push_back(filtered_aln);

list<string> use_this_seq;

modifyAlignment =

;

(use_this_seq.size() > 0) {

list< CRef< CBlast_def_line > >& bdlSet = bdlRef->

();

(accInfo != accType) {

use_this_seq.push_back(textSeqID);

modifyAlignment =

;

(!modifyAlignment) {

(modifyAlignment && use_this_seq.size() > 0) {

vector <string> useThisSeqs;

(list<string>, iter_seq, use_this_seq){

(seqID->

()) {

useThisSeqs.push_back(

+ *iter_seq);

useThisSeqs.push_back(

+ *iter_seq);

userObject->

().SetStr(

);

userObject->

(

, useThisSeqs);

sa_copy->

().push_back(userObject);

vector <CSeq_id::EAccessionInfo> accTypes)

success =

;

(previous_id.

() || !subjid->

(*previous_id))

(

= 0;

< accTypes.size();

++) {

(!currAlign.

()) {

currAlign = filtered_aln;

(!filtered_aln.

()) {

previous_id = subjid;

(success && !filtered_aln.

()) {

new_aln->

().push_back(filtered_aln);

Defines the alignment filtering class.

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

static bool RemoveSeqsOfAccessionTypeFromSeqInUse(list< string > &use_this_seq, objects::CSeq_id::EAccessionInfo accesionType)

function to remove sequences of accesionType from use_this_seq list

static bool GetTextSeqID(const list< CRef< objects::CSeq_id > > &ids, string *textSeqID=NULL)

static void GetUseThisSequence(const objects::CSeq_align &aln, list< TGi > &use_this_gi)

Extract use_this_gi info from blast alingment.

static bool MatchSeqInUseThisSeqList(list< string > &use_this_seq, string textSeqIDToMatch)

void x_RemoveExtraGis(CRef< objects::CSeq_align > sa)

void WriteSeqalignSet(const string &fname, const objects::CSeq_align_set &aln)

Write a seqalign to a file.

void FilterSeqalignsExt(const string &fname_in_seqaligns, const string &fname_out_seqaligns, CRef< CSeqDB > db)

Filter Seqaligns - extended file-based version.

CRef< CSeqDB > PrepareSeqDB(const string &fname_db, bool is_prot, const string &fname_gis_to_filter)

Load a SeqDB database with the given gi-list.

void ReadGiList(const string &fname, list< TGi > &list_gis, bool sorted=false)

Read a gi list from a file and, optionally, sort it.

void FilterByGiListFromFile(const objects::CSeq_align_set &full_aln, const string &fname_gis_to_filter, objects::CSeq_align_set &filtered_aln)

Filter Seqaligns using a gi-list stored in file.

EResultsFormat

EResultsFormat - output options for filtered seqaligns.

CRef< CSeq_align_set > FilterByAccessionType(const CSeq_align_set &seqalign, CRef< CScope > &scope, vector< CSeq_id::EAccessionInfo > accTypes)

virtual ~CSeqAlignFilter()

Destructor.

bool x_AddUseGiEntryInSeqalign(CRef< objects::CSeq_align > sa, TGi new_gi)

void x_ReadExtraGis(CConstRef< objects::CSeq_align > sa, vector< TGi > &vec_extra_gis)

Read the "use_this_gi" entries from a seqalign object.

void FilterBySeqDB(const objects::CSeq_align_set &full_aln, CRef< CSeqDB > db, objects::CSeq_align_set &filtered_aln)

Filter Seqaligns using a SeqDB object.

void FilterByGiList(const objects::CSeq_align_set &full_aln, const list< TGi > &list_gis, objects::CSeq_align_set &filtered_aln)

Filter Seqaligns using a list of integers as the gi-list.

void ReadGiVector(const string &fname, vector< TGi > &vec_gis, bool sorted=false)

Read a gi vector from a file and, optionally, sort it.

void x_WriteExtraGis(CRef< objects::CSeq_align > sa, const vector< TGi > &vec_extra_gis)

void ReadSeqalignSet(const string &fname, objects::CSeq_align_set &aln)

Read a seqalign set from file.

void x_CreateOusputSeqaligns(CConstRef< objects::CSeq_align > in_aln, TGi in_gi, objects::CSeq_align_set &out_aln, const vector< TGi > &out_gi_vec)

Create one or more seqalign objects for output, based on the given input seqalign and the list of gi'...

CRef< CSeq_align_set > FilterByTaxonomy(const CSeq_align_set &seqalign, CRef< CSeqDB > &seqdb, const set< int > &taxids)

void x_GenerateNewGis(TGi main_old_gi, const vector< TGi > &vec_old_extra_gis, const vector< TGi > &vec_out_gis, TGi &main_new_gi, vector< TGi > &vec_new_extra_gis)

Generate the list of gi's based on the old list and the newly available gi's.

CRef< objects::CSeq_align > x_UpdateGiInSeqalign(CConstRef< objects::CSeq_align > sa, unsigned int n_row, TGi old_gi, TGi new_gi, bool &success)

Change the gi of one of the sequences referenced in the seqalign object.

void FilterSeqaligns(const string &fname_in_seqaligns, const string &fname_out_seqaligns, const string &fname_gis_to_filter)

Filter Seqaligns - file-based version.

list< CRef< CSeq_id > > GetSeqIDs(int oid) const

Gets a list of sequence identifiers.

const CSeqDBGiList * GetGiList() const

Get GI list attached to this database.

bool SeqidToOid(const CSeq_id &seqid, int &oid) const

Translate a Seq-id to any matching OID.

CRef< CBlast_def_line_set > GetHdr(int oid) const

Get the ASN.1 header for the sequence.

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

bool GiToOid(TGi gi, int &oid) const

Translate a GI to an OID.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

#define GI_FROM(T, value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define TAX_ID_FROM(T, value)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

@ eSerial_AsnText

ASN.1 text.

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

EAccessionInfo

For IdentifyAccession (below)

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static int WorstRank(const CRef< CSeq_id > &id)

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

bool IsSetLinks(void) const

Check if a value has been assigned to Links data member.

TTaxid GetTaxid(void) const

Get the Taxid member data.

bool IsSetTaxid(void) const

Check if a value has been assigned to Taxid data member.

const TLinks & GetLinks(void) const

Get the Links member data.

const Tdata & Get(void) const

Get the member data.

void SetType(TType &value)

Assign a value to Type data member.

Tdata & Set(void)

Assign a value to data member.

TScore & SetScore(void)

Assign a value to Score data member.

vector< CRef< CScore > > TScore

void ResetExt(void)

Reset Ext data member.

list< CRef< CStd_seg > > TStd

void SetSegs(TSegs &value)

Assign a value to Segs data member.

bool IsDendiag(void) const

Check if variant Dendiag is selected.

TExt & SetExt(void)

Assign a value to Ext data member.

bool IsStd(void) const

Check if variant Std is selected.

list< CRef< CSeq_align > > Tdata

const TScore & GetScore(void) const

Get the Score member data.

list< CRef< CDense_diag > > TDendiag

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

TGi GetGi(void) const

Get the variant data.

TGi & SetGi(void)

Select the variant.

bool IsGi(void) const

Check if variant Gi is selected.

@ e_Gi

GenInfo Integrated Database.

list< CRef< CSeq_id > > TId

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

static CRef< CSeq_align > s_ModifySeqAlnWithFilteredSeqIDs(CRef< CBlast_def_line_set > &bdlRef, const set< TTaxId > &taxids, CRef< CSeq_align > &in_align)

static CRef< CSeq_align > s_UpdateSubjectInSeqalign(CRef< CSeq_align > &in_align, CRef< CSeq_id > &newSeqID)

static void s_GetFilteredRedundantGis(CRef< CSeqDB > db, int oid, vector< TGi > &gis)

static bool s_IncludeDeflineTaxid(const CBlast_def_line &def, const set< TTaxId > &user_tax_ids)

CRef< CSeq_align > s_UpdateSeqAlnWithFilteredSeqIDs(CRef< CSeqDB > filteredDB, int oid, CRef< CSeq_align > &in_align)

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