NCBI C++ ToolKit
gene_model_config.cpp
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1 /* $Id: gene_model_config.cpp 46313 2021-03-16 13:11:19Z shkeda $
2  * ===========================================================================
3  *
4  * PUBLIC DOMAIN NOTICE
5  * National Center for Biotechnology Information
6  *
7  * This software/database is a "United States Government Work" under the
8  * terms of the United States Copyright Act. It was written as part of
9  * the author's official duties as a United States Government employee and
10  * thus cannot be copyrighted. This software/database is freely available
11  * to the public for use. The National Library of Medicine and the U.S.
12  * Government have not placed any restriction on its use or reproduction.
13  *
14  * Although all reasonable efforts have been taken to ensure the accuracy
15  * and reliability of the software and data, the NLM and the U.S.
16  * Government do not and cannot warrant the performance or results that
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18  * Government disclaim all warranties, express or implied, including
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20  * purpose.
21  *
22  * Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Authors: Liangshou Wu
27  *
28  * File Description:
29  *
30  */
31 
32 #include <ncbi_pch.hpp>
33 
34 #include <gui/widgets/seq_graphic/gene_model_config.hpp>
35 #include <gui/widgets/seq_graphic/seqgraphic_conf.hpp>
36 #include <gui/widgets/seq_graphic/layout_group.hpp>
37 #include <gui/objutils/registry.hpp>
38 
39 
40 BEGIN_NCBI_SCOPE
41 USING_SCOPE(objects);
42 
43 
44 ///////////////////////////////////////////////////////////////////////////////
45 /// CGeneModelConfig implementation
46 ///
47 
48 static const char* const kDefProfile = "Default";
49 static const char* const kCDSKey = "GBPlugins.SeqGraphicGeneModelCDS";
50 
51 typedef SStaticPair<const char*, CGeneModelConfig::EMergeStyle> TStyleStr;
52 static const TStyleStr s_StyleStrs[] = {
53  { "Merge all", CGeneModelConfig::eMerge_All },
54  { "Merge pairs", CGeneModelConfig::eMerge_Pairs },
55  { "No merge", CGeneModelConfig::eMerge_No },
56  { "Single line", CGeneModelConfig::eMerge_OneLine },
57 };
58 
59 
60 typedef CStaticArrayMap<string, CGeneModelConfig::EMergeStyle> TStyleMap;
61 DEFINE_STATIC_ARRAY_MAP(TStyleMap, sm_StyleMap, s_StyleStrs);
62 
63 
64 CGeneModelConfig::EMergeStyle
65 CGeneModelConfig::StyleStrToValue(const string& style)
66 {
67  TStyleMap::const_iterator iter = sm_StyleMap.find(style);
68  if (iter != sm_StyleMap.end()) {
69  return iter->second;
70  }
71  NCBI_THROW(CException, eInvalid, "Invalid merge style string: " + style);
72 }
73 
74 
75 const string&
76 CGeneModelConfig::StyleValueToStr(CGeneModelConfig::EMergeStyle style)
77 {
78  TStyleMap::const_iterator iter;
79  for (iter = sm_StyleMap.begin(); iter != sm_StyleMap.end(); ++iter) {
80  if (iter->second == style) {
81  return iter->first;
82  }
83  }
84  return kEmptyStr;
85 }
86 
87 
88 typedef SStaticPair<const char*, CGeneModelConfig::ERenderingOption> TOptionStr;
89 static const TOptionStr s_OptionStrs[] = {
90  { "GeneOnly", CGeneModelConfig::eOption_GeneOnly },
91  { "MergeAll", CGeneModelConfig::eOption_MergeAll },
92  { "MergePairs", CGeneModelConfig::eOption_MergePairs },
93  { "ShowAll", CGeneModelConfig::eOption_ShowAll },
94  { "ShowAllButGenes", CGeneModelConfig::eOption_ShowAllButGenes },
95  { "SingleLine", CGeneModelConfig::eOption_SingleLine },
96 };
97 
98 
99 typedef CStaticArrayMap<string, CGeneModelConfig::ERenderingOption> TOptionMap;
100 DEFINE_STATIC_ARRAY_MAP(TOptionMap, sm_OptionMap, s_OptionStrs);
101 
102 
103 const string& CGeneModelConfig::OptionValueToStr(CGeneModelConfig::ERenderingOption option)
104 {
105  TOptionMap::const_iterator iter;
106  for (iter = sm_OptionMap.begin(); iter != sm_OptionMap.end(); ++iter) {
107  if (iter->second == option) {
108  return iter->first;
109  }
110  }
111  return kEmptyStr;
112 }
113 
114 
115 CGeneModelConfig::ERenderingOption CGeneModelConfig::OptionStrToValue(const string& option)
116 {
117  TOptionMap::const_iterator iter = sm_OptionMap.find(option);
118  if (iter != sm_OptionMap.end()) {
119  return iter->second;
120  }
121  NCBI_THROW(CException, eInvalid, "Invalid rendeirng option string: " + option);
122 }
123 
124 
125 void CGeneModelConfig::LoadSettings(CConstRef<CSeqGraphicConfig> g_conf,
126  const string& reg_path,
127  const string& profile)
128 {
129  if ( !m_CdsConfig ) {
130  m_CdsConfig.Reset(new CCdsConfig);
131  }
132 
133  if ( !m_GeneBoxConfig ) {
134  m_GeneBoxConfig.Reset(new CBoundaryParams(
135  true, false, CRgbaColor(0.0, 0.6f, 0.0f, 0.1f),
136  CRgbaColor(0.6f, 0.8f, 0.3f, 0.3f), 1.0));
137  }
138 
139  CGuiRegistry& registry = CGuiRegistry::GetInstance();
140  CRegistryReadView view =
141  CSGConfigUtils::GetReadView(registry, reg_path, profile, kDefProfile);
142  m_MergeStyle =
143  StyleStrToValue(view.GetString("CdsRnaMergeStyle", "No merge"));
144  m_ShowLMGeneLabel = view.GetBool("LandmarkGeneLabel", true);
145  m_LandmarkFeatLimit = view.GetInt("LandmarkFeatLimit", 199);
146  m_OverviewFeatCutoff = view.GetInt("OverviewFeatCutoff", 30);
147 
148  // load content settings
149  m_ShowGenes = view.GetBool("Genes", true);
150  m_ShowRNAs = view.GetBool("RNAs", true);
151  m_ShowCDSs = view.GetBool("CDSs", true);
152  m_ShowExons = view.GetBool("Exons", true);
153  m_ShowVDJCs = view.GetBool("VDJCs", true);
154  m_ShowGeneProducts = view.GetBool("GeneProdcuts", true);
155  m_ShowCDSProductFeats = view.GetBool("CDSProductFeats", false);
156  m_ShowNtRuler = view.GetBool("NtRuler", true);
157  m_ShowAaRuler = view.GetBool("AaRuler", true);
158  m_ShowHistogram = view.GetBool("Histogram", true);
159  m_CDSProfile = view.GetString("CDSProfile", kDefProfile);
160  m_HighlightMode = view.GetInt("HighlightMode", 0);
161  m_ShowLabel = view.GetBool("ShowLabel", true);
162 
163  m_HideNonCoding = view.GetBool("HideNonCoding", false);
164  m_HideModels = view.GetBool("HideModels", false);
165  m_CCDSOnly = view.GetBool("CCDSOnly", false);
166  m_SelectOnly = view.GetBool("SelectOnly", false);
167 
168  // load color settings
169  view = CSGConfigUtils::GetColorReadView(
170  registry, kCDSKey, m_CDSProfile, g_conf->GetColorTheme(), kDefProfile);
171  CSGConfigUtils::GetColor(view, "BGProtProduct", m_CdsConfig->m_bgProtProd);
172  CSGConfigUtils::GetColor(view, "FGProtProduct", m_CdsConfig->m_fgProtProd);
173  CSGConfigUtils::GetColor(view, "LabelProtProduct", m_CdsConfig->m_LabelProtProd);
174  CSGConfigUtils::GetColor(view, "SeqProtOriginal", m_CdsConfig->m_SeqProt);
175  CSGConfigUtils::GetColor(view, "SeqProtMismatch", m_CdsConfig->m_SeqProtMismatch);
176  CSGConfigUtils::GetColor(view, "SeqProtTranslated", m_CdsConfig->m_SeqProtTrans);
177 
178  // load size settings
179  view = CSGConfigUtils::GetSizeReadView(
180  registry, kCDSKey, m_CDSProfile, g_conf->GetSizeLevel(), kDefProfile);
181 
182  CSGConfigUtils::GetFont(view, "ProdFontFace", "ProdFontSize", m_CdsConfig->m_ProdFont);
183  CSGConfigUtils::GetFont(view, "TransFontFace", "TransFontSize", m_CdsConfig->m_TransFont);
184 }
185 
186 
187 void CGeneModelConfig::LoadSettingsPartial(
188  const string& reg_path,
189  const string& profile)
190 {
191 // if ( !m_CdsConfig ) {
192 // m_CdsConfig.Reset(new CCdsConfig);
193 // }
194 
195  if ( !m_GeneBoxConfig ) {
196  m_GeneBoxConfig.Reset(new CBoundaryParams(
197  true, false, CRgbaColor(0.0, 0.6f, 0.0f, 0.1f),
198  CRgbaColor(0.6f, 0.8f, 0.3f, 0.3f), 1.0));
199  }
200 
201  CGuiRegistry& registry = CGuiRegistry::GetInstance();
202  CRegistryReadView view =
203  CSGConfigUtils::GetReadView(registry, reg_path, profile, kDefProfile);
204  m_MergeStyle =
205  StyleStrToValue(view.GetString("CdsRnaMergeStyle", "No merge"));
206  m_ShowLMGeneLabel = view.GetBool("LandmarkGeneLabel", true);
207  m_LandmarkFeatLimit = view.GetInt("LandmarkFeatLimit", 199);
208  m_OverviewFeatCutoff = view.GetInt("OverviewFeatCutoff", 30);
209 
210  // load content settings
211  m_ShowGenes = view.GetBool("Genes", true);
212  m_ShowRNAs = view.GetBool("RNAs", true);
213  m_ShowCDSs = view.GetBool("CDSs", true);
214  m_ShowExons = view.GetBool("Exons", true);
215  m_ShowVDJCs = view.GetBool("VDJCs", true);
216  m_ShowGeneProducts = view.GetBool("GeneProdcuts", true);
217  m_ShowCDSProductFeats = view.GetBool("CDSProductFeats", false);
218 // m_ShowNtRuler = view.GetBool("NtRuler", true);
219 // m_ShowAaRuler = view.GetBool("AaRuler", true);
220  m_ShowNtRuler = true;
221  m_ShowAaRuler = true;
222  m_ShowHistogram = view.GetBool("Histogram", true);
223  m_CDSProfile = view.GetString("CDSProfile", kDefProfile);
224  m_HighlightMode = view.GetInt("HighlightMode", 0);
225  m_HideNonCoding = view.GetBool("HideNonCoding", false);
226  m_HideModels = view.GetBool("HideModels", false);
227  m_CCDSOnly = view.GetBool("CCDSOnly", false);
228  m_SelectOnly = view.GetBool("SelectOnly", false);
229 
230 }
231 
232 
233 void CGeneModelConfig::SaveSettings(CConstRef<CSeqGraphicConfig> g_conf,
234  const string& reg_path,
235  const string& profile) const
236 {
237  CGuiRegistry& registry = CGuiRegistry::GetInstance();
238  CRegistryWriteView view =
239  CSGConfigUtils::GetWriteView(registry, reg_path, profile, kDefProfile);
240  view.Set("CdsRnaMergeStyle", StyleValueToStr(m_MergeStyle));
241  view.Set("LandmarkGeneLabel", m_ShowLMGeneLabel);
242  view.Set("LandmarkFeatLimit", m_LandmarkFeatLimit);
243  view.Set("OverviewFeatCutoff", m_OverviewFeatCutoff);
244 
245  // save content settings
246  view.Set("Genes", m_ShowGenes);
247  view.Set("RNAs", m_ShowRNAs);
248  view.Set("CDSs", m_ShowCDSs);
249  view.Set("Exons", m_ShowExons);
250  view.Set("VDJCs", m_ShowVDJCs);
251  view.Set("GeneProdcuts", m_ShowGeneProducts);
252  view.Set("CDSProductFeats", m_ShowCDSProductFeats);
253  view.Set("NtRuler", m_ShowNtRuler);
254  view.Set("AaRuler", m_ShowAaRuler);
255  view.Set("Histogram", m_ShowHistogram);
256  view.Set("CDSProfile", m_CDSProfile);
257  view.Set("HighlightMode", m_HighlightMode);
258  view.Set("HideNonCoding", m_HideNonCoding);
259  view.Set("HideModels", m_HideModels);
260  view.Set("CCDSOnly", m_CCDSOnly);
261  view.Set("SelectOnly", m_SelectOnly);
262 
263  if (m_CdsConfig->m_Dirty) {
264  // save color settings
265  view = CSGConfigUtils::GetColorRWView(
266  registry, kCDSKey, m_CDSProfile, g_conf->GetColorTheme(), kDefProfile);
267  CSGConfigUtils::SetColor(view, "BGProtProduct", m_CdsConfig->m_bgProtProd);
268  CSGConfigUtils::SetColor(view, "FGProtProduct", m_CdsConfig->m_fgProtProd);
269  CSGConfigUtils::SetColor(view, "LabelProtProduct", m_CdsConfig->m_LabelProtProd);
270  CSGConfigUtils::SetColor(view, "SeqProtOriginal", m_CdsConfig->m_SeqProt);
271  CSGConfigUtils::SetColor(view, "SeqProtMismatch", m_CdsConfig->m_SeqProtMismatch);
272  CSGConfigUtils::SetColor(view, "SeqProtTrans", m_CdsConfig->m_SeqProtTrans);
273 
274  // save size settings
275  view = CSGConfigUtils::GetSizeRWView(
276  registry, kCDSKey, m_CDSProfile, g_conf->GetSizeLevel(), kDefProfile);
277  CSGConfigUtils::SetFont(view, "ProdFontFace", "ProdFontSize", m_CdsConfig->m_ProdFont);
278  CSGConfigUtils::SetFont(view, "TransFontFace", "TransFontSize", m_CdsConfig->m_TransFont);
279  }
280 }
281 
282 void CGeneModelConfig::UpdateSettings(const CSGConfigUtils::TKeyValuePairs& settings)
283 {
284  // override those default settings passed in through profile settings
285  ITERATE (CSGConfigUtils::TKeyValuePairs, iter, settings) {
286  try {
287  if (NStr::EqualNocase(iter->first, "Merge"))
288  m_MergeStyle = StyleStrToValue(iter->second);
289  else if (NStr::EqualNocase(iter->first, "LandmarkGeneLabel"))
290  m_ShowLMGeneLabel = NStr::StringToBool(iter->second);
291  else if (NStr::EqualNocase(iter->first, "Genes"))
292  m_ShowGenes = NStr::StringToBool(iter->second);
293  else if (NStr::EqualNocase(iter->first, "RNAs"))
294  m_ShowRNAs = NStr::StringToBool(iter->second);
295  else if (NStr::EqualNocase(iter->first, "CDSs"))
296  m_ShowCDSs = NStr::StringToBool(iter->second);
297  else if (NStr::EqualNocase(iter->first, "Exons"))
298  m_ShowExons = NStr::StringToBool(iter->second);
299  else if (NStr::EqualNocase(iter->first, "VDJCs"))
300  m_ShowVDJCs = NStr::StringToBool(iter->second);
301  else if (NStr::EqualNocase(iter->first, "CDSProductFeats"))
302  m_ShowCDSProductFeats = NStr::StringToBool(iter->second);
303  else if (NStr::EqualNocase(iter->first, "NtRuler"))
304  // m_ShowNtRuler = NStr::StringToBool(iter->second);
305  ; // suppress the warning
306  else if (NStr::EqualNocase(iter->first, "AaRuler"))
307  /// m_ShowAaRuler = NStr::StringToBool(iter->second);
308  ; // suppress the warning
309  else if (NStr::EqualNocase(iter->first, "Histogram"))
310  m_ShowHistogram = NStr::StringToBool(iter->second);
311  else if (NStr::EqualNocase(iter->first, "HighlightMode"))
312  m_HighlightMode = NStr::StringToInt(iter->second);
313  else if (NStr::EqualNocase(iter->first, "ShowLabel"))
314  m_ShowLabel = NStr::StringToBool(iter->second);
315  else if (NStr::EqualNocase(iter->first, "HideNonCoding"))
316  m_HideNonCoding = NStr::StringToBool(iter->second);
317  else if (NStr::EqualNocase(iter->first, "HideModels"))
318  m_HideModels = NStr::StringToBool(iter->second);
319  else if (NStr::EqualNocase(iter->first, "CCDSOnly"))
320  m_CCDSOnly = NStr::StringToBool(iter->second);
321  else if (NStr::EqualNocase(iter->first, "SelectOnly"))
322  m_SelectOnly = NStr::StringToBool(iter->second);
323  else if (NStr::EqualNocase(iter->first, "Options")) {
324  ERenderingOption option = OptionStrToValue(iter->second);
325  switch (option) {
326  case eOption_GeneOnly:
327  m_ShowGenes = true;
328  m_ShowRNAs = false;
329  m_ShowCDSs = false;
330  m_ShowExons = false;
331  m_ShowVDJCs = false;
332  break;
333  case eOption_MergeAll:
334  m_ShowGenes = false;
335  m_ShowRNAs = true;
336  m_ShowCDSs = true;
337  m_ShowExons = true;
338  m_ShowVDJCs = true;
339  m_MergeStyle = eMerge_All;
340  break;
341  case eOption_MergePairs:
342  m_ShowGenes = false;
343  m_ShowRNAs = true;
344  m_ShowCDSs = true;
345  m_ShowExons = true;
346  m_ShowVDJCs = true;
347  m_MergeStyle = eMerge_Pairs;
348  break;
349  case eOption_ShowAllButGenes:
350  m_ShowGenes = false;
351  m_ShowRNAs = true;
352  m_ShowCDSs = true;
353  m_ShowExons = true;
354  m_ShowVDJCs = true;
355  m_MergeStyle = eMerge_No;
356  break;
357  case eOption_ShowAll:
358  m_ShowGenes = true;
359  m_ShowRNAs = true;
360  m_ShowCDSs = true;
361  m_ShowExons = true;
362  m_ShowVDJCs = true;
363  m_MergeStyle = eMerge_No;
364  break;
365  case eOption_SingleLine:
366  m_ShowGenes = false;
367  m_ShowRNAs = true;
368  m_ShowCDSs = true;
369  m_ShowExons = true;
370  m_ShowVDJCs = true;
371  m_MergeStyle = eMerge_OneLine;
372  break;
373  default:
374  break;
375  }
376  } else
377  LOG_POST(Warning << "CGeneModelConfig::UpdateSettings() "
378  << "the setting is not supported: "
379  << iter->first << ":" << iter->second);
380  } catch (CException&) {
381  LOG_POST(Warning << "CGeneModelConfig::UpdateSettings() invalid setting - "
382  << iter->first << ":" << iter->second);
383  }
384  }
385 }
386 
387 
388 string CGeneModelConfig::SaveSettingsAsString(const string& preset_style) const
389 {
390  CSGConfigUtils::TKeyValuePairs settings;
391 
392  if ( !preset_style.empty() ) {
393  settings["profile"] = preset_style;
394  }
395 
396  settings["Merge"] = StyleValueToStr(m_MergeStyle);
397  settings["LandmarkGeneLabel"] = NStr::BoolToString(m_ShowLMGeneLabel);
398  settings["Genes"] = NStr::BoolToString(m_ShowGenes);
399  settings["RNAs"] = NStr::BoolToString(m_ShowRNAs);
400  settings["CDSs"] = NStr::BoolToString(m_ShowCDSs);
401  settings["Exons"] = NStr::BoolToString(m_ShowExons);
402  settings["VDJCs"] = NStr::BoolToString(m_ShowVDJCs);
403  settings["CDSProductFeats"] = NStr::BoolToString(m_ShowCDSProductFeats);
404  settings["NtRuler"] = NStr::BoolToString(m_ShowNtRuler);
405  settings["AaRuler"] = NStr::BoolToString(m_ShowAaRuler);
406 
407  settings["Histogram"] = NStr::BoolToString(m_ShowHistogram);
408 
409  settings["HideNonCoding"] = NStr::BoolToString(m_HideNonCoding);
410  settings["HideModels"] = NStr::BoolToString(m_HideModels);
411  settings["CCDSOnly"] = NStr::BoolToString(m_CCDSOnly);
412  settings["SelectOnly"] = NStr::BoolToString(m_SelectOnly);
413 
414  return CSGConfigUtils::ComposeProfileString(settings);
415 }
416 
417 
418 END_NCBI_SCOPE
CBoundaryParams
IBoundaryParams.
Definition: layout_group.hpp:199
CCdsConfig::m_SeqProtMismatch
CRgbaColor m_SeqProtMismatch
mismatched sequence color.
Definition: cds_glyph.hpp:85
CCdsConfig::m_Dirty
bool m_Dirty
dirty flag indicating any setting changed
Definition: cds_glyph.hpp:95
CCdsConfig::m_ProdFont
CGlTextureFont m_ProdFont
Definition: cds_glyph.hpp:91
CCdsConfig::m_LabelProtProd
CRgbaColor m_LabelProtProd
protein product label color.
Definition: cds_glyph.hpp:83
CCdsConfig::m_SeqProtTrans
CRgbaColor m_SeqProtTrans
translated sequence color.
Definition: cds_glyph.hpp:86
CCdsConfig::m_fgProtProd
CRgbaColor m_fgProtProd
protein product frorground color.
Definition: cds_glyph.hpp:82
CCdsConfig::m_SeqProt
CRgbaColor m_SeqProt
sequence color.
Definition: cds_glyph.hpp:84
CCdsConfig::m_bgProtProd
CRgbaColor m_bgProtProd
protein product background color.
Definition: cds_glyph.hpp:81
CCdsConfig::m_TransFont
CGlTextureFont m_TransFont
Definition: cds_glyph.hpp:92
CGeneModelConfig::m_CCDSOnly
bool m_CCDSOnly
Show only CCDS variants.
Definition: gene_model_config.hpp:137
CGeneModelConfig::m_ShowCDSProductFeats
bool m_ShowCDSProductFeats
CDS associated protein features.
Definition: gene_model_config.hpp:122
CGeneModelConfig::m_ShowGeneProducts
bool m_ShowGeneProducts
feature histogram on a gene.
Definition: gene_model_config.hpp:121
CGeneModelConfig::m_ShowNtRuler
bool m_ShowNtRuler
Show nucleotide ruler.
Definition: gene_model_config.hpp:123
CGeneModelConfig::m_MergeStyle
EMergeStyle m_MergeStyle
the way on how to merge CDSs and RNAs.
Definition: gene_model_config.hpp:128
CGeneModelConfig::OptionStrToValue
static ERenderingOption OptionStrToValue(const string &option)
Definition: gene_model_config.cpp:115
CGeneModelConfig::OptionValueToStr
static const string & OptionValueToStr(CGeneModelConfig::ERenderingOption option)
Definition: gene_model_config.cpp:103
CGeneModelConfig::StyleStrToValue
static EMergeStyle StyleStrToValue(const string &style)
Definition: gene_model_config.cpp:65
CGeneModelConfig::m_ShowAaRuler
bool m_ShowAaRuler
Show protein ruler.
Definition: gene_model_config.hpp:124
CGeneModelConfig::m_SelectOnly
bool m_SelectOnly
Show only Select/MANE variants.
Definition: gene_model_config.hpp:138
CGeneModelConfig::SaveSettings
void SaveSettings(CConstRef< CSeqGraphicConfig > g_conf, const string &reg_path, const string &profile) const
Definition: gene_model_config.cpp:233
CGeneModelConfig::UpdateSettings
void UpdateSettings(const CSGConfigUtils::TKeyValuePairs &settings)
Definition: gene_model_config.cpp:282
CGeneModelConfig::m_HideNonCoding
bool m_HideNonCoding
Hide transcripts without associated CDS.
Definition: gene_model_config.hpp:135
CGeneModelConfig::LoadSettingsPartial
void LoadSettingsPartial(const string &reg_path, const string &profile)
Definition: gene_model_config.cpp:187
CGeneModelConfig::LoadSettings
void LoadSettings(CConstRef< CSeqGraphicConfig > g_conf, const string &reg_path, const string &profile)
Definition: gene_model_config.cpp:125
CGeneModelConfig::m_ShowVDJCs
bool m_ShowVDJCs
show VDJ_segments and C_region
Definition: gene_model_config.hpp:120
CGeneModelConfig::m_GeneBoxConfig
CRef< CBoundaryParams > m_GeneBoxConfig
Definition: gene_model_config.hpp:141
CGeneModelConfig::m_ShowHistogram
bool m_ShowHistogram
show gene distribution histogram.
Definition: gene_model_config.hpp:125
CGeneModelConfig::ERenderingOption
ERenderingOption
rendering options on how to render features overall.
Definition: gene_model_config.hpp:69
CGeneModelConfig::eOption_SingleLine
@ eOption_SingleLine
merge all RNAs and CDSs into one line
Definition: gene_model_config.hpp:75
CGeneModelConfig::eOption_MergeAll
@ eOption_MergeAll
merge all RNAs and CDSs, show exons, no gene bar
Definition: gene_model_config.hpp:71
CGeneModelConfig::eOption_ShowAll
@ eOption_ShowAll
show all features individually
Definition: gene_model_config.hpp:74
CGeneModelConfig::eOption_MergePairs
@ eOption_MergePairs
merge each RNA and CDS pair, show exons, no gene bar
Definition: gene_model_config.hpp:72
CGeneModelConfig::eOption_ShowAllButGenes
@ eOption_ShowAllButGenes
show all RNAs, CDSs and exons, no gene bar
Definition: gene_model_config.hpp:73
CGeneModelConfig::eOption_GeneOnly
@ eOption_GeneOnly
show gene bar only
Definition: gene_model_config.hpp:70
CGeneModelConfig::SaveSettingsAsString
string SaveSettingsAsString(const string &preset_style) const
Definition: gene_model_config.cpp:388
CGeneModelConfig::m_CDSProfile
string m_CDSProfile
cds setting profile
Definition: gene_model_config.hpp:127
CGeneModelConfig::StyleValueToStr
static const string & StyleValueToStr(CGeneModelConfig::EMergeStyle style)
Definition: gene_model_config.cpp:76
CGeneModelConfig::m_CdsConfig
CRef< CCdsConfig > m_CdsConfig
Definition: gene_model_config.hpp:140
CGeneModelConfig::EMergeStyle
EMergeStyle
style on how to merge RNAs and CDSs.
Definition: gene_model_config.hpp:50
CGeneModelConfig::eMerge_OneLine
@ eMerge_OneLine
merge into one line
Definition: gene_model_config.hpp:54
CGeneModelConfig::eMerge_Pairs
@ eMerge_Pairs
merge each transcript and CDS pair
Definition: gene_model_config.hpp:52
CGeneModelConfig::eMerge_All
@ eMerge_All
merge all transcripts and CDSs
Definition: gene_model_config.hpp:53
CGeneModelConfig::eMerge_No
@ eMerge_No
show all feature individually
Definition: gene_model_config.hpp:51
CGeneModelConfig::m_ShowLMGeneLabel
bool m_ShowLMGeneLabel
landmark gene labels.
Definition: gene_model_config.hpp:115
CGeneModelConfig::m_HideModels
bool m_HideModels
Hide Model RefSeqs.
Definition: gene_model_config.hpp:136
CGeneModelConfig::m_ShowLabel
bool m_ShowLabel
Show labels.
Definition: gene_model_config.hpp:126
CGuiRegistry::GetInstance
static CGuiRegistry & GetInstance()
access the application-wide singleton
Definition: registry.cpp:400
CRegistryReadView
class CRegistryReadView provides a nested hierarchical view at a particular key.
Definition: reg_view.hpp:58
CRegistryReadView::GetInt
int GetInt(const string &key, int default_val=0) const
access a named key at this level, with no recursion
Definition: reg_view.cpp:230
CRegistryReadView::GetBool
bool GetBool(const string &key, bool default_val=false) const
Definition: reg_view.cpp:241
CRegistryReadView::GetString
string GetString(const string &key, const string &default_val=kEmptyStr) const
Definition: reg_view.cpp:246
CRegistryWriteView::Set
void Set(const string &key, int val)
access a named key at this level, with no recursion
Definition: reg_view.cpp:533
CRgbaColor
class CRgbaColor provides a simple abstraction for managing colors.
Definition: rgba_color.hpp:58
CSGConfigUtils::GetSizeReadView
static CRegistryReadView GetSizeReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")
Definition: config_utils.hpp:218
CSGConfigUtils::GetFont
static void GetFont(const CRegistryReadView &view, const string &face_key, const string &size_key, CGlTextureFont &f)
Definition: config_utils.cpp:121
CSGConfigUtils::ComposeProfileString
static string ComposeProfileString(const TKeyValuePairs &settings)
Definition: config_utils.cpp:102
CSGConfigUtils::GetColorReadView
static CRegistryReadView GetColorReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")
Create a read view specifically for 'Color' section.
Definition: config_utils.hpp:192
CSGConfigUtils::GetReadView
static CRegistryReadView GetReadView(const CGuiRegistry &reg, 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.
Definition: config_utils.cpp:43
CSGConfigUtils::GetWriteView
static CRegistryWriteView GetWriteView(CGuiRegistry &reg, const string &base_key, const string &curr_key, const string &def_key1="", const string &def_key2="", const string &def_key3="")
Definition: config_utils.cpp:65
CSGConfigUtils::GetColorRWView
static CRegistryWriteView GetColorRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")
Definition: config_utils.hpp:205
CSGConfigUtils::GetSizeRWView
static CRegistryWriteView GetSizeRWView(CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")
Definition: config_utils.hpp:231
CSGConfigUtils::SetColor
static void SetColor(CRegistryWriteView &view, const string &key, const CRgbaColor &color)
Definition: config_utils.hpp:317
CSGConfigUtils::GetColor
static void GetColor(const CRegistryReadView &view, const string &key, CRgbaColor &color)
Definition: config_utils.hpp:307
CSGConfigUtils::SetFont
static void SetFont(CRegistryWriteView &view, const string &face_key, const string &size_key, const CGlTextureFont &f)
Definition: config_utils.cpp:134
CSeqGraphicConfig::GetSizeLevel
const string & GetSizeLevel() const
Definition: seqgraphic_conf.hpp:441
CSeqGraphicConfig::GetColorTheme
const string & GetColorTheme() const
Definition: seqgraphic_conf.hpp:429
CStaticArrayMap
class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...
Definition: static_map.hpp:175
CStaticArrayMap::const_iterator
TBase::const_iterator const_iterator
Definition: static_map.hpp:179
registry
static CMemoryRegistry registry
Definition: cn3d_tools.cpp:81
option
#define option
USING_SCOPE
USING_SCOPE(objects)
TStyleMap
CStaticArrayMap< string, CGeneModelConfig::EMergeStyle > TStyleMap
Definition: gene_model_config.cpp:60
TOptionMap
CStaticArrayMap< string, CGeneModelConfig::ERenderingOption > TOptionMap
Definition: gene_model_config.cpp:99
TStyleStr
SStaticPair< const char *, CGeneModelConfig::EMergeStyle > TStyleStr
Definition: gene_model_config.cpp:51
kDefProfile
static const char *const kDefProfile
CGeneModelConfig implementation.
Definition: gene_model_config.cpp:48
s_OptionStrs
static const TOptionStr s_OptionStrs[]
Definition: gene_model_config.cpp:89
TOptionStr
SStaticPair< const char *, CGeneModelConfig::ERenderingOption > TOptionStr
Definition: gene_model_config.cpp:88
s_StyleStrs
static const TStyleStr s_StyleStrs[]
Definition: gene_model_config.cpp:52
kCDSKey
static const char *const kCDSKey
Definition: gene_model_config.cpp:49
DEFINE_STATIC_ARRAY_MAP
DEFINE_STATIC_ARRAY_MAP(TStyleMap, sm_StyleMap, s_StyleStrs)
gene_model_config.hpp
ITERATE
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
Definition: ncbimisc.hpp:815
LOG_POST
#define LOG_POST(message)
This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...
Definition: ncbidiag.hpp:226
NCBI_THROW
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
Definition: ncbiexpt.hpp:704
Warning
void Warning(CExceptionArgs_Base &args)
Definition: ncbiexpt.hpp:1191
CRef::Reset
void Reset(void)
Reset reference object.
Definition: ncbiobj.hpp:773
END_NCBI_SCOPE
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
BEGIN_NCBI_SCOPE
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
NStr::StringToBool
static bool StringToBool(const CTempString str)
Convert string to bool.
Definition: ncbistr.cpp:2819
kEmptyStr
#define kEmptyStr
Definition: ncbistr.hpp:123
NStr::StringToInt
static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)
Convert string to int.
Definition: ncbistr.cpp:630
NStr::BoolToString
static const string BoolToString(bool value)
Convert bool to string.
Definition: ncbistr.cpp:2813
NStr::EqualNocase
static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)
Case-insensitive equality of a substring with another string.
Definition: ncbistr.hpp:5352
layout_group.hpp
ncbi_pch.hpp
seqgraphic_conf.hpp
SStaticPair
Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...
Definition: static_set.hpp:60
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