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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/compare__with__biosample_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/compare_with_biosample.cpp Source File

wxWindowID

,

wxString& caption,

wxPoint& pos,

wxSize&

,

style )

: m_TopSeqEntry(seh), m_CmdProcessor(cmdProcessor), m_all_records(all_records)

(parent,

, caption, pos,

, style);

num_processed;

vector<string> unprocessed_ids;

use_dev_server(

);

compare_structured_comments(

);

(

diff : diff_vec)

seq_id = diff->GetSequenceId();

field = diff->GetFieldName();

= diff->GetSrcVal();

sample = diff->GetPureSampleVal();

sample_id = diff->GetBioSample();

tie(set_source, set_sample) =

[{sample_id, field}][seq_id];

set_sample.

(sample);

[{sample_id, field}][seq_id] = make_pair(set_source, set_sample);

vector<CRef <CSeq_id> > id_list;

id_list.push_back(ic);

->GetLabel(&

);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxFrame::Create( parent,

, caption, pos,

, style );

wxVisualAttributes attr = wxPanel::GetClassDefaultAttributes();

(attr.colBg != wxNullColour) {

SetOwnBackgroundColour(attr.colBg);

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

=

wxScrolledWindow(itemDialog1,

, wxDefaultPosition, wxSize(840, 870), wxHSCROLL| wxVSCROLL);

wxBoxSizer* top_sizer =

wxBoxSizer(wxVERTICAL);

wxMessageBox(

(

),

(

), wxOK);

wxMessageBox(

(

),

(

), wxOK);

wxArrayString itemChoiceStrings, itemChoiceStringsWritable;

((*it)->IsSetHeader() && (*it)->GetHeader().IsSetTitle() )

title = (*it)->GetHeader().GetTitle();

itemChoiceStrings.Add(wxString(title));

itemChoiceStringsWritable.Add(wxString(title));

wxBoxSizer* itemBoxSizer16 =

wxBoxSizer(wxHORIZONTAL);

top_sizer->Add(itemBoxSizer16, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

itemBoxSizer16->Add(itemButton24, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemButton24->SetToolTip(

(

));

itemBoxSizer16->Add(itemButton17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemButton17->SetToolTip(

(

));

wxButton* itemButton18 =

wxButton(

,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer16->Add(itemButton18, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemButton18->SetToolTip(

(

));

itemBoxSizer16->Add(itemButton19, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemButton19->SetToolTip(

(

));

itemBoxSizer16->Add(itemButton25, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemButton25->SetToolTip(

(

));

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

top_sizer->Add(itemBoxSizer4, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer5 =

wxBoxSizer(wxHORIZONTAL);

top_sizer->Add(itemBoxSizer5, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer13 =

wxBoxSizer(wxHORIZONTAL);

top_sizer->Add(itemBoxSizer13, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

itemBoxSizer13->Add(itemButton14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer13->Add(itemButton20, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer13->Add(itemButton21, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer13->Add(

, 0, wxALIGN_CENTER_VERTICAL | wxALL, 5);

itemBoxSizer13->Add(itemButton23, 0, wxALIGN_CENTER_VERTICAL | wxALL, 5);

wxButton* itemButton15 =

wxButton(

, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(itemButton15, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

->SetTable(gridAdapter,

);

->AutoSizeColumns();

l_height =

->GetColLabelSize();

->SetColLabelSize( 2 * l_height );

((*it)->IsSetHeader() && (*it)->GetHeader().IsSetTitle() )

title = (*it)->GetHeader().GetTitle();

(glyph_col >= 0 && glyph_col+1 <

->GetNumberCols())

expand_col->

().SetTitle(

);

expand_col->

().SetField_name(

);

expand_col->

().SetString();

name_col->

().SetTitle(

);

name_col->

().SetField_name(

);

name_col->

().SetString();

source_col->

().SetTitle(

);

source_col->

().SetField_name(

);

source_col->

().SetString();

sample_col->

().SetTitle(

);

sample_col->

().SetField_name(

);

sample_col->

().SetString();

sample_id_col->

().SetTitle(

);

sample_id_col->

().SetField_name(

);

sample_id_col->

().SetString();

->SetColumns().push_back(expand_col);

->SetColumns().push_back(name_col);

->SetColumns().push_back(source_col);

->SetColumns().push_back(sample_col);

->SetColumns().push_back(sample_id_col);

field, sample_id;

tie(sample_id, field) = diff.first;

(

&

: diff.second)

seq_id =

.first;

tie(set_source, set_sample) =

.second;

sample =

(set_sample,

);

->Assign(*

[seq_id]);

->SetData().SetId().push_back(

);

expand_col->

().SetString().push_back(

);

name_col->

().SetString().push_back(field);

sample_col->

().SetString().push_back(sample);

sample_id_col->

().SetString().push_back(sample_id);

num_rows =

->GetNumberRows();

(

= 0;

< num_rows; ++

)

values[bsh][field] =

;

new_desc->

(*src_desc_ci);

field = fi->first;

= fi->second;

biosource.

().ResetTaxname();

biosource.

().SetOrgname().ResetName();

biosource.

().SetTaxId(taxid);

(

&v : vals)

->SetSubtype(subtype);

biosource.

().SetOrgname().SetMod().push_back(

);

(

exception&)

(

&v : vals)

(

exception&)

wxMessageBox(

(

) + wxString(field),

(

), wxOK);

;

wxMessageDialog dlg(

,

(

),

(

),wxOK|wxCANCEL|wxCENTRE);

(dlg.ShowModal() == wxID_OK) {

(!

->IsSelection())

wxArrayInt wx_selected =

->GetSelectedRows();

(wx_selected.IsEmpty())

(

->GetSelectionBlockTopLeft().size() == 1 &&

->GetSelectionBlockTopLeft().size() ==

->GetSelectionBlockBottomRight().size())

top_row =

->GetSelectionBlockTopLeft()[0].GetRow();

bot_row =

->GetSelectionBlockBottomRight()[0].GetRow();

(

= top_row;

<= bot_row;

++)

selected.insert(

);

(

= 0;

< wx_selected.GetCount();

++)

selected.insert(wx_selected.Item(

));

std::set<int> selected;

(selected.empty())

wxMessageBox(

(

),

(

), wxOK);

(std::set<int>::const_iterator

= selected.begin();

!= selected.end(); ++

)

(

->IsRowShown(*

))

(sample_value.IsEmpty() && !source_value.IsEmpty())

(!sample_value.IsEmpty() && source_value.IsEmpty())

std::set<int> selected;

(selected.empty())

wxMessageBox(

(

),

(

), wxOK);

(std::set<int>::const_iterator

= selected.begin();

!= selected.end(); ++

)

(

->IsRowShown(*

))

(!sample_value.IsEmpty() && source_value != sample_value)

std::set<int> selected;

(selected.empty())

wxMessageBox(

(

),

(

), wxOK);

(std::set<int>::const_iterator

= selected.begin();

!= selected.end(); ++

)

(

->IsRowShown(*

))

(sample_value != source_value && !source_value.IsEmpty())

std::set<int> selected;

(selected.empty())

wxMessageBox(

(

),

(

), wxOK);

(std::set<int>::const_iterator

= selected.begin();

!= selected.end(); ++

)

(

->IsRowShown(*

))

(!sample_value.IsEmpty() && source_value != sample_value && field !=

(

) && field !=

(

))

list<string> old_vals;

list<string> new_vals;

vals(old_vals.begin(), old_vals.end());

vals.

(new_vals.begin(), new_vals.end());

(new_val != source_value)

std::set<int> selected;

(selected.empty())

wxMessageBox(

(

),

(

), wxOK);

(std::set<int>::const_iterator

= selected.begin();

!= selected.end(); ++

)

(

->IsRowShown(*

))

(sample_value != source_value && !source_value.IsEmpty() && field !=

(

) && field !=

(

))

list<string> old_vals;

list<string> new_vals;

vals(old_vals.begin(), old_vals.end());

vals.

(new_vals.begin(), new_vals.end());

(new_val != sample_value)

<<

;

field, sample_id;

tie(sample_id, field) = diff.first;

(

&

: diff.second)

seq_id =

.first;

tie(set_source, set_sample) =

.second;

sample =

(set_sample,

);

<< seq_id <<

<<field<<

<<

<<

<<sample<<

<<sample_id<<

;

report->SetTitle(

(

));

report->Show(

);

*

=

;

wxMessageBox(

(

),

(

), wxOK);

num_rows =

->GetNumberRows();

(

= 0;

< num_rows; ++

)

seq_id_str =

->GetData().GetId()[

]->GetSeqIdString();

list<string> sample_list;

new_values[pair<string, string>(sample_id, field)] = sample_list;

unordered_map<string, map<string, vector<string> > > delete_value, add_value;

unordered_map<string, string> change_organism;

field, sample_id;

tie(sample_id, field) = diff.first;

list<string> new_sample;

(new_values.

(diff.first) != new_values.

())

new_sample = new_values[diff.first];

tie(set_source, old_sample) = diff.second.

()->second;

vector<string> deleted_values;

set_difference(old_sample.

(), old_sample.

(), new_sample.begin(), new_sample.end(), inserter(deleted_values, deleted_values.end()));

vector<string> added_values;

set_difference(new_sample.begin(), new_sample.end(), old_sample.

(), old_sample.

(), inserter(added_values, added_values.end()));

(field ==

)

(added_values.size() == 1 && deleted_values.size() == 1)

change_organism[sample_id] = added_values.front();

(!deleted_values.empty())

delete_value[sample_id][field] = deleted_values;

(!added_values.empty())

add_value[sample_id][field] = added_values;

(

&diff : new_values)

field, sample_id;

tie(sample_id, field) = diff.first;

vector<string> new_sample(diff.second.begin(), diff.second.end());

(new_sample.empty())

add_value[sample_id][field] = new_sample;

sUrl =

;

sContentType =

;

sample_id_it = ids.

();

(sample_id_it != ids.

())

sample_id = *sample_id_it;

obj1.

(

, sample_id);

(!delete_value[sample_id].

())

(

&kv : delete_value[sample_id])

&field = kv.first;

(

&v : kv.second)

obj2.

(

, field);

obj2.

(

, v);

( !change_organism[sample_id].

())

chg_org.

(

, change_organism[sample_id]);

(!add_value[sample_id].

())

(

&kv : add_value[sample_id])

&field = kv.first;

(

&v : kv.second)

obj2.

(

, field);

obj2.

(

, v);

err = ss.str();

err =

;

wxMessageBox(wxString(err),

(

), wxOK);

has_error =

;

wxMessageBox(

(

),

(

), wxOK);

(!

.IsEmpty()) {

report->SetTitle(

(

));

report->Show(

);

wxWindow *win = FindWindowByLabel(

(

),

);

(dlg.ShowModal() == wxID_OK) {

wxMessageBox(

(

),

(

), wxOK);

wxMessageBox(

(

),

(

), wxOK);

wxWindow *win = FindWindowByLabel(

(

),

);

error_it = obj.

(

);

msg_it = obj.

(

);

(msg_it != obj.

() && msg_it->

.

() && !msg_it->value.GetArray().empty()) {

(

& resp_it : messages) {

(resp_it.IsObject()) {

& resp_obj = resp_it.

();

level_it = resp_obj.

(

);

message_it = resp_obj.find(

);

((level_it != resp_obj.end()) &&

(message_it != resp_obj.end()) &&

(level_it->value.GetValue().GetString() ==

) &&

unordered_map<string, vector<string> > messages;

(obj2.

(

) != obj2.

() && obj2.

(

) != obj2.

())

messages[level].push_back(

);

it = obj.

(

);

name(it2->name);

(obj2.

(

) == obj2.

())

validation_msg;

(obj2.

(

) != obj2.

())

(

==

&& obj2.

(

) != obj2.

())

validation_msg +=

+ attribute_name;

(obj2.

(

) != obj2.

())

(!attribute_value.empty())

validation_msg +=

+ attribute_value;

is_warning =

;

(obj2.

(

) != obj2.

())

(obj2.

(

) != obj2.

())

+=

+ short_name +

;

(short_name ==

|| short_name ==

|| short_name ==

)

wxMessageBox(wxString(

),

(

), wxOK);

validation_warning[

][name] = validation_msg;

validation_error[

][name] = validation_msg;

(

&m : validation_error)

messages[

].push_back(m.first);

(

&name : m.second)

= name.first;

(!name.second.empty())

+=

+ name.second;

messages[

].push_back(

);

(

&m : validation_warning)

messages[

].push_back(m.first);

(

&name : m.second)

= name.first;

(!name.second.empty())

+=

+ name.second;

messages[

].push_back(

);

(messages.empty())

(!messages[

].

())

report <<

;

(

&m : messages[

])

report << m <<

;

(!messages[

].

())

report <<

;

(

&m : messages[

])

report << m <<

;

(!messages[

].

())

report <<

;

(

&m : messages[

])

report << m <<

;

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxDialog::Create(parent,

, caption, pos,

, style);

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer4, 0, wxEXPAND | wxALL, 0);

itemBoxSizer4->Add(

, 1, wxALIGN_LEFT | wxALL, 5);

wxButton* itemButton5 =

wxBitmapButton(itemDialog1,

, wxArtProvider::GetBitmap(

(

)), wxDefaultPosition, wxDefaultSize, wxBU_AUTODRAW);

itemButton5->SetToolTip(

(

));

itemBoxSizer4->Add(itemButton5, 0, wxALIGN_CENTER_VERTICAL | wxTOP |wxBOTTOM | wxRIGHT, 5);

wxBoxSizer* itemBoxSizer6 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer6, 0, wxALIGN_CENTER_HORIZONTAL | wxALL, 5);

wxButton* itemButton7 =

wxButton(itemDialog1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0);

itemBoxSizer6->Add(itemButton7, 0, wxALIGN_CENTER_VERTICAL | wxALL, 5);

wxButton* itemButton8 =

wxButton(itemDialog1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0);

itemBoxSizer6->Add(itemButton8, 0, wxALIGN_CENTER_VERTICAL | wxALL, 5);

wxFileDialog dlg(

,

(

), wxEmptyString, wxEmptyString,

(

), wxFD_OPEN | wxFD_FILE_MUST_EXIST);

(dlg.ShowModal() == wxID_OK) {

wxNullBitmap;

vector< CRef< CBiosampleFieldDiff > > TBiosampleFieldDiffList

map< string, CRef< CSeq_descr > > TBioSamples

TBiosampleFieldDiffList GetBioseqDiffs(CBioseq_Handle bh, const string &biosample_accession, size_t &num_processed, vector< string > &unprocessed_ids, bool use_dev_server=false, bool compare_structured_comments=false, const string &expected_prefix="", TBioSamples *cache=NULL)

static bool IsStopWord(const string &value)

bool RemoveOrgMod(int subtype)

bool RemoveSubSource(int subtype)

void AddCommand(IEditCommand &command)

void SetButton(wxButton *button)

void OnAddToSample(wxCommandEvent &event)

void OnAddToSource(wxCommandEvent &event)

CRef< objects::CSeq_table > GetChoices(CRef< objects::CSeq_table > values_table)

CStringConstraintSelect * m_StringConstraintPanel

wxScrolledWindow * m_ScrolledWindow

void OnSyncButtonClick(wxCommandEvent &event)

ICommandProccessor * m_CmdProcessor

void CreateBiosampleUpdateWebService(wxCommandEvent &event)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

CRef< objects::CSeq_table > GetValuesTableFromSeqEntry()

CRef< objects::CSeqTable_column > m_id_col

void OnRefresh(wxCommandEvent &event)

void OnClickCancel(wxCommandEvent &event)

void x_AddTablePanel(CRef< objects::CSeq_table > values_table)

map< pair< string, string >, unordered_map< string, pair< set< string >, set< string > > > > m_DiffVec

~CCompareWithBiosample()

Destructor.

void Init()

Initialises member variables.

CSeqTableGridPanel * m_GridPanel

void OnCopyToSourceButtonClick(wxCommandEvent &event)

void OnNewAPIKey(wxCommandEvent &event)

wxButton * m_RefreshButton

map< string, CConstRef< CSeq_id > > m_ids

wxBoxSizer * m_GridPanelSizer

wxString x_ReportBiosampleUpdate(const string &str, bool &has_error)

CSeq_entry_Handle m_TopSeqEntry

bool IsReadOnlyColumn(string column_name)

void GetSelectedRows(std::set< int > &selected)

biosample_util::TBioSamples m_Cache

void CreateControls()

Creates the controls and sizers.

void OnCopyToSampleButtonClick(wxCommandEvent &event)

void x_ReadBioSampleApiKey()

CApplyEditconvertPanel * m_AecrPanel

CCompareWithBiosample()

Constructors.

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Compare with Biosample"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCLOSE_BOX|wxCAPTION|wxCLIP_CHILDREN|wxRESIZE_BORDER)

Creation.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void MakeReport(wxCommandEvent &event)

void SaveSettings() const

void OnClickOk(wxCommandEvent &event)

static bool ShowToolTips()

Should we show tooltips?

void OnOpenFile(wxCommandEvent &event)

string GetFilename() const

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

CFileLocDialog()

Constructors.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

static bool ShowToolTips()

Should we show tooltips?

void CreateControls()

Creates the controls and sizers.

void Init()

Initialises member variables.

bool Create(wxWindow *parent, wxWindowID id=13000, const wxString &caption=_("Select File with BioSample API Key"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void SetText(const wxString &text)

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

int GetInt(const string &key, int default_val=0) const

retrieve values by section and key.

CJson_Object push_back_object(void)

Add object type element to the end of the array.

Random-access iterator to access const JSON array element.

const_iterator begin(void) const

Return a random-access iterator to the first element in the array.

bool empty(void) const

Test if the array is empty.

const_iterator end(void) const

Return a random-access iterator that points just beyond the end of the array.

bool IsObject(void) const

CJson_ConstObject GetObject(void) const

Get JSON object contents of the node.

CJson_ConstArray GetArray(void) const

Get JSON array contents of the node.

std::string ToString(TJson_Write_Flags flags=fJson_Write_IndentWithSpace, unsigned int indent_char_count=4) const

Convert the contents of the node into string.

CJson_ConstValue GetValue(void) const

Get JSON value contents of the node.

Bidirectional iterator to access const JSON object element.

const CJson_ConstNode value

bool empty(void) const

Test if the object is empty.

const_iterator find(const CJson_Node::TKeyType &name) const

Return an iterator that points to the location of the element.

const_iterator begin(void) const

Return an iterator that points to the first element in the object.

const_iterator end(void) const

Return an iterator that points to the location after the last element.

bool GetBool(void) const

Get primitive value data.

TStringType GetString(void) const

bool ParseString(const TStringType &v)

Read JSON data from a UTF8 string.

bool ReadSucceeded(void) const

Test if the most recent read was successful.

CJson_Object SetObject(void)

Get JSON object contents of the node.

CJson_Array insert_array(const CJson_Node::TKeyType &name)

Insert array type element into the object.

void insert(const CJson_Node::TKeyType &name)

Insert null element into the object.

CJson_Object insert_object(const CJson_Node::TKeyType &name)

Insert object type element into the object.

@OrgMod.hpp User-defined methods of the data storage class.

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

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

void MakeColumnReadOnly(int pos, bool val=true)

void CollapseByCol(int col)

int GetCollapseColAndExpand(void)

void InitColumnCollapse(int col)

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

static const int chunk_size

static const char * kRegPath

static const char * kApiKeyPath

#define ID_COPY_TO_SAMPLE

#define ID_CREATE_BIOSAMPLE

#define ID_UPDATE_BIOSOURCE

#define ID_FILELOCTEXTCTRL

#define ID_REFRESH_BIOSAMPLE

#define ID_COPY_TO_SOURCE

#define ID_APIKEY_BIOSAMPLE

const char * kSequenceIdColLabel

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

CNcbiIstream & ContentStream(void) const

Get input stream.

int GetStatusCode(void) const

Get response status code.

void SetValue(CHeaderNameConverter name, CTempString value)

Remove all existing values with the name, set the new value.

CNcbiIstream & ErrorStream(void) const

Get input stream containing error message (e.g.

CHttpResponse g_HttpPost(const CUrl &url, CTempString data, const CHttpParam &param=CHttpParam())

Shortcut for POST request.

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

@ fParse_Default

By default in ParseIDs and IsValid, allow raw parsable non-numeric accessions and plausible local acc...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

vector< CSeq_id_Handle > TId

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

bool NcbiStreamCopy(CNcbiOstream &os, CNcbiIstream &is)

Copy the entire contents of stream "is" to stream "os".

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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 bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_Tokenize

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

@ eNocase

Case insensitive compare.

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

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

static const char label[]

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

const TOrg & GetOrg(void) const

Get the Org member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

void SetName(const TName &value)

Assign a value to Name data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

bool IsSetOrgname(void) const

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

bool IsSetName(void) const

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

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

const TColumns & GetColumns(void) const

Get the Columns member data.

void SetHeader(THeader &value)

Assign a value to Header data member.

vector< CRef< CSeqTable_column > > TColumns

void SetData(TData &value)

Assign a value to Data data member.

TNum_rows GetNum_rows(void) const

Get the Num_rows member data.

@ eField_id_location_id

location Seq-id

bool IsGenbank(void) const

Check if variant Genbank is selected.

TSource & SetSource(void)

Select the variant.

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

void ReportUsage(const wxString &dialog_name)

Report opening & accepting events in the editing package.

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

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

#define row(bind, expected)

wxString GetAbsolutePath(const wxString &localpath)

string ToStdString(const wxString &s)

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