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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sequence__search__tool_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence/sequence_search_tool.cpp Source File

.

.push_back(pair<string,string>(

,

.

.push_back(pair<string,string>(

,

name(

);

sl_ctx !=

;

;

;

& pattern,

&

)

m_PatternType(pt_type),

m_PatternFile(

)

wxBoxSizer * vSz =

wxBoxSizer(wxVERTICAL);

wxFlexGridSizer * sz =

wxFlexGridSizer(1, 4, 0, 0);

sz->AddGrowableCol(3);

->Add(sz, 0, wxGROW|wxALL, 0);

sz->Add(

wxStaticText( parent, wxID_STATIC,

(

),

wxDefaultPosition, wxDefaultSize, 0 ),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxDefaultPosition, wxDefaultSize,

0, (

wxString*)

);

sz->Add(

,1, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

sz->Add(

wxStaticText( parent, wxID_STATIC,

(

),

wxDefaultPosition, wxDefaultSize, 0 ),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxDefaultPosition, wxDefaultSize,

0, (

wxString*)

);

sz->Add(

,1, wxGROW|wxALIGN_CENTER_VERTICAL|wxALL, 5);

(

),

wxDefaultPosition, wxDefaultSize, 0 ),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

->Add(

wxStaticText( parent, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 ),

0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxDefaultPosition, wxDefaultSize,

0, (

wxString*)

);

bPattern = (

->GetSelection()==3);

(search_loc.

()) {

vector<CRef<CSeq_loc> > locs;

locs.back()->SetInt(*ref);

locs.push_back(search_loc);

->Assign(*(search_loc->

()));

locs.back()->SetWhole(*

);

sc_locs.push_back(sl);

searchString =

;

( (dir =

.

(

,

)).empty() ) {

.

(

,

,

,

dir =

.

(

,

);

(list<string>, iter, paths) {

(*iter ==

|| *iter ==

) {

( dir_name.empty() ) {

wxFileName fname(dir_name, wxEmptyString);

( !fname.DirExists(dir_name) ) {

cont = dir.GetFirst(&filename,

(

), wxDIR_FILES);

fname.SetFullName(filename);

wxString full_path = fname.GetFullPath();

list<string> pat_ids;

.EnumerateSections(&pat_ids);

(list<string>, pat_id, pat_ids) {

(*pat_id ==

) {

fName =

.Get(

,

);

(!fName.empty()) {

pattern =

.Get(*pat_id,

);

desc =

.Get(*pat_id,

);

(!fName.empty()) {

cont = dir.GetNext(&filename);

m_PatternType(

.GetPatternType())

sep(

);

it->m_Scope.GetPointer());

( ! s_locs.empty()) {

s_locs.resize(s_locs.size() - sep.size());

=

+ s_pat +

+ s_locs;

searchForward =

, searchReverse =

;

(expr.find(

) == 0 && expr.size() > 7) {

= expr.substr(7);

(

==

)

searchReverse =

;

(

==

)

searchForward =

;

(!searchForward && !searchReverse)

searchForward = searchReverse =

;

(seq_loc.

())

range.

() + seq_offset,

range.

() + seq_offset));

range.

() + seq_offset,

range.

() + seq_offset));

((

) coll.

() < max_coll_size) {

coll.

(make_pair(from, to));

start_pos = 0, num = 0;

(

= 0; i < num && max_coll_size > 0 && !

(); ++

) {

p0 = (

)(

.size() - p[1]);

p1 = (

)(

.size() - p[0]);

coll.

(make_pair(from, to));

((

) coll.

() >= max_coll_size) {

kMaxLen = 40;

*s = s1 +

+ s2;

& sequence,

& loc_name,

& strand,

& ctx_name)

kUpdateIncrement = 250;

(

>= kUpdateIncrement) {

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CObjectList * GetObjectList()

static CNcbiApplication * Instance(void)

Singleton method.

CObjectList Data structure representing a list of CObjects with associated Scopes and other optional ...

int AddRow(CObject *obj, objects::CScope *scope)

void AddObjectLabel(const string &name, CLabel::ELabelType type)

void SetString(int col, int row, const string &val)

void SetInteger(int col, int row, int val)

void Append(const CObjectList &list)

adds rows from the given list, the lists must have identical sets of columns

int AddColumn(EColumnType type, const string &name, int col=-1)

class CRegistryReadView provides a nested hierarchical view at a particular key.

string GetString(const string &key, const string &default_val=kEmptyStr) const

void Set(const string &key, int val)

access a named key at this level, with no recursion

virtual void UpdateContexts()

updates m_ContextCombo

void UpdateContextCombo(wxChoice *combo)

CRef< CDMSearchResult > m_TempResult

holds temporary results, guarded by Mutex

string m_Descr

human-readable description of the Job

int m_ResultsCount

total number of results

IDMSearchTool::TFilters m_Filters

holds the final results

CMutex m_Mutex

synchronizes access to the Job members

CRef< CAppJobError > m_Error

CObjectList m_AccList

accumulates found objects before they are transferred to m_ResultList

TScopedLocs & GetScopedLocs()

vector< SScopedLoc > TScopedLocs

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

static wxString ResolvePath(const wxString &path, const wxString &rel_name)

Utility function to hide the platform specifics of locating our standard directories and files.

IDMSearchQuery - abstract data mining query.

IDataMiningContext IDataMiningContext represents an abstract context for a Search.

virtual string GetDMContextName()=0

returns Name of the context to be used in UI

virtual CRef< objects::CScope > GetSearchScope()=0

virtual CRef< objects::CSeq_loc > GetSearchLoc()=0

iterator_bool insert(const value_type &val)

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

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.

virtual IAppJob::EJobState x_DoSearch()

performs searching, assuming that params are correct; Implement in derived classes

CRef< CSequenceSearchTool > m_Tool

void x_GetSequence(objects::CSeqVector &vec, const CRange< TSeqPos > &range, string *s)

virtual CObjectListTableModel * x_GetNewOLTModel() const

factory method creating new column handler for CObjectListWidget

virtual IDMSearchTool * x_GetTool()

virtual CIRef< IDMSearchForm > CreateSearchForm()

factory method for creating a form representing the tool

virtual IDMSearchTool::TUIToolFlags GetFlags(void)

special flags

wxChoice * m_PatternCombo

void x_UpdateFileList(void)

CSequenceSearchQuery::TScopedLocs TScopedLocs

CSequenceSearchQuery(TScopedLocs &locs, const string &pattern, TPatternType pt_type, const string &file)

CSequenceSearchQuery.

wxFlexGridSizer * m_pSearchSizer

CRegexp * m_Pattern

search patteern for "Exact Match" and "Wildcard" modes

virtual void x_LoadSettings(const CRegistryReadView &view)

virtual string GetName() const

returns unique name of the method that is used in UI to identify it

CSequenceSearchJob(CSequenceSearchQuery &query)

CSequenceSearchJob.

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual string ToString() const

Prepare a string representation of a query (for logging and debugging)

virtual bool IsCompatible(IDataMiningContext *context)

retuns true if the tool is compatible with the provided Search Context

CRef< CSequenceSearchQuery > m_Query

virtual void UpdateContexts()

updates m_ContextCombo

void x_AddToResults(CObject &obj, objects::CScope &scope, const string &sequence, const string &loc_name, const string &strand, const string &ctx_name)

virtual wxSizer * GetWidget(wxWindow *parent)

return a widget associated with the form; the form controls the lifetime of the widget (do not delete...

vector< ISeqLocSearchContext * > m_SeqLocContexts

virtual CIRef< IDMSearchQuery > ConstructQuery()

virtual IUITool * Clone() const

void x_GetMatches(const string &data, int start, TRangeCollection &coll, bool reverse)

"offset" argument defines the sequence position corresponding to the fisrt character in "data"

TPatternType m_PatternType

CSequenceSearchForm(CSequenceSearchTool &tool)

list< TDescPattern > TDescPatList

wxFlexGridSizer * m_pPatternSizer

virtual void x_SaveSettings(CRegistryWriteView view) const

pair< string, string > TDescPattern

TPatternType m_PatternType

IAppJob::EJobState x_SearchSequence(TScopedLocs &scoped_locs)

virtual void x_SetupColumns(CObjectList &obj_list)

add custom columns if needed

virtual bool x_ValidateParams()

returns true if Job params are correct, implement in derived classes

string m_PatternFile

regular expression to apply

TPatternType GetPatternType()

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual CRef< CSearchJobBase > x_CreateJob(IDMSearchQuery &query)

implementing CSearchToolBase pure virtual function

CSequenceSearchQuery::TScopedLocs TScopedLocs

TPatternType m_PatternType

CSequenceSearchTool()

CSequenceSearchTool.

virtual string GetDescription() const

returns a detailed description of the method that is used in UI

static TFileList m_FileList

CSequenceSearchForm.

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

TRange GetTotalRange(void) const

const CSeq_id * GetId(void) const

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

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,...

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

position_type GetLength(void) const

const TOffset * GetResults(size_t idx) const

Get location of pattern/subpattern for the last GetMatch().

CTempString GetMatch(CTempString str, size_t offset=0, size_t idx=0, TMatch flags=fMatch_default, bool noreturn=false)

Get matching pattern and subpatterns.

int NumFound() const

Get number of patterns + subpatterns.

static string WildcardToRegexp(CTempString mask)

Convert wildcard mask to regular expression.

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

bool Set(const string &section, const string &name, const string &value, TFlags flags=0, const string &comment=kEmptyStr)

Set the configuration parameter value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ eForwardSearch

Search in a forward direction.

@ fWithCommas

Use commas as thousands separator.

@ eNocase

Case insensitive compare.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_interval > > Tdata

const Tdata & Get(void) const

Get the member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

unsigned int

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

const GenericPointer< typename T::ValueType > T2 value

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

#define row(bind, expected)

CRef< objects::CScope > m_Scope

CRef< objects::CSeq_loc > m_Loc

static CS_CONTEXT * context

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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