64 static const string kBaseKey =
"GBPlugins.SixframeTrans";
137 int t_off = (seq_len - to) % 3;
156 if (!
x_Translate(objs, orig_seq, tbl, start,
false)) {
164 if (!
x_Translate(objs, rev_comp_seq, tbl, start,
true)) {
175 const string& orig_seq,
182 size_t length = orig_seq.size();
184 typedef vector< CRef<CTranslationGlyph> > TTRans;
188 for (
size_t idx = 0; idx < 3; ++idx) {
191 prot->GetTranslation().reserve(length/3);
192 prots.push_back(
prot);
199 string tmp_codon =
"NNN";
200 int orf_starts[3] = {-1, -1, -1};
204 tmp_codon[shift] = orig_seq[
i];
209 string codon = tmp_codon;
218 tmp_codon[2] = orig_seq[
i];
220 tmp_codon[0] = tmp_codon[1];
221 tmp_codon[1] = tmp_codon[2];
227 prots[shift]->GetTranslation().push_back(res);
231 prots[shift]->GetStopCodons().push_back(curr_pos);
232 if (orf_starts[shift] > -1) {
233 prots[shift]->GetOrfs().push_back(
TSeqRange(orf_starts[shift], curr_pos));
234 orf_starts[shift] = -1;
239 prots[shift]->GetStartCodons().push_back(curr_pos);
240 if (orf_starts[shift] == -1) {
241 orf_starts[shift] = curr_pos;
248 for (
size_t idx = 0; idx < 3; ++idx) {
282 if (tax.
Init(&time_out, 3)) {
301 gc_id = node->
GetGC();
319 , m_SubsetAltStart(
false)
341 const CSeq_id&
id =
dynamic_cast<const CSeq_id&
>(
object.object.GetObject());
342 return new CSFTransDS(
object.scope.GetObject(),
id);
348 static string sid(
"six_frames_trans_ds_type");
355 static string slabel(
"Six-frame Translation Data Source Type");
382 if (iter != sm_TransMap.end()) {
392 for (iter = sm_TransMap.begin(); iter != sm_TransMap.end(); ++iter) {
393 if (iter->second == trans) {
416 if (iter != sm_OptionMap.end()) {
426 for (iter = sm_OptionMap.begin(); iter != sm_OptionMap.end(); ++iter) {
427 if (iter->second == opt) {
436 "Graphical View Six-frame Translation Track");
442 , m_Trans(eTrans_Adaptive)
508 if (preset_style.empty()) {
569 "invalid translation setting:" << iter->second);
581 if ( !preset_style.empty() ) {
582 settings[
"profile"] = preset_style;
601 string link =
"https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG";
625 if (
range.GetLength() < 3)
636 range.GetFrom() > buffer_len ?
range.GetFrom() - buffer_len : 0,
637 range.GetTo() + buffer_len > max_r ? max_r :
range.GetTo() + buffer_len);
644 ", Translating in six-frame..." :
", Translating in three-frame..."
669 string msg =
"No translation is available with visible range > " +
675 label->SetConfig(c_config);
691 x_SetStatus(
", failed on doing translatinon", 100);
692 LOG_POST(
Error <<
"CSixFramesTransTrack::x_OnJobCompleted() "
693 "notification for job does not contain results.");
721 if ( !objs.empty() ) {
754 x_SetStatus(
", failed on doing translatinon", 100);
766 vector<pair<EStrandOption, wxString> > options =
773 for (
auto&& opt : options) {
775 item = menu.AppendRadioItem(
kContentBaseID + opt.first, opt.second);
780 wxMenuItemList& item_list = menu.GetMenuItems();
781 ITERATE (wxMenuItemList, iter, item_list) {
799 wxMenuItem* item =
NULL;
802 int radio_item_base = 0;
803 item = menu.AppendCheckItem(
kContentBaseID + radio_item_base++,
wxT(
"Highlight Codons"));
805 item = menu.AppendCheckItem(
kContentBaseID + radio_item_base++,
wxT(
"Enable alternative Start"));
807 item = menu.AppendCheckItem(
kContentBaseID + radio_item_base++,
wxT(
"ATG/GTG/TTG Start Codons"));
813 menu.AppendSeparator();
816 typedef vector< pair<int, string> >
TItems;
824 for (
size_t i = 0;
i < items.size(); ++
i) {
825 item = menu.AppendRadioItem(
kContentBaseID + radio_item_base +
static_cast<int>(
i),
831 wxMenuItemList& item_list = menu.GetMenuItems();
832 ITERATE (wxMenuItemList, iter, item_list) {
834 bool checked = (*iter)->IsChecked();
840 }
else if (
id == 1) {
859 id -= radio_item_base;
880 wxMenuItem* item =
NULL;
882 typedef vector< pair<int, string> >
TItems;
889 for (
size_t i = 0;
i < items.size(); ++
i) {
891 if (items[
i].
first == curr_gc) {
897 wxMenuItemList& item_list = menu.GetMenuItems();
898 ITERATE (wxMenuItemList, iter, item_list) {
900 bool checked = (*iter)->IsChecked();
902 if (curr_gc != items[
id].
first) {
923 string frames_b =
"Three";
927 frames_a =
"+1, +2, +3)";
931 frames_a =
"+1, +2, +3, -1, -2, -3)";
934 frames_a =
"-1, -2, -3)";
940 string title = frames_b;
941 title +=
"-frame translations (top -> bottom: ";
945 title +=
", Genetic code: ";
960 if ((*code)->GetId() == gc_id) {
1024 config->SetLegend_text(
"anchor_10");
1030 int orf_threshold = view.
GetInt(
"OrfThreshold", 20);
1031 bool hl_codons = view.
GetBool(
"HighlightCodons",
true);
1032 bool alt_start =
false;
1033 bool subset_alt_start =
false;
1038 if (orf_threshold != 0 && orf_threshold != 20 &&
1039 orf_threshold != 100 && orf_threshold != 250 &&
1055 "invalid translation setting:" << iter->second);
1059 string help =
"Six-frame translations<br>";
1062 help +=
"From top to bottom: forward translation +1, +2 and +3<br>";
1065 help +=
"From top to bottom: reverse translation -1, -2 and -3<br>";
1068 help +=
"From top to bottom: forward translation +1, +2 and +3 or reverse translation -1, -2 and -3 based on current orientaion<br>";
1071 help +=
"From top to bottom: forward translation +1, +2 and +3, and reverse translation -1, -2 and -3<br>";
1076 help +=
"Regions highlighted with Green are start codons<br>";
1077 help +=
"Regions highlighted with Red are stop codons<br>";
1078 help +=
"Regions highlighted with Gray are ORFs<br>";
1082 "ShowOption",
"Translation strand",
option,
1083 "Translation direction option");
1084 choice->SetValues().push_back(
1087 "Forward translations",
1088 "Show forward direction translations (+1, +2, +3)",
1090 choice->SetValues().push_back(
1093 "Reverse translations",
1094 "Show reverse direction translations (-1, -2, -3)",
1096 choice->SetValues().push_back(
1099 "Left-to-right translations",
1100 "Show left-to-right translations",
1102 choice->SetValues().push_back(
1106 "Show all six-frame translations",
1108 config->SetChoice_list().push_back(choice);
1112 "Setting for highlighting ORFs based on number of codons"
1115 orf_choice->SetValues().push_back(
1117 "0",
"Highlight all ORFs",
"Highlight all ORFs",
""));
1119 orf_choice->SetValues().push_back(
1121 "20",
"Highlight ORFs (>= 20 codons)",
1122 "Highlight ORFs equal or longer than 20 codons",
""));
1124 orf_choice->SetValues().push_back(
1126 "100",
"Highlight ORFs (>= 100 codons)",
1127 "Highlight ORFs equal or longer than 100 codons",
""));
1129 orf_choice->SetValues().push_back(
1131 "250",
"Highlight ORFs (>= 250 codons)",
1132 "Highlight ORFs equal or longer than 250 codons",
""));
1134 orf_choice->SetValues().push_back(
1137 "Do not highlight ORFs",
""));
1139 config->SetChoice_list().push_back(orf_choice);
1141 config->SetCheck_boxes().push_back(
1143 "HighlightCodons",
"Highlight codons",
1144 "Highlight codon",
"",
1147 config->SetCheck_boxes().push_back(
1149 "AltStart",
"Enable alternative start",
1150 "Enable alternative initiation codon",
"",
1153 config->SetCheck_boxes().push_back(
1155 "SubsetAltStart",
"ATG/GTG/TTG Start Codons",
1156 "Enable ATG and two other alternative start codons (gcode = 11)",
"",
CAppJobNotification Notification send by CAppJobEventTranslator.
void SetShowBackground(bool flag)
void SetBgColor(const CRgbaColor &flag)
void SetShowBoundary(bool flag)
CDataTrack - a abstract base class for layout tracks which need to deal with background data retrieva...
virtual void Update(bool layout_only)
Update content and layout including the bounding box.
static const CTrans_table & GetTransTable(int id)
static const CGenetic_code_table & GetCodeTable(void)
void Add(CSeqGlyph *obj)
Append a layout object to the end.
void SetObjects(const CLayoutGroup::TObjectList &objs)
CLayoutGroup & SetGroup()
CRef< CLayeredLayout > m_Layered
CRef< CSimpleLayout > m_Simple
void SetLayoutPolicy(ILayoutPolicy *policy)
Set policy on how to deploy the layout of its children.
static CGuiRegistry & GetInstance()
access the application-wide singleton
CLayoutGroup is a container of CSeqGlyphs (layout objects).
void SetLayoutPolicy(ILayoutPolicy *policy)
Set policy on how to deploy the layout of its children.
void SetConfig(const CBoundaryParams *conf)
Set composition boundary parameters.
void PushBack(CSeqGlyph *obj)
Append a layout object to the end.
void SetTitle(const string &label, const string &default_title=NcbiEmptyString)
@ eIcon_Content
icon id for setting content
@ eIcon_Settings
icon id for track settings
@ eIcon_Help
icon id for track help
ILayoutTrackHost * m_LTHost
Top level host owning the tracks.
string GetTitle() const
get the track title.
virtual void x_OnIconClicked(TIconID id)
Mouse left-click event handler on an icon.
const string & GetProfile() const
void x_SetStatus(const string &msg, int progress)
void SetMsg(const string &msg)
static void RegisterIconImage(const TIconAlias &key, const string &img_file)
register the image for an icon.
void SetProfile(const string &preset_style)
CLayoutTrack inline method implmentation.
CRef< CSeqGraphicConfig > m_gConfig
global configuration.
int TIconID
use int as TIconID instead of EIconID.
void x_RegisterIcon(const SIconInfo &icon)
register track icons.
int GetPgcode(void) const
bool IsSetPgcode(void) const
bool IsSetGcode(void) const
bool IsSetMgcode(void) const
int GetMgcode(void) const
class CRegistryReadView provides a nested hierarchical view at a particular key.
int GetInt(const string &key, int default_val=0) const
access a named key at this level, with no recursion
bool GetBool(const string &key, bool default_val=false) const
string GetString(const string &key, const string &default_val=kEmptyStr) const
CRenderingContext offers the basic context and utility methods for rendering layout objects in featur...
CRef< CSGSequenceDS > GetSeqDS() const
const TSeqRange & GetVisSeqRange() const
bool IsFlippedStrand() const
class CRgbaColor provides a simple abstraction for managing colors.
CSFTransDSType - Six-frames translation data source type.
virtual bool IsSharable() const
check if the data source can be shared.
virtual string GetExtensionLabel() const
returns a displayable label for this extension ( please capitalize the key words - "My Extension" )
virtual ISGDataSource * CreateDS(SConstScopedObject &object) const
create an instance of the layout track type using default settings.
virtual string GetExtensionIdentifier() const
returns the unique human-readable identifier for the extension the id should use lowercase letters se...
CSFTransDS - Six-frames translation data source.
bool m_SubsetAltStart
allow ATG (Met) and two alternative start codons: GTG (Val), TTG (Leu) for gcode = 11
bool m_AltStart
allow alternative start codon
CSFTransDS(objects::CScope &scope, const objects::CSeq_id &id)
CSFTransDS.
void DoTranslation(const TSeqRange &range, objects::ENa_strand strand=objects::eNa_strand_both)
do Six-frames translation.
void SetGeneticCode(int id)
CSFTransDS inline methods.
int GetGeneticCode() const
bool GetSubsetAltStart() const
void SetSubsetAltStart(bool value)
CSFTranslationJob - Graphical view six-frame translation job.
bool m_SubsetAltStart
allow ATG (Met) and two alternative start codons: GTG (Val), TTG (Leu) for gcode = 11
CSFTranslationJob(const string &desc, CBioseq_Handle handle, const TSeqRange &range, ENa_strand strand=eNa_strand_both)
void SetGeneticCode(int id)
bool x_Translate(CSeqGlyph::TObjects &objs, const string &orig_seq, const CTrans_table &tbl, TSeqPos start, bool negative)
Do translation for three frame shifts.
ENa_strand m_Strand
Translated strand (plus, minus, both)
TSeqRange m_Range
target range
virtual EJobState x_Execute()
method truly doing the job.
void SetSubsetAltStart(bool value)
bool m_AltStart
allow alternative start codon
CBioseq_Handle m_Handle
target sequence
static CRegistryReadView GetSizeReadView(const CGuiRegistry ®, const string &base_key, const string §, const string &key, const string &def_sect="")
static void GetFont(const CRegistryReadView &view, const string &face_key, const string &size_key, CGlTextureFont &f)
static string ComposeProfileString(const TKeyValuePairs &settings)
static CRegistryReadView GetColorReadView(const CGuiRegistry ®, const string &base_key, const string §, const string &key, const string &def_sect="")
Create a read view specifically for 'Color' section.
static CRegistryReadView GetReadView(const CGuiRegistry ®, const string &base_key, const string &curr_key, const string &def_key1="", const string &def_key2="", const string &def_key3="")
read/readwrite view creation helper methods.
static void GetColor(const CRegistryReadView &view, const string &key, CRgbaColor &color)
TJobID x_LaunchJob(IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")
Launch either a background or foreground job.
virtual bool AllJobsFinished() const
void SetJobListener(CEventHandler *listener)
Set JobDispatcher listener.
virtual void ClearJobID(TJobID job_id)
void SetDepth(int depth)
Set the annotation selector resolving depth.
virtual void DeleteAllJobs()
Remove waiting jobs from queue or cancel the unfinished jobs.
objects::CBioseq_Handle m_Handle
CSGJobResult – the data structure holding the seqgraphic job results.
TSeqPos GetSequenceLength() const
objects::CSeq_id_Handle GetBestIdHandle() const
static bool IsMitochondrion(const objects::CBioseq_Handle &handle)
static bool IsPlastid(const objects::CBioseq_Handle &handle)
CRenderingContext * m_Context
the rendering context
list< CRef< CSeqGlyph > > TObjects
const string & GetSizeLevel() const
int GetObjectSpace() const
bool GetShowComments() const
const string & GetColorTheme() const
CSeqGraphicJob – the base class of seqgraphic job for handling the job status such as reporting the p...
virtual void SetTaskTotal(int total)
virtual void SetTaskName(const string &name)
virtual void SetTaskCompleted(int completed)
set total finished task number.
virtual void AddTaskCompleted(int delta)
set to add newly finished task number.
static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)
virtual TTrackMap CreateTracks(SConstScopedObject &object, ISGDataSourceContext *ds_context, CRenderingContext *r_cntx, const SExtraParams ¶ms=SExtraParams(), const TAnnotMetaDataList &src_annots=TAnnotMetaDataList()) const
create a layout track based on the input objects and extra parameters.
virtual string GetExtensionLabel() const
returns a displayable label for this extension ( please capitalize the key words - "My Extension" )
virtual CRef< objects::CTrackConfigSet > GetSettings(const string &profile, const TKeyValuePairs &settings, const CTempTrackProxy *track_proxy) const
virtual void RegisterIconImages() const
virtual string GetExtensionIdentifier() const
returns the unique human-readable identifier for the extension the id should use lowercase letters se...
CSixFramesTransTrack – A special track for doing six-frames translation of the current sequence.
virtual const CTrackTypeInfo & GetTypeInfo() const override
virtual void Update(bool layout_only) override
Update content and layout including the bounding box.
@ eTrans_Adaptive
do translation only for under certain zoom level
@ eTrans_Always
do translation for all resolution
@ eOpt_All
show translation for both directions
@ eOpt_LeftToRight
Choose what to show based on orientation.
@ eOpt_Forward
show forward translations
@ eOpt_Reverse
show reverse translations
string m_GCName
genetic code name.
void x_InitGeneticCodeName(int gc_id)
virtual string GetFullTitle() const override
get a more meaningful title.
objects::ENa_strand m_TransStrand
the sequence strand for the current translation
CSixFramesTransTrack(CSFTransDS *ds, CRenderingContext *r_cntx)
static const string & OptionValueToStr(EStrandOption opt)
static CTrackTypeInfo m_TypeInfo
TSeqRange x_GetCurrentTransRange() const
TSeqRange m_TransRange
the sequence range current translation is done.
void x_AddTranslations(const CSGJobResult &result)
virtual void x_LoadSettings(const string &preset_style, const TKeyValuePairs &settings) override
load the track settings.
static const string & TransValueToStr(ETranslation trans)
virtual void x_OnJobCompleted(CAppJobNotification ¬ify) override
virtual ~CSixFramesTransTrack()
CRef< CBoundaryParams > m_GroupConf
virtual void x_UpdateData() override
update track content.
static EStrandOption OptionStrToValue(const string &opt)
void x_OnGeneticIconClicked()
virtual void x_OnIconClicked(TIconID id) override
Mouse left-click event handler on an icon.
virtual void x_SaveSettings(const string &preset_style) override
save part of settings to a profile string.
void x_OnContentIconClicked()
static ETranslation TransStrToValue(const string &trans)
void x_OnSettingIconClicked()
void SetGCName(const string &gc_name)
CRef< CTranslationConfig > m_Config
class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...
TBase::const_iterator const_iterator
bool GetTaxId4GI(TGi gi, TTaxId &tax_id_out)
bool LoadNode(TTaxId tax_id, const ITaxon1Node **ppNode=NULL)
static CRef< objects::CChoice > CreateChoice(const string &name, const string &disp_name, const string &curr_val, const string &help, bool optional=false)
static CRef< objects::CCheckBox > CreateCheckBox(const string &name, const string &disp_n, const string &help_text, const string &legend_txt, bool value, bool optional=false)
static CRef< objects::CChoiceItem > CreateChoiceItem(const string &name, const string &disp_name, const string &help, const string &legend_txt, bool optional=false)
CTrackTypeInfo - holds description of a layout track type.
const string & GetDescr() const
const string & GetId() const
char GetCodonResidue(int state) const
bool IsAltStart(int state) const
static int NextCodonState(int state, unsigned char ch)
void SetOrfHighlightColor(const CRgbaColor &color)
void SetSeqColor(const CRgbaColor &color)
void SetLabelBgColor(const CRgbaColor &color)
CGlTextureFont & GetSeqFont()
bool GetHighlightCodons() const
void SetStartCodonColor(const CRgbaColor &color)
CTranslationConfig inline methods.
void SetOrfSeqColor(const CRgbaColor &color)
CGlTextureFont & GetStrandFont()
void SetStopCodonColor(const CRgbaColor &color)
int GetOrfThreshold() const
void SetHighlightCodons(bool f)
void SetCommentColor(const CRgbaColor &color)
void SetShowLabel(bool f)
void SetOrfThreshold(int val)
void SetConfig(CTranslationConfig *config)
CTranslationGlyph inline methods.
virtual void LTH_PopupMenu(wxMenu *menu)=0
show track-specific context menu.
ISGDSManager is seqgraphic data source manage that serves as an data source context.
virtual CIRef< ISGDataSource > GetDS(const string &type, SConstScopedObject &object)=0
Get a seqgraphic data source instance of the specified type.
virtual TTaxGeneticCode GetMGC() const =0
virtual TTaxGeneticCode GetGC() const =0
static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)
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.
SStrictId_Tax::TId TTaxId
Taxon id type.
#define TAX_ID_FROM(T, value)
#define LOG_POST(message)
This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...
void Error(CExceptionArgs_Base &args)
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
void Warning(CExceptionArgs_Base &args)
void SetFontFace(EFontFace face, bool use_bitmap_overrides=true)
void SetFontSize(unsigned int size)
Set/get font size in points.
CGlPoint< TModelUnit > TModelPoint
void Set(float r, float g, float b)
set the color from an Fl_Color
CRef< CObject > GetResult() const
returns non-null pointer only if Completed or Running and has temporary results available
virtual bool IsCanceled() const override
EJobState
Job states (describe FSM)
static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)
Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...
CConstRef< CSeq_id > GetSeqId(void) const
EAccessionInfo
For IdentifyAccession (below)
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,...
const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)
Return the org-ref associated with a given sequence.
@ eGetId_ForceGi
return only a gi-based seq-id
TTaxId GetTaxId(const CSeq_id &id, TGetFlags flags=0)
Get taxonomy id of bioseq Return -1 if sequence is not found Return 0 if sequence doesn't have taxono...
TSeqPos GetBioseqLength(void) const
const CSeq_id_Handle & GetSeq_id_Handle(void) const
Get handle of id used to obtain this bioseq handle.
CScope & GetScope(void) const
Get scope this handle belongs to.
CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const
Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.
@ 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.
position_type GetLength(void) const
TThisType IntersectionWith(const TThisType &r) const
TThisType & Set(position_type from, position_type to)
CRange< TSeqPos > TSeqRange
typedefs for sequence ranges
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
static bool StringToBool(const CTempString str)
Convert string to bool.
static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)
Convert string to int.
static const string BoolToString(bool value)
Convert bool to string.
static string IntToString(int value, TNumToStringFlags flags=0, int base=10)
Convert int to string.
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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)
Convert numeric value to string.
@ fWithCommas
Use commas as thousands separator.
unsigned int usec
microseconds (modulo 1,000,000)
static const char label[]
TTo GetTo(void) const
Get the To member data.
TFrom GetFrom(void) const
Get the From member data.
Tdata & Set(void)
Assign a value to data member.
list< CRef< CGenetic_code > > Tdata
const Tdata & Get(void) const
Get the member data.
ENa_strand
strand of nucleic acid
@ eNa_strand_both
in forward orientation
range(_Ty, _Ty) -> range< _Ty >
constexpr bool empty(list< Ts... >) noexcept
double value_type
The numeric datatype used by the parser.
double f(double x_, const double &y_)
SStaticPair< const char *, CSixFramesTransTrack::ETranslation > TTranslationStr
CSixFramesTransTrack.
DEFINE_STATIC_ARRAY_MAP(TTransMap, sm_TransMap, s_TransStrs)
static const string kDefProfile
static const int kMaxOrfLen
static const TTranslationStr s_TransStrs[]
static const string kTrackTitle
SStaticPair< const char *, CSixFramesTransTrack::EStrandOption > TOptionStr
static const TOptionStr s_OptionStrs[]
CStaticArrayMap< string, CSixFramesTransTrack::ETranslation > TTransMap
CStaticArrayMap< string, CSixFramesTransTrack::EStrandOption > TOptionMap
static const TSeqPos kTransRangeLimit
largest sequence range we will do sequence translations.
static const int kContentBaseID
static const string kBaseKey
A help struct for storing information about a icon.
Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...
void UseDefaultMarginWidth(wxMenu &menu)
Using default menu item margin width.
wxString ToWxString(const string &s)