NCBI C++ ToolKit
Functions | Variables
subprep_util.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objects/submit/Contact_info.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/biblio/Affil.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/general/Name_std.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/PCRReactionSet.hpp>
#include <objects/seqfeat/PCRReaction.hpp>
#include <objects/seqfeat/PCRPrimerSet.hpp>
#include <objects/seqfeat/PCRPrimer.hpp>
#include <objects/seqfeat/PCRPrimerSeq.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/IUPACaa.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <gui/widgets/wx/wx_utils.hpp>
#include <gui/widgets/object_list/object_list_widget.hpp>
#include <gui/objutils/cmd_composite.hpp>
#include <gui/objutils/cmd_create_desc.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <gui/objutils/cmd_del_desc.hpp>
#include <gui/objutils/cmd_del_seq_feat.hpp>
#include <gui/objutils/descriptor_change.hpp>
#include <gui/objutils/cmd_add_seqentry.hpp>
#include <gui/objutils/cmd_change_bioseq_set.hpp>
#include <gui/widgets/wx/file_extensions.hpp>
#include <gui/widgets/wx/csv_exporter.hpp>
#include <gui/widgets/edit/field_type_constants.hpp>
#include <gui/widgets/edit/biosource_autocomplete.hpp>
#include <gui/packages/pkg_sequence_edit/subprep_util.hpp>
#include <gui/packages/pkg_sequence_edit/featedit_util.hpp>
#include <objects/seqtable/SeqTable_multi_data.hpp>
#include <objects/seqtable/SeqTable_column_info.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <algo/align/prosplign/prosplign.hpp>
#include <objtools/readers/source_mod_parser.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <wx/msgdlg.h>
#include <objtools/edit/cds_fix.hpp>
+ Include dependency graph for subprep_util.cpp:

Go to the source code of this file.

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Functions

TWizardNameList GetWizardNameList ()
 
CSourceRequirements::EWizardType GetWizardTypeFromName (string wizard_name)
 
static bool OneRowOk (CRef< objects::CSeq_id > id, CRef< objects::CSeqTable_column > id_col, objects::CSeq_entry_Handle seh)
 
void FixTableAfterImport (CRef< objects::CSeq_table > input_table)
 
string FindBadRows (CRef< objects::CSeq_table > src, CRef< objects::CSeq_table > dst, objects::CSeq_entry_Handle seh)
 
CRef< objects::CSeqTable_column > FindSeqIDColumn (const objects::CSeq_table &table)
 
int FindRowForSeqId (CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeq_id > id)
 
int CountColumnRowConflicts (CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)
 
int CountTableColumnConflicts (CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)
 
void DeleteTableRow (CRef< objects::CSeq_table > table, int row)
 
static void CombineColumns (CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)
 
int CombineTables (CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)
 
bool SaveTableFile (wxWindow *parent, wxString &save_file_dir, wxString &save_file_name, CRef< objects::CSeq_table > values_table)
 
bool AreAllColumnValuesTheSame (CRef< objects::CSeqTable_column > col, string default_val)
 
bool AreAnyColumnValuesMissing (CRef< objects::CSeqTable_column > col)
 
bool DoesColumnHaveValue (CRef< objects::CSeqTable_column > col, string val)
 
bool AreAnyColumnValuesPresent (CRef< objects::CSeqTable_column > col, string default_val)
 
static void s_ExtendIntervalToEnd (objects::CSeq_interval &ival, objects::CBioseq_Handle bsh)
 
bool AddProteinToSeqEntry (const objects::CSeq_entry *protein, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool create_general_only)
 
static void s_ReportMixError ()
 
void ParseTitlesToNewSeqEntries (CRef< objects::CSeq_entry > entry)
 
bool AddSeqEntryToSeqEntry (const objects::CSeq_entry *entry, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool &has_nuc, bool &has_prot, bool create_general_only)
 
string CheckFeatureAnnotation (objects::CSeq_entry_Handle entry, bool &is_ok)
 
vector< stringGetTrueFalseList ()
 
bool IsSynonymForTrue (const string &val)
 
bool IsSynonymForFalse (const string &val)
 
bool IsTrueFalseList (const vector< string > &choices)
 
int AddFeatureToSeqTable (const objects::CSeq_feat &f, CRef< objects::CSeq_table > table)
 
static bool s_OkToAddFeature (const objects::CSeq_feat &f1, const objects::CSeq_feat &f2, const TFeatureSeqTableColumnList &reqs)
 
CRef< objects::CSeq_table > GetFeaturesFromSeqEntry (objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)
 
void AddFeatureSeqTableRowToSeqEntry (CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, unsigned int row, TFeatureSeqTableColumnList &vecColEditFactories, CRef< CCmdComposite > cmd)
 
CRef< CCmdCompositeAddFeatureSeqTableToSeqEntry (CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)
 
void MergeStringVectors (vector< string > &problems, vector< string > add)
 
static void AddProblemsToColumn (CRef< objects::CSeqTable_column > val_col, CRef< CFeatureSeqTableColumnBase > rule_col, vector< string > &problems)
 
void RemoveProblemsColumn (CRef< objects::CSeq_table > values_table)
 
CRef< CFeatureSeqTableColumnBaseGetColumnRuleForFeatureSeqTable (CRef< objects::CSeqTable_column > col, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)
 
void AddProblemsColumnToFeatureSeqTable (CRef< objects::CSeq_table > table, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)
 
bool HasLocalIntFeatureId (const objects::CSeq_feat &feat)
 
CRef< CCmdCompositeRemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry (objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)
 
wxString GetAsnSqnExtensions ()
 
bool IsWizardObject (const objects::CUser_object &user)
 
CRef< objects::CUser_object > MakeWizardObject ()
 
void SetWizardFieldInSeqEntryNoUndo (objects::CSeq_entry_Handle entry, string field_name, string value)
 
bool IsBankItSubmissionObject (const objects::CUser_object &user)
 
CRef< objects::CUser_object > MakeBankItSubmissionObject ()
 
string GetFieldFromWizardObject (const objects::CUser_object &user, string field_name)
 
string GetDescAlternateEmailAddress (const objects::CSeqdesc &desc)
 
string GetAlternateEmailAddress (objects::CSeq_entry_Handle entry)
 
void SetUserAlternateEmailAddress (objects::CUser_object &u, string alt_email)
 
void SetAlternateEmailAddress (objects::CSeq_entry_Handle entry, string alt_email)
 
bool IsValidEmail (string email)
 
static void AddIdsFromSeqEntryToTable (const objects::CSeq_entry &entry, CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeqTable_column > pos_col, CRef< objects::CSeqTable_column > np_col, CRef< objects::CSeqTable_column > title_col, int &pos, size_t &row)
 
static CRef< objects::CSeqTable_column > s_MakeIdTableIdCol ()
 
static CRef< objects::CSeqTable_column > s_MakePosCol ()
 
static CRef< objects::CSeqTable_column > s_MakeNpCol ()
 
static CRef< objects::CSeqTable_column > s_MakeTitleCol ()
 
void AddIdsFromSeqEntryToTable (const objects::CSeq_entry &entry, CRef< objects::CSeq_table > table)
 
CRef< objects::CSeq_table > GetIdsFromSeqEntry (const objects::CSeq_entry &entry)
 
static string GetIdValueFromColumn (CRef< objects::CSeqTable_column > id_col, int pos)
 
CRef< objects::CSeqTable_column > GetSeqIdProblems (CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)
 
string SummarizeIdProblems (CRef< objects::CSeqTable_column > problems)
 
CRef< objects::CSeqTable_column > GetReplacementSeqIds (CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)
 
static void TransformSeqAnnot (objects::CSeq_annot &annot, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id)
 
static void TransformSeqAnnots (objects::CBioseq &bioseq, CRef< objects::CSeq_id > seq_id, CRef< objects::CSeq_id > new_seq_id)
 
void ApplyReplacementIds (objects::CSeq_entry &entry, CRef< objects::CSeq_table > table)
 
bool AlreadyHasFeature (objects::CBioseq_Handle bh, string key, string comment)
 
bool AlreadyHasFeature (objects::CBioseq_Handle bh, objects::CSeqFeatData::ESubtype subtype)
 

Variables

static TWizardName s_WizardNames []
 
static int k_NumWizardNames = sizeof (s_WizardNames) / sizeof (TWizardName)
 
const string kBankitSubmissionLabel = "Submission"
 
const string kBankItAltEmailPrefix = "ALT EMAIL:"
 
const string kSMARTComment = "SmartComment"
 
const string kIdTooLong = "ID is too long"
 
const string kIdDuplicate = "duplicate"
 
const string kIdMissing = "Missing ID"
 

Function Documentation

◆ AddFeatureSeqTableRowToSeqEntry()

void AddFeatureSeqTableRowToSeqEntry ( CRef< objects::CSeq_table >  table,
objects::CSeq_entry_Handle  entry,
objects::CSeqFeatData::ESubtype  subtype,
unsigned int  row,
TFeatureSeqTableColumnList vecColEditFactories,
CRef< CCmdComposite cmd 
)

◆ AddFeatureSeqTableToSeqEntry()

CRef<CCmdComposite> AddFeatureSeqTableToSeqEntry ( CRef< objects::CSeq_table >  table,
objects::CSeq_entry_Handle  entry,
objects::CSeqFeatData::ESubtype  subtype,
const TFeatureSeqTableColumnList reqs,
const TFeatureSeqTableColumnList opts 
)

◆ AddFeatureToSeqTable()

int AddFeatureToSeqTable ( const objects::CSeq_feat &  f,
CRef< objects::CSeq_table >  table 
)

◆ AddIdsFromSeqEntryToTable() [1/2]

void AddIdsFromSeqEntryToTable ( const objects::CSeq_entry &  entry,
CRef< objects::CSeq_table >  table 
)

◆ AddIdsFromSeqEntryToTable() [2/2]

static void AddIdsFromSeqEntryToTable ( const objects::CSeq_entry &  entry,
CRef< objects::CSeqTable_column >  id_col,
CRef< objects::CSeqTable_column >  pos_col,
CRef< objects::CSeqTable_column >  np_col,
CRef< objects::CSeqTable_column >  title_col,
int pos,
size_t &  row 
)
static

Definition at line 1621 of file subprep_util.cpp.

References ITERATE, and row.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ AddProblemsColumnToFeatureSeqTable()

void AddProblemsColumnToFeatureSeqTable ( CRef< objects::CSeq_table >  table,
const TFeatureSeqTableColumnList reqs,
const TFeatureSeqTableColumnList opts 
)

◆ AddProblemsToColumn()

static void AddProblemsToColumn ( CRef< objects::CSeqTable_column >  val_col,
CRef< CFeatureSeqTableColumnBase rule_col,
vector< string > &  problems 
)
static

◆ AddProteinToSeqEntry()

bool AddProteinToSeqEntry ( const objects::CSeq_entry *  protein,
objects::CSeq_entry_Handle  seh,
CRef< CCmdComposite cmd,
bool  create_general_only 
)

◆ AddSeqEntryToSeqEntry()

bool AddSeqEntryToSeqEntry ( const objects::CSeq_entry *  entry,
objects::CSeq_entry_Handle  seh,
CRef< CCmdComposite cmd,
bool has_nuc,
bool has_prot,
bool  create_general_only 
)

◆ AlreadyHasFeature() [1/2]

bool AlreadyHasFeature ( objects::CBioseq_Handle  bh,
objects::CSeqFeatData::ESubtype  subtype 
)

Definition at line 2051 of file subprep_util.cpp.

References f().

◆ AlreadyHasFeature() [2/2]

bool AlreadyHasFeature ( objects::CBioseq_Handle  bh,
string  key,
string  comment 
)

◆ ApplyReplacementIds()

void ApplyReplacementIds ( objects::CSeq_entry &  entry,
CRef< objects::CSeq_table >  table 
)

◆ AreAllColumnValuesTheSame()

bool AreAllColumnValuesTheSame ( CRef< objects::CSeqTable_column >  col,
string  default_val 
)

◆ AreAnyColumnValuesMissing()

bool AreAnyColumnValuesMissing ( CRef< objects::CSeqTable_column >  col)

◆ AreAnyColumnValuesPresent()

bool AreAnyColumnValuesPresent ( CRef< objects::CSeqTable_column >  col,
string  default_val 
)

◆ CheckFeatureAnnotation()

string CheckFeatureAnnotation ( objects::CSeq_entry_Handle  entry,
bool is_ok 
)

Definition at line 968 of file subprep_util.cpp.

References all, and NStr::NumericToString().

Referenced by CSubPrep_panel::x_UpdateFeatureStatus().

◆ CombineColumns()

static void CombineColumns ( CRef< objects::CSeqTable_column >  dst_id,
CRef< objects::CSeqTable_column >  dst_col,
CRef< objects::CSeqTable_column >  src_id,
CRef< objects::CSeqTable_column >  src_col 
)
static

Definition at line 483 of file subprep_util.cpp.

References FindRowForSeqId(), i, and row.

Referenced by CombineTables().

◆ CombineTables()

int CombineTables ( CRef< objects::CSeq_table >  dst,
const objects::CSeq_table &  src 
)

◆ CountColumnRowConflicts()

int CountColumnRowConflicts ( CRef< objects::CSeqTable_column >  dst_id,
CRef< objects::CSeqTable_column >  dst_col,
CRef< objects::CSeqTable_column >  src_id,
CRef< objects::CSeqTable_column >  src_col 
)

Definition at line 393 of file subprep_util.cpp.

References NStr::Equal(), FindRowForSeqId(), i, NStr::IsBlank(), and row.

Referenced by CountTableColumnConflicts().

◆ CountTableColumnConflicts()

int CountTableColumnConflicts ( CRef< objects::CSeq_table >  dst,
const objects::CSeq_table &  src 
)

◆ DeleteTableRow()

void DeleteTableRow ( CRef< objects::CSeq_table >  table,
int  row 
)

Definition at line 432 of file subprep_util.cpp.

References NON_CONST_ITERATE, row, and table.

Referenced by FixTableAfterImport().

◆ DoesColumnHaveValue()

bool DoesColumnHaveValue ( CRef< objects::CSeqTable_column >  col,
string  val 
)

Definition at line 656 of file subprep_util.cpp.

References NStr::Equal(), row, and val.

Referenced by CSubmissionPrepMainPanel::CreateVirusMoleculeOptions().

◆ FindBadRows()

string FindBadRows ( CRef< objects::CSeq_table >  src,
CRef< objects::CSeq_table >  dst,
objects::CSeq_entry_Handle  seh 
)

◆ FindRowForSeqId()

int FindRowForSeqId ( CRef< objects::CSeqTable_column >  id_col,
CRef< objects::CSeq_id >  id 
)

Definition at line 377 of file subprep_util.cpp.

References row.

Referenced by CombineColumns(), and CountColumnRowConflicts().

◆ FindSeqIDColumn()

CRef<objects::CSeqTable_column> FindSeqIDColumn ( const objects::CSeq_table &  table)

Definition at line 365 of file subprep_util.cpp.

References ITERATE, NULL, and table.

Referenced by CombineTables(), CountTableColumnConflicts(), FindBadRows(), and FixTableAfterImport().

◆ FixTableAfterImport()

void FixTableAfterImport ( CRef< objects::CSeq_table >  input_table)

◆ GetAlternateEmailAddress()

string GetAlternateEmailAddress ( objects::CSeq_entry_Handle  entry)

◆ GetAsnSqnExtensions()

wxString GetAsnSqnExtensions ( )

Definition at line 1419 of file subprep_util.cpp.

References wxT.

Referenced by CSubmitBlockDlg::OnExportBtnClick(), and CSubPrep_panel::OnSaveBtnClick().

◆ GetColumnRuleForFeatureSeqTable()

CRef<CFeatureSeqTableColumnBase> GetColumnRuleForFeatureSeqTable ( CRef< objects::CSeqTable_column >  col,
const TFeatureSeqTableColumnList reqs,
const TFeatureSeqTableColumnList opts 
)

◆ GetDescAlternateEmailAddress()

string GetDescAlternateEmailAddress ( const objects::CSeqdesc &  desc)

◆ GetFeaturesFromSeqEntry()

CRef<objects::CSeq_table> GetFeaturesFromSeqEntry ( objects::CSeq_entry_Handle  entry,
const objects::CSeq_feat &  feat,
const TFeatureSeqTableColumnList reqs 
)

◆ GetFieldFromWizardObject()

string GetFieldFromWizardObject ( const objects::CUser_object &  user,
string  field_name 
)

◆ GetIdsFromSeqEntry()

CRef<objects::CSeq_table> GetIdsFromSeqEntry ( const objects::CSeq_entry &  entry)

◆ GetIdValueFromColumn()

static string GetIdValueFromColumn ( CRef< objects::CSeqTable_column >  id_col,
int  pos 
)
static

Definition at line 1756 of file subprep_util.cpp.

References eContent, and str().

Referenced by GetSeqIdProblems().

◆ GetReplacementSeqIds()

CRef<objects::CSeqTable_column> GetReplacementSeqIds ( CRef< objects::CSeq_table >  new_ids,
CRef< objects::CSeq_table >  old_ids,
size_t  max_len 
)

◆ GetSeqIdProblems()

CRef<objects::CSeqTable_column> GetSeqIdProblems ( CRef< objects::CSeq_table >  new_ids,
CRef< objects::CSeq_table >  old_ids,
size_t  max_len 
)

◆ GetTrueFalseList()

vector<string> GetTrueFalseList ( )

Definition at line 1041 of file subprep_util.cpp.

Referenced by CFeatureTableCommandConverter::GetChoices().

◆ GetWizardNameList()

TWizardNameList GetWizardNameList ( )

Definition at line 121 of file subprep_util.cpp.

References i, k_NumWizardNames, and s_WizardNames.

Referenced by CSubPrepIntroPanel::CreateControls(), and CSubPrep_panel::Init().

◆ GetWizardTypeFromName()

CSourceRequirements::EWizardType GetWizardTypeFromName ( string  wizard_name)

◆ HasLocalIntFeatureId()

bool HasLocalIntFeatureId ( const objects::CSeq_feat &  feat)

◆ IsBankItSubmissionObject()

bool IsBankItSubmissionObject ( const objects::CUser_object &  user)

◆ IsSynonymForFalse()

bool IsSynonymForFalse ( const string val)

◆ IsSynonymForTrue()

bool IsSynonymForTrue ( const string val)

◆ IsTrueFalseList()

bool IsTrueFalseList ( const vector< string > &  choices)

Definition at line 1074 of file subprep_util.cpp.

References IsSynonymForFalse(), and IsSynonymForTrue().

◆ IsValidEmail()

bool IsValidEmail ( string  email)

◆ IsWizardObject()

bool IsWizardObject ( const objects::CUser_object &  user)

◆ MakeBankItSubmissionObject()

CRef<objects::CUser_object> MakeBankItSubmissionObject ( )

◆ MakeWizardObject()

CRef<objects::CUser_object> MakeWizardObject ( )

◆ MergeStringVectors()

void MergeStringVectors ( vector< string > &  problems,
vector< string add 
)

Definition at line 1297 of file subprep_util.cpp.

References NStr::IsBlank().

Referenced by AddProblemsToColumn().

◆ OneRowOk()

static bool OneRowOk ( CRef< objects::CSeq_id >  id,
CRef< objects::CSeqTable_column >  id_col,
objects::CSeq_entry_Handle  seh 
)
static

Definition at line 170 of file subprep_util.cpp.

References b, ITERATE, RelaxedMatch(), and row.

Referenced by FindBadRows().

◆ ParseTitlesToNewSeqEntries()

void ParseTitlesToNewSeqEntries ( CRef< objects::CSeq_entry >  entry)

Definition at line 866 of file subprep_util.cpp.

References NON_CONST_ITERATE.

Referenced by AddSeqEntryToSeqEntry().

◆ RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry()

CRef<CCmdComposite> RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry ( objects::CSeq_entry_Handle  entry,
const objects::CSeq_feat &  feat,
const TFeatureSeqTableColumnList reqs 
)

◆ RemoveProblemsColumn()

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

◆ s_ExtendIntervalToEnd()

static void s_ExtendIntervalToEnd ( objects::CSeq_interval &  ival,
objects::CBioseq_Handle  bsh 
)
static

Definition at line 700 of file subprep_util.cpp.

References eNa_strand_minus, and len.

Referenced by AddProteinToSeqEntry(), and s_GetCDSLoc().

◆ s_MakeIdTableIdCol()

static CRef<objects::CSeqTable_column> s_MakeIdTableIdCol ( )
static

Definition at line 1662 of file subprep_util.cpp.

References kSequenceIdColLabel.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_MakeNpCol()

static CRef<objects::CSeqTable_column> s_MakeNpCol ( )
static

Definition at line 1680 of file subprep_util.cpp.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_MakePosCol()

static CRef<objects::CSeqTable_column> s_MakePosCol ( )
static

Definition at line 1671 of file subprep_util.cpp.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_MakeTitleCol()

static CRef<objects::CSeqTable_column> s_MakeTitleCol ( )
static

Definition at line 1689 of file subprep_util.cpp.

Referenced by AddIdsFromSeqEntryToTable(), and GetIdsFromSeqEntry().

◆ s_OkToAddFeature()

static bool s_OkToAddFeature ( const objects::CSeq_feat &  f1,
const objects::CSeq_feat &  f2,
const TFeatureSeqTableColumnList reqs 
)
static

◆ s_ReportMixError()

static void s_ReportMixError ( )
static

Definition at line 859 of file subprep_util.cpp.

References NULL, and wxT.

Referenced by AddSeqEntryToSeqEntry().

◆ SaveTableFile()

bool SaveTableFile ( wxWindow *  parent,
wxString &  save_file_dir,
wxString &  save_file_name,
CRef< objects::CSeq_table >  values_table 
)

◆ SetAlternateEmailAddress()

void SetAlternateEmailAddress ( objects::CSeq_entry_Handle  entry,
string  alt_email 
)

◆ SetUserAlternateEmailAddress()

void SetUserAlternateEmailAddress ( objects::CUser_object &  u,
string  alt_email 
)

◆ SetWizardFieldInSeqEntryNoUndo()

void SetWizardFieldInSeqEntryNoUndo ( objects::CSeq_entry_Handle  entry,
string  field_name,
string  value 
)

◆ SummarizeIdProblems()

string SummarizeIdProblems ( CRef< objects::CSeqTable_column >  problems)

◆ TransformSeqAnnot()

static void TransformSeqAnnot ( objects::CSeq_annot &  annot,
CRef< objects::CSeq_id >  seq_id,
CRef< objects::CSeq_id >  new_seq_id 
)
static

Definition at line 1959 of file subprep_util.cpp.

References Begin().

Referenced by TransformSeqAnnots().

◆ TransformSeqAnnots()

static void TransformSeqAnnots ( objects::CBioseq &  bioseq,
CRef< objects::CSeq_id >  seq_id,
CRef< objects::CSeq_id >  new_seq_id 
)
static

Definition at line 1973 of file subprep_util.cpp.

References NON_CONST_ITERATE, and TransformSeqAnnot().

Referenced by ApplyReplacementIds().

Variable Documentation

◆ k_NumWizardNames

int k_NumWizardNames = sizeof (s_WizardNames) / sizeof (TWizardName)
static

Definition at line 118 of file subprep_util.cpp.

Referenced by GetWizardNameList(), and GetWizardTypeFromName().

◆ kBankItAltEmailPrefix

const string kBankItAltEmailPrefix = "ALT EMAIL:"

◆ kBankitSubmissionLabel

const string kBankitSubmissionLabel = "Submission"

Definition at line 1495 of file subprep_util.cpp.

Referenced by IsBankItSubmissionObject(), and MakeBankItSubmissionObject().

◆ kIdDuplicate

const string kIdDuplicate = "duplicate"

Definition at line 1752 of file subprep_util.cpp.

Referenced by GetSeqIdProblems(), and SummarizeIdProblems().

◆ kIdMissing

const string kIdMissing = "Missing ID"

Definition at line 1753 of file subprep_util.cpp.

Referenced by GetSeqIdProblems().

◆ kIdTooLong

const string kIdTooLong = "ID is too long"

Definition at line 1751 of file subprep_util.cpp.

Referenced by GetSeqIdProblems(), and SummarizeIdProblems().

◆ kSMARTComment

const string kSMARTComment = "SmartComment"

◆ s_WizardNames

TWizardName s_WizardNames[]
static
Initial value:
= {
TWizardName(CSourceRequirements::eWizardType_igs, "Intergenic Spacer (IGS) sequences"),
TWizardName(CSourceRequirements::eWizardType_d_loop, "D-loops and control regions")
}
pair< CSourceRequirements::EWizardType, string > TWizardName

Definition at line 108 of file subprep_util.cpp.

Referenced by GetWizardNameList(), and GetWizardTypeFromName().

Modified on Mon May 27 04:35:30 2024 by modify_doxy.py rev. 669887