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NCBI C++ ToolKit: src/gui/widgets/aln_multiple/alnmulti_model.cpp Source File

m_StyleCatalog(

),

m_EnableScoring(

),

m_isDataReadSync(

)

min_scale = 1 / (max_sym_w * 0.75);

min_scale =

(min_scale, 0.01);

b_invert_others)

vector<TNumrow>::iterator iter = std::find(rows.begin(), rows.end(),

(consensus_idx));

(!b_invert_others) {

(iter != rows.end())

(iter == rows.end())

rows.push_back(consensus_idx);

n_rows = rows.size();

(n_rows || b_invert_others) {

vector<TNumrow> v_items;

(b_invert_others) {

vector<bool> new_visible(

(), ! b_visible);

(vector<TNumrow>, it, rows) {

new_visible[*it] = b_visible;

vector<SRowRecord*> vis_recs;

vis_recs.reserve(b_visible ? rows.size()

: new_visible.size() - rows.size());

(

!= master_row && new_visible[

]) {

vis_recs.push_back(&rec);

v_items.reserve(vis_recs.size());

(vector<SRowRecord*>, it, vis_recs) {

v_items.reserve(n_rows);

vector<TLine> v_indices;

v_indices.reserve(n_rows);

(vector<TNumrow>, it, rows) {

(b_old_vis != b_visible &&

!= master_row) {

v_indices.push_back(line);

v_items.push_back(

);

(Y < rcL.

() || Y > rcL.

())

->GetHeightPixels();

vector<TNumrow> nothing;

(

= 0;

<

; ++

) {

->GetColumnText(

, s);

.emplace_back(rec, s);

(

= 0;

<

; ++

) {

(

= 0;

<

; ++

) {

(

= 0;

<

; ++

) {

(

= 0;

<

; ++

) {

.emplace_back(rec, pos);

(

= 0;

<

; ++

) {

(pos >= 0 && pos < n_vis) {

= 0, line = pos;

( ;

< (

) rows.size() && line < n_vis;

++ ) {

new_vis[line] = p_rec;

(ins_i < pos) {

(ins_i < n_vis) {

pane_rows_n = aln_rows_n;

vector<int> vVisibleRowPos;

vVisibleRows.resize(pane_rows_n);

vVisibleRowPos.resize(pane_rows_n);

RowToRec.resize(aln_rows_n);

(

== consensus_idx)

(

== MasterRow) {

vVisibleRows[i_line] = &RowToRec[

];

}

(std::exception& e) {

line = p_rec ? p_rec->

: -1;

->SetDisplayStyle(style);

->UpdateOnStyleChanged();

(

total_H = 0,

= 0;

<

;

++ ) {

(new_master_row != -1) {

pNewMaster = rec.

;

vector<int> vDelItems;

vDelItems.push_back(rec.

);

->UpdateOnAnchorChanged();

(method->GetName() == name) {

entries_n = v_entries.size();

(

= 0;

< entries_n;

++ ) {

(

= 0;

<

;

++ ) {

static const int kColorGradNumber

virtual void x_CompleteInsertion()

performs update after all items have been inserted

virtual void EnableBackgroundProcessing(bool en)

virtual bool CanChangeMasterRow() const

changes Master (Anchor) and performs necessary updates

virtual void CreateConsensus(void)

Creates consenus row if it is not already created.

virtual void OnScoringFinished()

SRowRecord & x_GetRecordByRow(TNumrow row)

virtual int GetLineByRowNum(TNumrow row) const

virtual void SetDefaultMethod(const string &method_name)

virtual void x_UpdateMinScale()

CScoreCache::IListener * m_Listener

const CRowStyleCatalog * m_StyleCatalog

virtual void UpdateSortOrder(void)

enables auto sorting of rows, sorts rows using x_SortRows() and performs necessary updates

virtual bool AddScoringMethod(IScoringMethod *method)

adds scoring method; model assumes ownership of the method, it will be deleted automatically

CAlnMultiModel()

number of gradient colors in alignment

virtual CWidgetDisplayStyle * GetDisplayStyle()

virtual TNumrow GetLinesCount() const

NUmber of visible lines.

TRowRecVector m_vVisibleRows

line number SRowRecord* for visible rows

virtual string GetDefaultMethod(void)

bool m_EnableScoring

scoring support

virtual TSortState GetColumnSortState(TColumnType type)

returns sorting state for the specified column

virtual int GetLineByModelY(int Y) const

CIRef< IAlignRow > m_DataConsensusRow

IAligRow corresponding to consensus in the data.

virtual const IScoringMethod * GetCurrentMethod() const

virtual TIndex x_GetItemIndex(const TItem &item)

virtual void x_ClearItems(void)

virtual void x_CreateDisplayStyle()

virtual int GetLineHeight(TLine line) const

@ kMasterRowIndex

dummy master row index used in selection logic

virtual void x_UpdateOnCoordsChanged()

virtual void UpdateOnScoringChanged(const TSeqRange &range=TSeqRange::GetEmpty())

virtual IAlignRow * GetConsensusRow()

virtual void x_DoUpdateRowPositions(void)

recalculates vertical coordinates of row objects

CRef< CScoreCache > m_ScoreCache

virtual void x_InsertItem(TIndex index, const TItemEntry &entry)

inserts item, but does not updates all data structures

virtual void OnScoringProgress(float progress, const string &msg)

virtual void CreateRows(void)

Creates IAlignRow objects for each row in the data source.

virtual void x_EraseMarkedItems(void)

deletes all marked items in a single pass, performs neccessary updates

const size_t GetNumRows() const

Get number of rows registered in model.

virtual void EnableAutoSorting(bool b_en)

enables auto sorting but does not perform any updates

vector< SRowRecord > TRowToRecMap

virtual void SLM_InvertSingleItem(TIndex index)

virtual void SetRowOrder(const vector< TNumrow > &rows, int pos=0)

disables auto sorting, reorders rows in alignment so that rows from the given vector appear in the sp...

virtual int GetFocusedItemIndex() const

virtual TItem x_GetItem(TIndex index) const

virtual void SetStyleCatalog(const CRowStyleCatalog *catalog)

virtual void ClearRows(void)

Update handlers.

virtual bool IsRendererFocused()

virtual void UpdateOnRowHChanged(void)

updates model after row height changed

virtual void SetListener(CScoreCache::IListener *listener)

virtual IAlignRow * GetMasterRow()

list< CIRef< IScoringMethod > > TMethods

virtual bool SetMasterRow(TNumrow new_row)

virtual IAlignRow * GetRowByLine(TLine line)

all Y coordinates are OpenGL Viewport coordinates (not widget coords) "index" is a line index (not ro...

virtual bool IsItemSelected(int index) const

virtual bool x_SortRows(void)

This is a sorting callback automatically invoked by CAlnMultiModel when necessary.

virtual void SetShownElements(int shown_mask)

CRef< CConsensusRow > m_ConsensusRow

int GetRowState(TNumrow row) const

returns a combination of IAlignRow::EState flags

virtual void UpdateOnStyleChanged(void)

vector< int > m_vVisibleRowPos

bottom positions for visible rows[line]

virtual void x_UpdateOnVisibilityChanged(void)

CWidgetDisplayStyle * m_Style

virtual bool x_IsItemSelected(TIndex index) const

virtual void x_SetEntries(const TEntryVector &v_entries)

TMethods m_Methods

registered scoring methods

virtual IAlignRow * x_CreateRow(TNumrow row)

factory method for creating IAlignRow instances

TRowToRecMap m_RowToRec

map storing records for all rows

virtual void x_SelectItem(TIndex index, bool b_sel)

updates line numbers in SRowRecords

virtual int GetLinePosY(TLine line) const

IAlignRow * x_GetRowByLine(int Index)

virtual void UpdateOnDataChanged()

virtual ~CAlnMultiModel()

virtual void SLM_SelectAll(bool bSelect)

virtual void x_MarkItemForErase(TIndex index)

mark item for deletion

virtual bool x_UsingAutoSort() const

IAlignRow::TColumnType TColumnType

bool m_AutoSort

sorting support

void SetVisible(vector< TNumrow > rows, bool b_visible, bool b_invert_others=false)

makes specified rows visible/hidden, if b_invert_others == "true" then visibility of all rows not in ...

virtual const TMethods & GetMethods()

CIRef< IAlignRow > m_MasterRow

IAligRow corresponding to Anchor.

virtual void ResetCurrentMethod()

virtual void SetDataSource(IAlnMultiDataSource *p_ds)

virtual int GetShownElements()

returns mask of shown elements - header, ruler, master row, alignment, track matrix

virtual void x_DoUpdateRowsOrder(void)

performs sorting by invoking x_SortRows() and updates line numbers

virtual bool SortByColumn(TColumnType type, bool ascending)

sorts visible rows by specified column, return "false" if sorting is not supported (nothin happened)

vector< SRowRecord * > TRowRecVector

IAlnMultiDataSource * m_DataSource

virtual bool SetCurrentMethod(const string &name, const TSeqRange &range=TSeqRange::GetEmpty())

void x_DoUpdateRowLines(void)

virtual TIndex x_GetItemsCount() const

virtual void SLM_SelectSingleItem(TIndex index)

class CAlnVecRow - implementation of IAlignRow for CAlnVec-based alignments.

void SetConsensus(CConsensusRow *crow)

virtual void SetDisplayStyle(const CRowDisplayStyle *style)

virtual void SetScoreCache(CScoreCache *cache)

Class CConsensusRow - Simple interface to a row that represents the consensus for rendering purposes.

void SetHandle(const IAlignRowHandle *h)

vector< TPair > TPairVector

void Sort(TPairVector &data)

CRowDisplayStyle is a base class representing a display style for IAlignRow.

CRowStyleCatalog is a collection of CRowDisplayStyle-s assigned to rows in alignment.

const CRowDisplayStyle * GetStyleForRow(TNumrow row) const

virtual void OnScoringFinished()=0

virtual void OnScoringProgress(float progress, const string &msg)=0

const IScoringAlignment * GetAlignment() const

void SetScoringMethod(IScoringMethod *method)

void SetAlignment(const IScoringAlignment *aln)

void CalculateScores(const TSeqRange &range=TSeqRange::GetEmpty())

Recalculate scores using current method; resets scores if no method is selected.

IScoringMethod * GetScoringMethod()

void EnableBackgoundProcessing(bool en)

void SetListener(IListener *listener)

void SetGradNumber(int grad_n)

Sets the number of score gradations.

void InsertItems(const TItemVector &v_items, const TIndexVector &v_indices, bool b_update)

vector< TItem > TItemVector

void DeleteItems(const TIndexVector &vIndices, bool b_update)

bool InsertItem(TIndex index, const TItem &item, bool b_update)

vector< TItemEntry > TEntryVector

virtual void SLM_SelectAll(bool bSelect=true)

virtual bool SLM_IsItemSelected(TIndex index) const

virtual void SLM_FocusItem(TIndex index)

virtual void SLM_InvertSingleItem(TIndex index)

virtual TIndex SLM_GetFocusedItemIndex() const

virtual void SLM_SelectSingleItem(TIndex index)

void SetItems(const TItemVector &vItems, bool b_update, bool b_keep_selection=false)

pair< TItem, bool > TItemEntry

IAlignRowHandle provides an abstract way to access alignment row data.

Interface IAlignRow - abstracts row rendering in Multiple Alignment Widget.

virtual int GetRowNum() const =0

Returns index of row in IAlnMultiDataSource.

virtual void SetRowState(int mask, bool b_set)=0

Set/Clear Row State.

virtual int GetHeightPixels() const =0

Returns height of the row in pixels.

@ ePctIdentity

% identity to consensus or anchor

@ ePctCoverage

% coverage to anchor

@ eMismatches

% number of mismatches to anchor/consensus

Alignment explorer interface.

IAlnMultiDataSource - interface to a data source representing an abstract multiple alignment.

virtual IAlnExplorer::EAlignType GetAlignType() const =0

virtual const IAlignRowHandle * GetRowHandle(TNumrow row) const =0

virtual bool IsDataReadSync() const

virtual TSeqPos GetAlnStart(void) const =0

virtual int GetConsensusRow() const =0

returns index of the Consensus row or -1 if it doesn't exist

virtual bool CanChangeAnchor(void) const =0

virtual TNumrow GetNumRows(void) const =0

number of rows in alignment

virtual TSeqPos GetAlnStop(void) const =0

virtual bool SetAnchor(TNumrow anchor)=0

virtual bool IsSetAnchor(void) const =0

Anchoring methods.

virtual TNumrow GetAnchor(void) const =0

virtual void SetCreateConsensus(bool b)=0

virtual void CreateConsensus()=0

IAlnExplorer::TNumrow TNumrow

IScoringMethod represents an abstract algorithm for calculating alignment scores and assigning colors...

static const char * catalog

unsigned int TSeqPos

Type for sequence locations and lengths.

#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 NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void SetModelLimitsRect(const TModelRect &R)

TModelRect & GetModelLimitsRect(void)

void SetAdjustmentPolicy(int adjust_x, int adjust_y)

void EnableZoom(bool en_x, bool en_y)

virtual TModelUnit GetMetric(EMetric metric, const char *text=NULL, int len=-1) const

TModelRect & GetVisibleRect(void)

void SetMinScaleX(TModelUnit scale)

CGlRect< TModelUnit > TModelRect

void SetOriginType(EOriginType type_x, EOriginType type_y)

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

unsigned int

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

constexpr auto sort(_Init &&init)

Multi-threading – classes, functions, and features.

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

#define row(bind, expected)

SRowRecord is a record representing a single alignment row.

CIRef< IAlignRow > m_Row

row object ptr

static bool PRecLineLess(const SRowRecord *rec1, const SRowRecord *rec2)

TLine m_Line

visual line index

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