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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuAlignmentCollection_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuAlignmentCollection.cpp Source File

12

: m_seqAligns(), m_rowSources(), m_firstCd(0), m_seqTable()

14

AddAlignment(cd,alignUse, uniqueSeqId, scoped);

20

: m_seqAligns(), m_rowSources(), m_firstCd(0), m_seqTable()

46

vector<RowSource> srcs;

48 for

(

unsigned int

j = 0; j < srcs.size(); j++)

69

list< CRef< CUpdate_align > >& pending = cd->

SetPending

();

70

list< CRef< CUpdate_align > >::iterator lit = pending.begin();

73 for

(; lit != pending.end(); ++lit)

75 if

((*lit)->IsSetSeqannot())

114

list< CRef< CSeq_align > >& alignList = cd->

GetSeqAligns

();

115

list< CRef< CSeq_align > >::iterator lit = alignList.begin();

140 for

(; lit != alignList.end(); ++lit)

213 if

(SeqID->

IsGi

() || SeqID->

IsPdb

()) {

216 result

"<Non-gi/pdb Sequence Types Unsupported>"

;

229

gi = SeqID->

GetGi

();

231

}

else if

(SeqID->

IsPdb

() && !ignorePDBs) {

242 bool

getSlave =

true

;

266 for

(

unsigned int i

= 0;

< rows.size();

++)

326

vector<RowSource> src;

330 else if

(src.size() ==1)

332 if

((src[0].cd ==

m_firstCd

) && (!includeSelf))

335 return

(src.rbegin())->cd;

340

vector<RowSource> src;

344

vector<RowSource>::reverse_iterator rit = src.rbegin();

345 for

(; rit != src.rend(); rit++)

359

vector<RowSource> src;

377 for

(;

< num;

++)

383

childless.push_back(

);

403

rowVec.push_back(*sit);

406 for

(; cit != cdRowsMap.

end

(); ++cit)

411

vector<int>& cdRows = cit->second;

419

vector<RowSource> src;

421 for

(

unsigned int i

= 0;

< src.size();

++)

434 for

(

int i

= 0;

< num;

++)

437

colRows.push_back(

);

483

list< CRef< CSeqdesc > >::const_iterator j;

486 if

(seqEntry->

IsSeq

()) {

492 if

((*j)->IsTitle()) {

493 return

((*j)->GetTitle());

497 if

((*j)->GetPdb().GetCompound().size() > 0) {

498 return

((*j)->GetPdb().GetCompound().front());

520 int result

= -1, index = -1;

521

vector<int>::iterator vit, vend = rows.end(), vrow = vend;

526 for

(vit = rows.begin(),

= 0; vit != vend; ++vit, ++

) {

527 if

(rowToMatch == *vit) {

532 if

(!inclusive && vrow != vend) {

535 result

= (index != -1) ? (

int

) rows.size() : -1;

544 for

(

int i

= 0;

< num;

++)

559 for

(

unsigned int i

= 0;

< rows.size();

++)

575

CDense_diag::TStarts::const_iterator pos=DenDiag->GetStarts().begin();

589

CDense_diag::TStarts::const_iterator pos=DenDiag->GetStarts().begin();

593 return

(*pos)+(

len

) - 1;

619 for

(

int i

= 0;

< numRow; ++

)

675 int

Start, Start2, Stop=-1, Stop2=-1,

Len

;

679 for

(iter=pDenDiagSet->begin(); iter!=pDenDiagSet->end(); iter++) {

680 Len

= (*iter)->GetLen();

681

Start = (*iter)->GetStarts().front();

682

Start2 = (*iter)->GetStarts().back();

684 if

((Stop >= 0) && ((Start <= Stop) || (Start2 <= Stop2))) {

687

Stop = Start +

Len

- 1;

688

Stop2 = Start2 +

Len

- 1;

708 if

(ppAlignedResidues ==

NULL

)

710

ppAlignedResidues =

new char

*[numRows];

712 else if

(!forceRecompute)

718 for

(

int i

= 0;

< numRows;

++)

764

vector<CCdCore*> cds;

766 for

(

unsigned int i

= 0;

< cds.size();

++)

778

vector<CDFamilyIterator> cdits;

780 for

(

unsigned int i

= 0;

< cdits.size();

++)

783 tmp

.setAlignment(family, cdits[

]);

785 if

(start == family.

begin

())

825 if

(matches.size() <= 0)

859 LOG_POST

(

"The alignment of the master in cd "

<<malign.

getFirstCD

()->

GetAccession

()<<

" does not match with that of its parent and its content is not used.\n"

);

867 if

(!deltaStatus.second)

869 delete

deltaStatus.first;

870 LOG_POST

(

"The master of cd "

<<malign.

getFirstCD

()->

GetAccession

()<<

" is not properly aligned to its parent and its content is not used."

);

874 for

(

int i

= 1;

< num;

++)

892

pair<BlockModel*, bool> resultStatus = malign.

m_blockTable

[

] + *(deltaStatus.first);

893 if

(resultStatus.second)

895 bool

IsLegit =

true

;

897 bool

shouldAdd =

true

;

906

IsLegit = (resultStatus.first)->isValid(seqLen, blockIndex);

907 if

(IsLegit && !seqAlign.

Empty

()) {

918

blockIndex+1<<

" in order to fit it into its parental block. This row is not used."

);

922 if

(IsLegit && (parentRow >= 0)) {

929

". It is thus not used to make the tree."

);

938

vector<int> seqIdMatches;

942 for

(

unsigned int i

= 0;

< seqIdMatches.size();

++)

945

pRow = seqIdMatches[

];

980

found =

bmp

->contain(bar);

992

vector<RowSource> sources;

994 for

(

unsigned int i

= 0;

< sources.size();

++)

1066 for

(; sit != normalRows.

end

(); ++sit)

1090 for

(; sit != normalRows.

end

(); ++sit)

1093 if

(slave != master)

void addRowSources(const vector< int > &rows, CCdCore *cd, bool scoped=true)

bool GetGI(int row, TGi &gi, bool ignorePDBs=true) const

bool GetSeqEntryForRow(int row, CRef< CSeq_entry > &seqEntry) const

bool Get_GI_or_PDB_String_FromAlignment(int row, std::string &result) const

bool GetBioseqForRow(int rowId, CRef< CBioseq > &bioseq)

bool wasMaster(int row) const

void getNormalRowsNotInChild(vector< int > &childless, bool excludeMaster=false) const

void GetAlignedResiduesForRow(int row, char *&)

void mapRows(const AlignmentCollection &ac, const set< int > &rows, set< int > &convertedRows) const

void addNormalAlignment(CCdCore *cd, bool uniqueSeqId=false, bool scoped=true)

bool GetSpeciesForRow(int row, string &species) const

int GetNumPendingRows() const

vector< CRef< CBioseq > > m_bioseqs

bool IsNonOverlapping(const CRef< CSeq_align > &align, int &blockIndex) const

RowSourceTable m_rowSources

CCdCore * GetLeafDescendentCD(int row, bool includeSelf=false) const

string GetSequenceForRow(int row)

void convertToCDRows(const vector< int > &colRows, CDRowsMap &cdRows) const

void GetAllSequences(vector< string > &sequences)

void removeRowSourcesForCD(CCdCore *cd)

int GetAlignmentLength(int row=0) const

void addPendingAlignment(CCdCore *cd, bool uniqueSeqId=false, bool scoped=true)

int GetRowsWithSameSeqID(int rowToMatch, vector< int > &rows, bool inclusive=true) const

int getCDs(vector< CCdCore * > &cds)

bool AreNonOverlapping() const

int getCDsOutofScope(vector< CCdCore * > &cds)

bool IsPdb(int row) const

void getAllRowsForCD(CCdCore *cd, vector< int > &colRows) const

const RowSource & GetRowSource(int row) const

CCdCore * GetScopedLeafCD(int row) const

int FindSeqInterval(const CSeq_interval &seqLoc) const

void GetAlignedResiduesForAll(char **&ppAlignedResidues, bool forceRecompute)

CRef< CSeq_align > getSeqAlign(int row) const

const RowSourceTable & GetRowSourceTable() const

CCdCore * getFirstCD() const

void AddSequence(CCdCore *cd)

bool isInstanceOf(MultipleAlignment *ma)

int GetRowsWithSeqID(const CRef< CSeq_id > &SeqID, vector< int > &rows) const

int GetLowerBound(int row) const

bool IsPending(int row) const

void AddAlignment(CCdCore *cd, CCdCore::AlignmentUsage alignUse=CCdCore::USE_PENDING_ALIGNMENT, bool uniqueSeqId=false, bool scoped=true)

int mapRow(const AlignmentCollection &ac, int row) const

bool isRowInScope(int row) const

bool isCDInScope(CCdCore *cd) const

int GetUpperBound(int row) const

CCdCore * GetSeniorMemberCD(int row, bool scopedOnly=true) const

string GetDefline(int row) const

vector< CRef< CSeq_align > > m_seqAligns

bool GetSeqIDForRow(int row, CRef< CSeq_id > &SeqID) const

virtual ~AlignmentCollection()

void convertFromCDRows(CCdCore *cd, const vector< int > &cdRows, set< int > &colRows) const

int getCDsInScope(vector< CCdCore * > &cds)

BlockModel * completeCastTo(const BlockModel &target) const

CRef< CSeq_id > getSeqId() const

bool contain(const BlockModel &rhs) const

CRef< CSeq_align > toSeqAlign(const BlockModel &master) const

bool blockMatch(const BlockModel &bm) const

bool GetBioseqForIndex(int seqIndex, CRef< CBioseq > &bioseq)

bool AddSequence(CRef< CSeq_entry > seqAntry)

bool AddPendingSeqAlign(CRef< CSeq_align > seqAlign)

TGi GetGIFromSequenceList(int SeqIndex) const

bool AddSeqAlign(CRef< CSeq_align > seqAlign)

int GetSeqIndex(const CRef< CSeq_id > &SeqID) const

const list< CRef< CSeq_align > > & GetSeqAligns() const

string GetSpeciesForIndex(int SeqIndex)

string GetAccession(int &Version) const

int getAllCD(vector< CCdCore * > &cds) const

void getChildren(vector< CCdCore * > &cds, CCdCore *parentCD) const

bool isBlockAligned() const

void copyRowSource(int currentRow, const AlignmentCollection &malign, int rowInAc)

const cd_utils::BlockModel & getBlockModel(int row) const

int appendAlignment(MultipleAlignment &malign, bool includeUnScoped=true)

bool setAlignment(const CDFamily &family)

bool transferToCD(CCdCore *cd=0)

bool findParentalEquivalent(const cd_utils::BlockModel &bar, int &pRow, bool inputAsChild=true) const

bool locateChildRow(const cd_utils::BlockModel &childRow, int &pRow) const

int transferOneRow(CCdCore *cd, int row)

bool extractAlignedSubset(const AlignmentCollection &ac, const set< int > &normalRows, int master)

bool findParentalCastible(const cd_utils::BlockModel &bar, int &pRow) const

vector< cd_utils::BlockModel > m_blockTable

int getCDs(vector< CCdCore * > &cds)

void removeEntriesForCD(vector< int > &colRows, CCdCore *cd)

int getCDsOutofScope(vector< CCdCore * > &cds)

void convertToCDRows(const vector< int > &colRows, CDRowsMap &cdRows) const

int findEntries(int row, vector< RowSource > &src, bool scopedOnly=false) const

int convertFromCDRow(CCdCore *cd, int cdRows) const

bool isCDInScope(CCdCore *cd) const

void addEntry(int row, CCdCore *cd, int rowInCD, bool normal=true, bool scoped=true)

void convertFromCDRows(CCdCore *cd, const vector< int > &cdRows, set< int > &colRows) const

bool isEntryInScope(const RowSource &rs) const

int getCDsInScope(vector< CCdCore * > &cds)

bool isRowInCD(int row, CCdCore *cd) const

const RowSource & findEntry(int row) const

bool findSequence(CRef< CSeq_id > seqId, CRef< CBioseq > &bioseq) const

void addSequences(vector< CRef< CBioseq > > &bioseqVec, bool grouped=false)

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator begin() const

const_iterator end() const

pre_order_iterator begin() const

TDendiag::const_iterator TDendiag_cit

CSeq_align::C_Segs::TDendiag TDendiag

void SetAlignedResiduesOnSequence(const CRef< CSeq_align > &align, const string &sequenceString, char *&pAlignedRes, bool isMaster=false)

bool GetFirstOrLastDenDiag(const CRef< CSeq_align > &seqAlign, bool firstOrLast, CRef< CDense_diag > &dd)

bool GetSeqID(const CRef< CSeq_align > &seqAlign, CRef< CSeq_id > &SeqID, bool getSlave=true)

bool GetDDSetFromSeqAlign(const CSeq_align &align, const TDendiag *&dd)

int GetNumAlignedResidues(const CRef< CSeq_align > &align)

bool SeqIdsMatch(const CRef< CSeq_id > &id1, const CRef< CSeq_id > &id2)

bool GetNcbieaaString(const CBioseq &bioseq, string &str)

int GetMMDBId(const CBioseq &bioseq)

string GetSeqIDStr(const CRef< CSeq_id > &SeqID)

bool Empty(const CNcbiOstrstream &src)

thread_local unique_ptr< FtaMsgPost > bmp

unsigned int TSeqPos

Type for sequence locations and lengths.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty â pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

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

#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.

bool IsSetPending(void) const

contains alignments from update or "lower panel" Check if a value has been assigned to Pending data m...

TPending & SetPending(void)

Assign a value to Pending data member.

void SetSequences(TSequences &value)

Assign a value to Sequences data member.

const TId & GetId(void) const

Get the Id member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsPdb(void) const

Check if variant Pdb is selected.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

TTo GetTo(void) const

Get the To member data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsAlign(void) const

Check if variant Align is selected.

void SetData(TData &value)

Assign a value to Data data member.

const Tdata & Get(void) const

Get the member data.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TData & GetData(void) const

Get the Data member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

unsigned int

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

const CConstRef< CSeq_id > GetAccession(const CSeq_id_Handle &id_handle)

#define row(bind, expected)

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