NCBI C++ ToolKit
editing_action_features.hpp
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1 /* $Id: editing_action_features.hpp 45436 2020-08-03 17:23:15Z asztalos $
2  * ===========================================================================
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5  * National Center for Biotechnology Information
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8  * terms of the United States Copyright Act. It was written as part of
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15  * and reliability of the software and data, the NLM and the U.S.
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22  * Please cite the author in any work or product based on this material.
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26  * Authors: Igor Filippov
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28 
29 #ifndef _EDITING_ACTION_FEATURES_H_
30 #define _EDITING_ACTION_FEATURES_H_
31 
32 #include <corelib/ncbistd.hpp>
44 
47 
49 
51 {
52 public:
54  const CSeqFeatData::ESubtype subtype,
55  const CSeqFeatData::E_Choice feat_type,
56  const string& ncRNA_class,
57  const string& name);
58 
59  virtual void SetFeat(CSeq_feat_Handle fh);
63 
64  // use these two functions together
65  static bool s_IsSetncRNAClass(const objects::CRNA_ref& rna_ref);
66  static const string& s_GetncRNAClass(const objects::CRNA_ref& rna_ref);
67 protected:
68  virtual void Find(EActionType action);
69  virtual void FindRelated(EActionType action);
70  virtual void Modify(EActionType action);
71  virtual void SwapContext(IEditingAction* source);
72  virtual bool SameObject();
73  bool OtherFeatIs(const CSeqFeatData::ESubtype subtype);
74  void FindFeatForAnotherFeat(EActionType action, SAnnotSelector other_selector);
75  void FindRelatedFeatForAnotherFeat(EActionType action, SAnnotSelector other_selector); // TODO - same as FindRelated ?
76  void FindOrCreateProtFeat(EActionType action);
78  void GoToProtFeature(void);
79  void GoToOrigFeature(void);
80 
81  bool x_TestGeneForFeature(const CSeq_loc& gene_loc, const CSeq_loc& feat_loc, CScope& scope, bool& exact, TSeqPos& diff);
84 
85  void RemoveGeneXref(void);
89 
90  virtual void ResetScope();
93  string m_ncRNAclass;
96 
100 };
101 
103 {
104 public:
106  const CSeqFeatData::ESubtype subtype,
107  const CSeqFeatData::E_Choice feat_type,
108  const string& ncRNA_class);
109 protected:
110  virtual bool IsSetValue(void);
111  virtual void SetValue(const string &value);
112  virtual string GetValue(void);
113  virtual void ResetValue(void);
114 };
115 
117 {
118 public:
120  const CSeqFeatData::ESubtype subtype,
121  const CSeqFeatData::E_Choice feat_type,
122  const string& ncRNA_class);
123 protected:
124  virtual bool IsSetValue(void);
125  virtual void SetValue(const string &value);
126  virtual string GetValue(void);
127  virtual void ResetValue(void);
128 };
129 
131 {
132 public:
134  const CSeqFeatData::ESubtype subtype,
135  const CSeqFeatData::E_Choice feat_type,
136  const string& ncRNA_class,
137  const string &qual, const string &name = "CEditingActionFeatGbQual");
138 protected:
139  virtual void Modify(EActionType action);
140  virtual bool IsSetValue(void);
141  virtual void SetValue(const string &value);
142  virtual string GetValue(void);
143  virtual void ResetValue(void);
144 protected:
145  string m_qual;
147  bool m_erase;
148 };
149 
151 {
152 public:
154  const CSeqFeatData::ESubtype subtype,
155  const CSeqFeatData::E_Choice feat_type,
156  const string& ncRNA_class,
157  const string &qual1, const string &qual2);
158 protected:
159  virtual void Modify(EActionType action);
160  string m_qual2;
161 };
162 
163 
165 {
166 public:
168  const CSeqFeatData::ESubtype subtype,
169  const CSeqFeatData::E_Choice feat_type,
170  const string& ncRNA_class,
171  const string &qual);
172 protected:
173  virtual bool IsSetValue(void);
174  virtual void SetValue(const string &value);
175  virtual string GetValue(void);
176  virtual void ResetValue(void);
177 };
178 
180 {
181 public:
183  const CSeqFeatData::ESubtype subtype,
184  const CSeqFeatData::E_Choice feat_type,
185  const string& ncRNA_class,
186  const string &qual);
187 protected:
188  virtual bool IsSetValue(void);
189  virtual void SetValue(const string &value);
190  virtual string GetValue(void);
191  virtual void ResetValue(void);
192 };
193 
195 {
196 public:
198  const CSeqFeatData::ESubtype subtype,
199  const CSeqFeatData::E_Choice feat_type,
200  const string& ncRNA_class);
201 protected:
202  virtual void Modify(EActionType action);
203  virtual bool IsSetValue(void);
204  virtual void SetValue(const string &value);
205  virtual string GetValue(void);
206  virtual void ResetValue(void);
207 private:
209  bool m_erase;
210 };
211 
213 {
214 public:
216  const CSeqFeatData::ESubtype subtype,
217  const CSeqFeatData::E_Choice feat_type,
218  const string& ncRNA_class);
219 protected:
220  virtual bool IsSetValue(void);
221  virtual void SetValue(const string &value);
222  virtual string GetValue(void);
223  virtual void ResetValue(void);
224 };
225 
227 {
228 public:
230  const CSeqFeatData::ESubtype subtype,
231  const CSeqFeatData::E_Choice feat_type,
232  const string& ncRNA_class);
233 protected:
234  virtual bool IsSetValue(void);
235  virtual void SetValue(const string &value);
236  virtual string GetValue(void);
237  virtual void ResetValue(void);
238 };
239 
241 {
242 public:
244  const CSeqFeatData::ESubtype subtype,
245  const CSeqFeatData::E_Choice feat_type,
246  const string& ncRNA_class);
247 protected:
248  virtual bool IsSetValue(void);
249  virtual void SetValue(const string &value);
250  virtual string GetValue(void);
251  virtual void ResetValue(void);
252 };
253 
255 {
256 public:
258  const CSeqFeatData::ESubtype subtype,
259  const CSeqFeatData::E_Choice feat_type,
260  const string& ncRNA_class);
261 protected:
262  virtual bool IsSetValue(void);
263  virtual void SetValue(const string &value);
264  virtual string GetValue(void);
265  virtual void ResetValue(void);
266 private:
267  string GetIntervalString(const CSeq_interval& seq_int);
268 };
269 
271 {
272 public:
274  const CSeqFeatData::ESubtype subtype,
275  const CSeqFeatData::E_Choice feat_type,
276  const string& ncRNA_class);
277 protected:
278  virtual void Modify(EActionType action);
279  virtual bool IsSetValue(void);
280  virtual void SetValue(const string &value);
281  virtual string GetValue(void);
282  virtual void ResetValue(void);
283 private:
285 };
286 
287 
289 {
290 public:
292  const CSeqFeatData::ESubtype subtype,
293  const CSeqFeatData::E_Choice feat_type,
294  const string& ncRNA_class, const string &qual);
295 protected:
296  virtual void Modify(EActionType action);
297  virtual bool IsSetValue(void);
298  virtual void SetValue(const string &value);
299  virtual string GetValue(void);
300  virtual void ResetValue(void);
301 private:
302  string m_qual;
305  bool m_erase;
306 };
307 
309 {
310 public:
312  const CSeqFeatData::ESubtype subtype,
313  const CSeqFeatData::E_Choice feat_type,
314  const string& ncRNA_class);
315 protected:
316  virtual bool IsSetValue(void);
317  virtual void SetValue(const string &value);
318  virtual string GetValue(void);
319  virtual void ResetValue(void);
320 };
321 
323 {
324 public:
326  const CSeqFeatData::ESubtype subtype,
327  const CSeqFeatData::E_Choice feat_type,
328  const string& ncRNA_class);
329 protected:
330  virtual bool IsSetValue(void);
331  virtual void SetValue(const string &value);
332  virtual string GetValue(void);
333  virtual void ResetValue(void);
334 };
335 
337 {
338 public:
340  const CSeqFeatData::ESubtype subtype,
341  const CSeqFeatData::E_Choice feat_type,
342  const string& ncRNA_class);
343 protected:
344  virtual bool IsSetValue(void);
345  virtual void SetValue(const string &value);
346  virtual string GetValue(void);
347  virtual void ResetValue(void);
348 private:
350 };
351 
353 {
354 public:
356  const CSeqFeatData::ESubtype subtype,
357  const CSeqFeatData::E_Choice feat_type,
358  const string& ncRNA_class);
359 protected:
360  virtual bool IsSetValue(void);
361  virtual void SetValue(const string &value);
362  virtual string GetValue(void);
363  virtual void ResetValue(void);
364 };
365 
367 {
368 public:
370  const CSeqFeatData::ESubtype subtype,
371  const CSeqFeatData::E_Choice feat_type,
372  const string& ncRNA_class);
373 protected:
374  virtual bool IsSetValue(void);
375  virtual void SetValue(const string &value);
376  virtual string GetValue(void);
377  virtual void ResetValue(void);
378 };
379 
381 {
382 public:
384  const CSeqFeatData::ESubtype subtype,
385  const CSeqFeatData::E_Choice feat_type,
386  const string& ncRNA_class);
387 protected:
388  virtual bool IsSetValue(void);
389  virtual void SetValue(const string &value);
390  virtual string GetValue(void);
391  virtual void ResetValue(void);
392 };
393 
395 {
396 public:
398  const CSeqFeatData::ESubtype subtype,
399  const CSeqFeatData::E_Choice feat_type,
400  const string& ncRNA_class);
401 protected:
402  virtual bool IsSetValue(void);
403  virtual void SetValue(const string &value);
404  virtual string GetValue(void);
405  virtual void ResetValue(void);
406 };
407 
409 {
410 public:
412  const CSeqFeatData::ESubtype subtype,
413  const CSeqFeatData::E_Choice feat_type,
414  const string& ncRNA_class);
415 protected:
416  virtual void Modify(EActionType action);
417  virtual bool IsSetValue(void);
418  virtual void SetValue(const string &value);
419  virtual string GetValue(void);
420  virtual void ResetValue(void);
421 private:
422  string *m_syn;
423  bool m_erase;
424  string m_qual;
426 };
427 
429 {
430 public:
432  const CSeqFeatData::ESubtype subtype,
433  const CSeqFeatData::E_Choice feat_type,
434  const string& ncRNA_class);
435 protected:
436  virtual bool IsSetValue(void);
437  virtual void SetValue(const string &value);
438  virtual string GetValue(void);
439  virtual void ResetValue(void);
440 };
441 
443 {
444 public:
446  const CSeqFeatData::ESubtype subtype,
447  const CSeqFeatData::E_Choice feat_type,
448  const string& ncRNA_class);
449 protected:
450  virtual void Modify(EActionType action);
451  virtual bool IsSetValue(void);
452  virtual void SetValue(const string &value);
453  virtual string GetValue(void);
454  virtual void ResetValue(void);
455 private:
456  string *m_activity;
457  bool m_erase;
458  string m_qual;
460 };
461 
463 {
464 public:
466  const CSeqFeatData::ESubtype subtype,
467  const CSeqFeatData::E_Choice feat_type,
468  const string& ncRNA_class);
469 protected:
470  virtual bool IsSetValue(void);
471  virtual void SetValue(const string &value);
472  virtual string GetValue(void);
473  virtual void ResetValue(void);
474 };
475 
477 {
478 public:
480  const CSeqFeatData::ESubtype subtype,
481  const CSeqFeatData::E_Choice feat_type,
482  const string& ncRNA_class);
483 protected:
484  virtual bool IsSetValue(void);
485  virtual void SetValue(const string &value);
486  virtual string GetValue(void);
487  virtual void ResetValue(void);
488 };
489 
491 {
492 public:
494  const CSeqFeatData::ESubtype subtype,
495  const CSeqFeatData::E_Choice feat_type,
496  const string& ncRNA_class);
497 protected:
498  virtual void Modify(EActionType action);
499  virtual bool IsSetValue(void);
500  virtual void SetValue(const string &value);
501  virtual string GetValue(void);
502  virtual void ResetValue(void);
503  virtual void Find(EActionType action);
504  virtual void FindRelated(EActionType action);
505 private:
506  string *m_ec;
507  bool m_erase;
508  string m_qual;
510 };
511 
513 {
514 public:
516  const CSeqFeatData::ESubtype subtype,
517  const CSeqFeatData::E_Choice feat_type,
518  const string& ncRNA_class);
519 protected:
520  virtual void Modify(EActionType action);
521  virtual bool IsSetValue(void);
522  virtual void SetValue(const string &value);
523  virtual string GetValue(void);
524  virtual void ResetValue(void);
525 // virtual void Find(EActionType action);
526 // virtual void FindRelated(EActionType action);
527 private:
528  string *m_function;
529  bool m_erase;
530  string m_qual;
532 };
533 
535 {
536 public:
538  const CSeqFeatData::ESubtype subtype,
539  const CSeqFeatData::E_Choice feat_type,
540  const string& ncRNA_class);
541 protected:
542  virtual void Modify(EActionType action);
543  virtual bool IsSetValue(void);
544  virtual void SetValue(const string &value);
545  virtual string GetValue(void);
546  virtual void ResetValue(void);
547  virtual void Find(EActionType action);
548  virtual void FindRelated(EActionType action);
549 private:
550  string *m_name;
551  bool m_erase;
552  string m_qual;
554 };
555 
556 
558 {
559 public:
561  const CSeqFeatData::ESubtype subtype,
562  const CSeqFeatData::E_Choice feat_type,
563  const string& ncRNA_class,
564  const string &name);
565 protected:
566  virtual bool IsSetValue(void);
567  virtual void SetValue(const string &value);
568  virtual string GetValue(void);
569  virtual void ResetValue(void);
570  virtual void FindRelated(EActionType action);
571 };
572 
574 {
575 public:
577  const CSeqFeatData::ESubtype subtype,
578  const CSeqFeatData::E_Choice feat_type,
579  const string& ncRNA_class)
580  : CEditingActionFeatGeneLocus(seh, subtype, feat_type, ncRNA_class, "CEditingActionFeatGeneLocusPlain") {}
581 protected:
582  virtual void Find(EActionType action);
583 };
584 
586 {
587 public:
589  const CSeqFeatData::ESubtype subtype,
590  const CSeqFeatData::E_Choice feat_type,
591  const string& ncRNA_class)
592  : CEditingActionFeatGeneLocus(seh, subtype, feat_type, ncRNA_class, "CEditingActionFeatGeneLocusRna") {}
593  virtual void SetFeat(CSeq_feat_Handle fh);
594 protected:
595  virtual bool SameObject();
596  virtual void Find(EActionType action);
597 };
598 
600 {
601 public:
603  const CSeqFeatData::ESubtype subtype,
604  const CSeqFeatData::E_Choice feat_type,
605  const string& ncRNA_class)
606  : CEditingActionFeatGeneLocus(seh, subtype, feat_type, ncRNA_class, "CEditingActionFeatGeneLocusCdsGeneProt") {}
607  virtual void SetFeat(CSeq_feat_Handle fh);
608 protected:
609  virtual void Find(EActionType action);
610 };
611 
612 
614 {
615 public:
617  const CSeqFeatData::ESubtype subtype,
618  const string& ncRNA_class);
619  virtual void SetFeat(CSeq_feat_Handle fh);
620 protected:
621  virtual bool SameObject();
622  virtual void Find(EActionType action);
623  virtual void FindRelated(EActionType action);
624 };
625 
627 {
628 public:
630  const CSeqFeatData::ESubtype subtype,
631  const string& ncRNA_class);
632  virtual void SetFeat(CSeq_feat_Handle fh);
633 protected:
634  virtual bool SameObject();
635  virtual void Find(EActionType action);
636  virtual void FindRelated(EActionType action);
637 };
638 
640 {
641 public:
643  const CSeqFeatData::ESubtype subtype,
644  const string& ncRNA_class);
645  virtual void SetFeat(CSeq_feat_Handle fh);
646 protected:
647  virtual bool SameObject();
648  virtual void Find(EActionType action);
649  virtual void FindRelated(EActionType action);
650 };
651 
653 {
654 public:
656  const CSeqFeatData::ESubtype subtype,
657  const string& ncRNA_class);
658  virtual void SetFeat(CSeq_feat_Handle fh);
659 protected:
660  virtual bool SameObject();
661  virtual void Find(EActionType action);
662  virtual void FindRelated(EActionType action);
663 };
664 
666 {
667 public:
669  const CSeqFeatData::ESubtype subtype,
670  const string& ncRNA_class);
671  virtual void SetFeat(CSeq_feat_Handle fh);
672 protected:
673  virtual bool SameObject();
674  virtual void Find(EActionType action);
675  virtual void FindRelated(EActionType action);
676 };
677 
679 {
680 public:
682  const CSeqFeatData::ESubtype subtype,
683  const CSeqFeatData::E_Choice feat_type,
684  const string& ncRNA_class);
685 protected:
686  virtual bool IsSetValue(void);
687  virtual void SetValue(const string &value);
688  virtual string GetValue(void);
689  virtual void ResetValue(void);
690 };
691 
693  string field,
694  const CSeqFeatData::ESubtype subtype,
695  const CSeqFeatData::E_Choice feat_type,
696  const string& ncRNA_class);
697 
699  string field,
700  const CSeqFeatData::ESubtype subtype,
701  const string& ncRNA_class);
702 
704  string field,
705  const CSeqFeatData::ESubtype subtype,
706  const string& ncRNA_class = kEmptyStr);
708 
709 #endif
710  // _EDITING_ACTION_FEATURES_H_
User-defined methods of the data storage class.
User-defined methods of the data storage class.
CBioseq_Handle –.
CEditingActionFeatActivity(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void Modify(EActionType action)
virtual void SetValue(const string &value)
CEditingActionFeatAllele(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
CEditingActionFeatAnticodon(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
string GetIntervalString(const CSeq_interval &seq_int)
virtual void SetValue(const string &value)
CEditingActionFeatCodonStart(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
CEditingActionFeatCodonsRecognized(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
CEditingActionFeatComment(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void Modify(EActionType action)
CEditingActionFeatDbxref(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void SetValue(const string &value)
CEditingActionFeatDesc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
CEditingActionFeatDualVal1(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual)
CEditingActionFeatDualVal2(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual)
virtual void SetValue(const string &value)
virtual void Modify(EActionType action)
virtual void FindRelated(EActionType action)
virtual void Find(EActionType action)
CEditingActionFeatEcNumber(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void SetValue(const string &value)
CEditingActionFeatEvidence(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
CEditingActionFeatException(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void SetValue(const string &value)
CEditingActionFeatFunction(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void Modify(EActionType action)
virtual void Modify(EActionType action)
CEditingActionFeatGbQualTwoNames(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual1, const string &qual2)
virtual void SetValue(const string &value)
virtual void Modify(EActionType action)
CEditingActionFeatGbQual(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual, const string &name="CEditingActionFeatGbQual")
virtual void SetFeat(CSeq_feat_Handle fh)
CEditingActionFeatGeneLocusCdsGeneProt(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void Find(EActionType action)
CEditingActionFeatGeneLocusPlain(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void Find(EActionType action)
virtual void SetFeat(CSeq_feat_Handle fh)
CEditingActionFeatGeneLocusRna(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
CEditingActionFeatGeneLocus(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &name)
virtual void FindRelated(EActionType action)
virtual void SetValue(const string &value)
CEditingActionFeatLocus_tag(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void SetValue(const string &value)
CEditingActionFeatMaploc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
CEditingActionFeatNcRnaClass(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
CEditingActionFeatPartial(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void Modify(EActionType action)
virtual void SetValue(const string &value)
virtual void Find(EActionType action)
virtual void FindRelated(EActionType action)
CEditingActionFeatProduct(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
CEditingActionFeatPseudo(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
CEditingActionFeatRegion(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
CEditingActionFeatRnaQual(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &qual)
virtual void Modify(EActionType action)
virtual void SetValue(const string &value)
virtual void FindRelated(EActionType action)
virtual void Find(EActionType action)
virtual void SetFeat(CSeq_feat_Handle fh)
CEditingActionFeatRnaToGeneComment(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
virtual void SetFeat(CSeq_feat_Handle fh)
virtual void Find(EActionType action)
virtual void FindRelated(EActionType action)
CEditingActionFeatRnaToGeneDesc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
virtual void FindRelated(EActionType action)
virtual void SetFeat(CSeq_feat_Handle fh)
CEditingActionFeatRnaToGeneLocus_tag(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
virtual void SetFeat(CSeq_feat_Handle fh)
virtual void Find(EActionType action)
virtual void FindRelated(EActionType action)
CEditingActionFeatRnaToGeneMaploc(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
CEditingActionFeatRnaToGeneSynonym(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
virtual void SetFeat(CSeq_feat_Handle fh)
virtual void FindRelated(EActionType action)
virtual void Find(EActionType action)
CEditingActionFeatSynonym(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void Modify(EActionType action)
virtual void SetValue(const string &value)
CEditingActionFeatTranscriptId(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void SetValue(const string &value)
virtual void Modify(EActionType action)
CEditingActionFeatTranslExcept(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
const CGenetic_code_table & m_code_table
CEditingActionFeatTranslTable(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
virtual void SetValue(const string &value)
virtual void SetValue(const string &value)
CEditingActionFeatTranslation(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
CScope –.
Definition: scope.hpp:92
CSeq_entry_Handle –.
CSeq_feat_Handle –.
CRef< CSeq_loc > x_GetSublocOnBioseq(CBioseq_Handle bsh, const CSeq_loc &loc)
void SetFeatForAnotherFeat(CSeq_feat_Handle fh, const CSeqFeatData::ESubtype subtype)
CSeq_feat_Handle x_FindGeneForFeature(const CSeq_loc &loc, CScope &scope, CSeqFeatData::ESubtype subtype)
virtual void SwapContext(IEditingAction *source)
CSeq_feat_Handle GetFeatHandle(void)
void FindFeatForAnotherFeat(EActionType action, SAnnotSelector other_selector)
virtual void SetFeat(CSeq_feat_Handle fh)
CSeqFeatData::ESubtype GetActionFeatSubtype()
CRef< CSeq_feat > m_EditedFeat
IEditingActionFeat(CSeq_entry_Handle seh, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class, const string &name)
CSeq_entry_Handle GetCurrentSeqEntryHandleFromFeatHandle(CSeq_feat_Handle fh)
virtual void Find(EActionType action)
bool MatchBioseqConstraintForFeatHandle(CSeq_feat_Handle fh)
CRef< CSeq_feat > m_SavedEditedFeat
virtual void FindRelated(EActionType action)
static const string & s_GetncRNAClass(const objects::CRNA_ref &rna_ref)
bool OtherFeatIs(const CSeqFeatData::ESubtype subtype)
CRef< CSeq_loc > x_MergeFeatureLocation(const CSeq_loc &loc, CScope &scope)
static bool s_IsSetncRNAClass(const objects::CRNA_ref &rna_ref)
virtual void Modify(EActionType action)
bool x_TestGeneForFeature(const CSeq_loc &gene_loc, const CSeq_loc &feat_loc, CScope &scope, bool &exact, TSeqPos &diff)
void FindRelatedFeatForAnotherFeat(EActionType action, SAnnotSelector other_selector)
void FindRelatedOrCreateProtFeat(EActionType action)
void FindOrCreateProtFeat(EActionType action)
Include a standard set of the NCBI C++ Toolkit most basic headers.
USING_SCOPE(objects)
IEditingActionFeat * CreateActionCdsGeneProt(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class=kEmptyStr)
IEditingActionFeat * CreateActionFeat(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
IEditingActionFeat * CreateActionRna(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
unsigned int TSeqPos
Type for sequence locations and lengths.
Definition: ncbimisc.hpp:875
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define kEmptyStr
Definition: ncbistr.hpp:123
E_Choice
Choice variants.
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
const CharType(& source)[N]
Definition: pointer.h:1149
SAnnotSelector –.
TFeatSubtype GetFeatSubtype(void) const
Modified on Sat May 18 11:39:40 2024 by modify_doxy.py rev. 669887