NCBI C++ ToolKit
names.cpp
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1 /* $Id: names.cpp 87240 2019-08-12 11:18:21Z fongah2 $
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
17  * may be obtained by using this software or data. The NLM and the U.S.
18  * Government disclaim all warranties, express or implied, including
19  * warranties of performance, merchantability or fitness for any particular
20  * purpose.
21  *
22  * Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Author: Kevin Bealer
27  *
28  * File Description:
29  * Define names and value types for options known to blast4.
30  *
31  */
32 
33 #include <ncbi_pch.hpp>
34 #include <objects/blast/names.hpp>
35 #include <objects/blast/blast__.hpp>
36 #include <objects/scoremat/scoremat__.hpp>
37 #include <corelib/ncbimtx.hpp>
38 
39 BEGIN_NCBI_SCOPE
40 
41 BEGIN_objects_SCOPE // namespace ncbi::objects::
42 
43 CBlast4Field::TFieldMap CBlast4Field::m_Fields;
44 CBlast4Field & CBlast4Field::Get(EBlastOptIdx opt)
45 {
46  {
47  DEFINE_STATIC_MUTEX(mx);
48  CMutexGuard guard(mx);
49  if (m_Fields.count(opt) == 0) {
50  switch (opt) {
51  //case eBlastOpt_Program:
52  case eBlastOpt_WordThreshold:
53  m_Fields[opt] = CBlast4Field("WordThreshold", CBlast4_value::e_Integer);
54  break;
55  //case eBlastOpt_LookupTableType: // not found
56  case eBlastOpt_WordSize:
57  m_Fields[opt] = CBlast4Field("WordSize", CBlast4_value::e_Integer);
58  break;
59  //case eBlastOpt_AlphabetSize: //not found
60  case eBlastOpt_MBTemplateLength:
61  m_Fields[opt] = CBlast4Field("MBTemplateLength", CBlast4_value::e_Integer);
62  break;
63  case eBlastOpt_MBTemplateType:
64  m_Fields[opt] = CBlast4Field("MBTemplateType", CBlast4_value::e_Integer);
65  break;
66  case eBlastOpt_FilterString:
67  m_Fields[opt] = CBlast4Field("FilterString", CBlast4_value::e_String);
68  break;
69  case eBlastOpt_MaskAtHash:
70  m_Fields[opt] = CBlast4Field("MaskAtHash", CBlast4_value::e_Boolean);
71  break;
72  case eBlastOpt_DustFiltering:
73  m_Fields[opt] = CBlast4Field("DustFiltering", CBlast4_value::e_Boolean);
74  break;
75  case eBlastOpt_DustFilteringLevel:
76  m_Fields[opt] = CBlast4Field("DustFilteringLevel", CBlast4_value::e_Integer);
77  break;
78  case eBlastOpt_DustFilteringWindow:
79  m_Fields[opt] = CBlast4Field("DustFilteringWindow", CBlast4_value::e_Integer);
80  break;
81  case eBlastOpt_DustFilteringLinker:
82  m_Fields[opt] = CBlast4Field("DustFilteringLinker", CBlast4_value::e_Integer);
83  break;
84  case eBlastOpt_SegFiltering:
85  m_Fields[opt] = CBlast4Field("SegFiltering", CBlast4_value::e_Boolean);
86  break;
87  case eBlastOpt_SegFilteringWindow:
88  m_Fields[opt] = CBlast4Field("SegFilteringWindow", CBlast4_value::e_Integer);
89  break;
90  case eBlastOpt_SegFilteringLocut:
91  m_Fields[opt] = CBlast4Field("SegFilteringLocut", CBlast4_value::e_Real);
92  break;
93  case eBlastOpt_SegFilteringHicut:
94  m_Fields[opt] = CBlast4Field("SegFilteringHicut", CBlast4_value::e_Real);
95  break;
96  case eBlastOpt_RepeatFiltering:
97  m_Fields[opt] = CBlast4Field("RepeatFiltering", CBlast4_value::e_Boolean);
98  break;
99  case eBlastOpt_RepeatFilteringDB:
100  m_Fields[opt] = CBlast4Field("RepeatFilteringDB", CBlast4_value::e_String);
101  break;
102  case eBlastOpt_StrandOption:
103  m_Fields[opt] = CBlast4Field("StrandOption", CBlast4_value::e_Strand_type);
104  break;
105  case eBlastOpt_QueryGeneticCode:
106  m_Fields[opt] = CBlast4Field("QueryGeneticCode", CBlast4_value::e_Integer);
107  break;
108  case eBlastOpt_WindowSize:
109  m_Fields[opt] = CBlast4Field("WindowSize", CBlast4_value::e_Integer);
110  break;
111  //case eBlastOpt_SeedContainerType: // not found
112  //case eBlastOpt_SeedExtensionMethod: // not found
113  //case eBlastOpt_XDropoff: //not found
114  case eBlastOpt_GapXDropoff:
115  m_Fields[opt] = CBlast4Field("GapXDropoff", CBlast4_value::e_Real);
116  break;
117  case eBlastOpt_GapXDropoffFinal:
118  m_Fields[opt] = CBlast4Field("GapXDropoffFinal", CBlast4_value::e_Real);
119  break;
120  case eBlastOpt_GapTrigger:
121  m_Fields[opt] = CBlast4Field("GapTrigger", CBlast4_value::e_Real);
122  break;
123  case eBlastOpt_GapExtnAlgorithm:
124  m_Fields[opt] = CBlast4Field("GapExtnAlgorithm", CBlast4_value::e_Integer);
125  break;
126  case eBlastOpt_HitlistSize:
127  m_Fields[opt] = CBlast4Field("HitlistSize", CBlast4_value::e_Integer);
128  //case eBlastOpt_MaxNumHspPerSequence: // not found
129  break;
130  case eBlastOpt_CullingLimit:
131  m_Fields[opt] = CBlast4Field("Culling", CBlast4_value::e_Integer);
132  break;
133  case eBlastOpt_EvalueThreshold:
134  m_Fields[opt] = CBlast4Field("EvalueThreshold", CBlast4_value::e_Cutoff);
135  break;
136  case eBlastOpt_CutoffScore:
137  m_Fields[opt] = CBlast4Field("CutoffScore", CBlast4_value::e_Cutoff);
138  break;
139  case eBlastOpt_PercentIdentity:
140  m_Fields[opt] = CBlast4Field("PercentIdentity", CBlast4_value::e_Real);
141  break;
142  case eBlastOpt_QueryCovHspPerc:
143  m_Fields[opt] = CBlast4Field("QueryCovHspPerc", CBlast4_value::e_Real);
144  break;
145  case eBlastOpt_MaxHspsPerSubject:
146  m_Fields[opt] = CBlast4Field("MaxHspsPerSubject", CBlast4_value::e_Integer);
147  break;
148  case eBlastOpt_SumStatisticsMode:
149  m_Fields[opt] = CBlast4Field("SumStatistics", CBlast4_value::e_Boolean);
150  break;
151  case eBlastOpt_LongestIntronLength:
152  m_Fields[opt] = CBlast4Field("LongestIntronLength", CBlast4_value::e_Integer);
153  break;
154  case eBlastOpt_GappedMode: // same as !ungapped mode
155  m_Fields[opt] = CBlast4Field("UngappedMode", CBlast4_value::e_Boolean);
156  break;
157  case eBlastOpt_ComplexityAdjMode: // -RMH-
158  m_Fields[opt] = CBlast4Field("ComplexityAdjustMode", CBlast4_value::e_Boolean);
159  break;
160  case eBlastOpt_MaskLevel: // -RMH-
161  m_Fields[opt] = CBlast4Field("MaskLevel", CBlast4_value::e_Integer);
162  break;
163  case eBlastOpt_MatrixName:
164  m_Fields[opt] = CBlast4Field("MatrixName", CBlast4_value::e_String);
165  break;
166  //case eBlastOpt_MatrixPath: // not found
167  case eBlastOpt_MatchReward:
168  m_Fields[opt] = CBlast4Field("MatchReward", CBlast4_value::e_Integer);
169  break;
170  case eBlastOpt_MismatchPenalty:
171  m_Fields[opt] = CBlast4Field("MismatchPenalty", CBlast4_value::e_Integer);
172  break;
173  case eBlastOpt_GapOpeningCost:
174  m_Fields[opt] = CBlast4Field("GapOpeningCost", CBlast4_value::e_Integer);
175  break;
176  case eBlastOpt_GapExtensionCost:
177  m_Fields[opt] = CBlast4Field("GapExtensionCost", CBlast4_value::e_Integer);
178  break;
179  //case eBlastOpt_FrameShiftPenalty: // not found
180  case eBlastOpt_OutOfFrameMode:
181  m_Fields[opt] = CBlast4Field("OutOfFrameMode", CBlast4_value::e_Boolean);
182  break;
183  case eBlastOpt_DbLength:
184  m_Fields[opt] = CBlast4Field("DbLength", CBlast4_value::e_Big_integer);
185  break;
186  //case eBlastOpt_DbSeqNum: // not found
187  case eBlastOpt_EffectiveSearchSpace:
188  m_Fields[opt] = CBlast4Field("EffectiveSearchSpace", CBlast4_value::e_Big_integer);
189  break;
190  case eBlastOpt_DbGeneticCode:
191  m_Fields[opt] = CBlast4Field("DbGeneticCode", CBlast4_value::e_Integer);
192  break;
193  case eBlastOpt_PHIPattern:
194  m_Fields[opt] = CBlast4Field("PHIPattern", CBlast4_value::e_String);
195  break;
196  case eBlastOpt_InclusionThreshold:
197  m_Fields[opt] = CBlast4Field("InclusionThreshold", CBlast4_value::e_Real);
198  break;
199  case eBlastOpt_PseudoCount:
200  m_Fields[opt] = CBlast4Field("PseudoCountWeight", CBlast4_value::e_Integer);
201  break;
202  case eBlastOpt_GapTracebackAlgorithm:
203  m_Fields[opt] = CBlast4Field("GapTracebackAlgorithm", CBlast4_value::e_Integer);
204  break;
205  case eBlastOpt_CompositionBasedStats:
206  m_Fields[opt] = CBlast4Field("CompositionBasedStats", CBlast4_value::e_Integer);
207  break;
208  case eBlastOpt_SmithWatermanMode:
209  m_Fields[opt] = CBlast4Field("SmithWatermanMode", CBlast4_value::e_Boolean);
210  break;
211  case eBlastOpt_UnifiedP:
212  m_Fields[opt] = CBlast4Field("UnifiedP", CBlast4_value::e_Integer);
213  break;
214  case eBlastOpt_WindowMaskerDatabase:
215  m_Fields[opt] = CBlast4Field("WindowMaskerDatabase", CBlast4_value::e_String);
216  break;
217  case eBlastOpt_WindowMaskerTaxId:
218  m_Fields[opt] = CBlast4Field("WindowMaskerTaxId", CBlast4_value::e_Integer);
219  break;
220  case eBlastOpt_ForceMbIndex: // corresponds to -use_index flag
221  m_Fields[opt] = CBlast4Field("ForceMbIndex", CBlast4_value::e_Boolean);
222  break;
223  case eBlastOpt_MbIndexName: // corresponds to -index_name flag
224  m_Fields[opt] = CBlast4Field("MbIndexName", CBlast4_value::e_String);
225  break;
226  case eBlastOpt_BestHitScoreEdge:
227  m_Fields[opt] = CBlast4Field("BestHitScoreEdge", CBlast4_value::e_Real);
228  break;
229  case eBlastOpt_BestHitOverhang:
230  m_Fields[opt] = CBlast4Field("BestHitOverhang", CBlast4_value::e_Real);
231  break;
232  case eBlastOpt_SubjectBestHit: // corresponds to -subject_besthit flag
233  m_Fields[opt] = CBlast4Field("UseSubjectBestHit", CBlast4_value::e_Boolean);
234  break;
235  case eBlastOpt_IgnoreMsaMaster:
236  m_Fields[opt] = CBlast4Field("IgnoreMsaMaster", CBlast4_value::e_Boolean);
237  break;
238  case eBlastOpt_DomainInclusionThreshold: // options for DELTA-BLAST
239  m_Fields[opt] = CBlast4Field("DomainInclusionThreshold", CBlast4_value::e_Real);
240  break;
241 
242  // Added to provide access to these options, they don't have a usage in
243  case eBlastOpt_Culling:
244  m_Fields[opt] = CBlast4Field("Culling", CBlast4_value::e_Boolean);
245  break;
246  case eBlastOpt_EntrezQuery:
247  m_Fields[opt] = CBlast4Field("EntrezQuery", CBlast4_value::e_String);
248  break;
249  case eBlastOpt_FinalDbSeq:
250  m_Fields[opt] = CBlast4Field("FinalDbSeq", CBlast4_value::e_Integer);
251  break;
252  case eBlastOpt_FirstDbSeq:
253  m_Fields[opt] = CBlast4Field("FirstDbSeq", CBlast4_value::e_Integer);
254  break;
255  case eBlastOpt_GiList:
256  m_Fields[opt] = CBlast4Field("GiList", CBlast4_value::e_Integer_list);
257  break;
258  case eBlastOpt_DbFilteringAlgorithmId:
259  m_Fields[opt] = CBlast4Field("DbFilteringAlgorithmId",CBlast4_value::e_Integer);
260  break;
261  case eBlastOpt_DbFilteringAlgorithmKey:
262  m_Fields[opt] = CBlast4Field("DbFilteringAlgorithmKey",CBlast4_value::e_String);
263  break;
264  case eBlastOpt_SubjectMaskingType:
265  m_Fields[opt] = CBlast4Field("SubjectMaskingType", CBlast4_value::e_Integer);
266  break;
267  case eBlastOpt_HspRangeMax:
268  m_Fields[opt] = CBlast4Field("HspRangeMax", CBlast4_value::e_Integer);
269  break;
270  case eBlastOpt_LCaseMask:
271  m_Fields[opt] = CBlast4Field("LCaseMask", CBlast4_value::e_Query_mask);
272  break;
273  case eBlastOpt_MatrixTable:
274  m_Fields[opt] = CBlast4Field("MatrixTable", CBlast4_value::e_Matrix);
275  break;
276  case eBlastOpt_NegativeGiList:
277  m_Fields[opt] = CBlast4Field("NegativeGiList", CBlast4_value::e_Integer_list);
278  break;
279  case eBlastOpt_RequiredEnd:
280  m_Fields[opt] = CBlast4Field("RequiredEnd", CBlast4_value::e_Integer);
281  break;
282  case eBlastOpt_RequiredStart:
283  m_Fields[opt] = CBlast4Field("RequiredStart", CBlast4_value::e_Integer);
284  break;
285  case eBlastOpt_UseRealDbSize:
286  m_Fields[opt] = CBlast4Field("UseRealDbSize", CBlast4_value::e_Boolean);
287  break;
288  case eBlastOpt_TaxidList:
289  m_Fields[opt] = CBlast4Field("TaxidList", CBlast4_value::e_Integer_list);
290  break;
291  case eBlastOpt_NegativeTaxidList:
292  m_Fields[opt] = CBlast4Field("NegativeTaxidList", CBlast4_value::e_Integer_list);
293  break;
294 
295 // List of web-related options
296  case eBlastOpt_Web_BlastSpecialPage:
297  m_Fields[opt] = CBlast4Field("Web_BlastSpecialPage", CBlast4_value::e_String);
298  break;
299  case eBlastOpt_Web_EntrezQuery:
300  m_Fields[opt] = CBlast4Field("Web_EntrezQuery", CBlast4_value::e_String);
301  break;
302  case eBlastOpt_Web_JobTitle:
303  m_Fields[opt] = CBlast4Field("Web_JobTitle", CBlast4_value::e_String);
304  break;
305  case eBlastOpt_Web_NewWindow:
306  m_Fields[opt] = CBlast4Field("Web_NewWindow", CBlast4_value::e_Boolean);
307  break;
308  case eBlastOpt_Web_OrganismName:
309  m_Fields[opt] = CBlast4Field("Web_OrganismName", CBlast4_value::e_String);
310  break;
311  case eBlastOpt_Web_RunPsiBlast:
312  m_Fields[opt] = CBlast4Field("Web_RunPsiBlast", CBlast4_value::e_Boolean);
313  break;
314  case eBlastOpt_Web_ShortQueryAdjust:
315  m_Fields[opt] = CBlast4Field("Web_ShortQueryAdjust", CBlast4_value::e_Boolean);
316  break;
317  case eBlastOpt_Web_StepNumber:
318  m_Fields[opt] = CBlast4Field("Web_StepNumber", CBlast4_value::e_Integer);
319  break;
320  case eBlastOpt_Web_DBInput:
321  m_Fields[opt] = CBlast4Field("Web_DBInput", CBlast4_value::e_Boolean);
322  break;
323  case eBlastOpt_Web_DBGroup:
324  m_Fields[opt] = CBlast4Field("Web_DBGroup", CBlast4_value::e_String);
325  break;
326  case eBlastOpt_Web_DBSubgroupName:
327  m_Fields[opt] = CBlast4Field("Web_DBSubgroupName", CBlast4_value::e_String);
328  break;
329  case eBlastOpt_Web_DBSubgroup:
330  m_Fields[opt] = CBlast4Field("Web_DBSubgroup", CBlast4_value::e_String);
331  break;
332  case eBlastOpt_Web_ExclModels:
333  m_Fields[opt] = CBlast4Field("Web_ExclModels", CBlast4_value::e_Boolean);
334  break;
335  case eBlastOpt_Web_ExclSeqUncult:
336  m_Fields[opt] = CBlast4Field("Web_SeqUncult", CBlast4_value::e_Boolean);
337  break;
338 
339  default:
340  ERR_POST(Warning << "Undefined remote BLAST options used");
341  m_Fields[opt] = CBlast4Field("-", CBlast4_value::e_not_set);
342  break;
343  }
344  }
345  }
346  _ASSERT(m_Fields.count(opt) != 0);
347  return m_Fields[opt];
348 }
349 
350 const string & CBlast4Field::GetName(EBlastOptIdx opt)
351 {
352  return CBlast4Field::Get(opt).GetName();
353 }
354 
355 const string & CBlast4Field::GetName() const
356 {
357  return m_Name;
358 }
359 
360 CBlast4_value::E_Choice CBlast4Field::GetType() const
361 {
362  return m_Type;
363 }
364 
365 bool CBlast4Field::Match(const CBlast4_parameter & p) const
366 {
367  return (p.CanGetName() &&
368  p.CanGetValue() &&
369  p.GetValue().Which() == m_Type &&
370  p.GetName() == m_Name);
371 }
372 
373 string CBlast4Field::GetString(const CBlast4_parameter & p) const
374 {
375  _ASSERT(Match(p));
376  return p.GetValue().GetString();
377 }
378 
379 bool CBlast4Field::GetBoolean(const CBlast4_parameter & p) const
380 {
381  _ASSERT(Match(p));
382  return p.GetValue().GetBoolean();
383 }
384 
385 Int8 CBlast4Field::GetBig_integer(const CBlast4_parameter & p) const
386 {
387  _ASSERT(Match(p));
388  return p.GetValue().GetBig_integer();
389 }
390 
391 CConstRef<CBlast4_cutoff>
392 CBlast4Field::GetCutoff(const CBlast4_parameter & p) const
393 {
394  _ASSERT(Match(p));
395  return CConstRef<CBlast4_cutoff>(& p.GetValue().GetCutoff());
396 }
397 
398 int CBlast4Field::GetInteger(const CBlast4_parameter & p) const
399 {
400  _ASSERT(Match(p));
401  return p.GetValue().GetInteger();
402 }
403 
404 list<int> CBlast4Field::GetIntegerList (const CBlast4_parameter & p) const
405 {
406  _ASSERT(Match(p));
407  return p.GetValue().GetInteger_list();
408 }
409 
410 CConstRef<CPssmWithParameters>
411 CBlast4Field::GetMatrix(const CBlast4_parameter & p) const
412 {
413  _ASSERT(Match(p));
414  return CConstRef<CPssmWithParameters>(& p.GetValue().GetMatrix());
415 }
416 
417 CConstRef<CBlast4_mask>
418 CBlast4Field::GetQueryMask(const CBlast4_parameter & p) const
419 {
420  _ASSERT(Match(p));
421  return CConstRef<CBlast4_mask>(& p.GetValue().GetQuery_mask());
422 }
423 
424 double CBlast4Field::GetReal(const CBlast4_parameter & p) const
425 {
426  _ASSERT(Match(p));
427  return p.GetValue().GetReal();
428 }
429 
430 EBlast4_strand_type
431 CBlast4Field::GetStrandType(const CBlast4_parameter & p) const
432 {
433  _ASSERT(Match(p));
434  return p.GetValue().GetStrand_type();
435 }
436 
437 const char* kBlast4SearchInfoReqName_Search("search");
438 const char* kBlast4SearchInfoReqName_Alignment("alignment");
439 const char* kBlast4SearchInfoReqValue_Status("status");
440 const char* kBlast4SearchInfoReqValue_Title("title");
441 const char* kBlast4SearchInfoReqValue_Subjects("subjects");
442 const char* kBlast4SearchInfoReqValue_PsiIterationNum("psi_iteration_number");
443 
444 /// Auxiliary function to consistently build the Blast4-get-search-info-reply
445 /// names
446 string Blast4SearchInfo_BuildReplyName(const string& name, const string& value)
447 {
448  return name + string("-") + value;
449 }
450 
451 END_objects_SCOPE // namespace ncbi::objects::
452 
453 END_NCBI_SCOPE
blast__.hpp
CBlast4Field
Field properties for options in a Blast4 parameter list.
Definition: names.hpp:164
CBlast4Field::GetBoolean
bool GetBoolean(const CBlast4_parameter &p) const
Verify parameter name and type, and get boolean value.
Definition: names.cpp:379
CBlast4Field::m_Name
string m_Name
Field name string as used in Blast4_parameter objects.
Definition: names.hpp:218
CBlast4Field::GetName
static const string & GetName(EBlastOptIdx opt)
Definition: names.cpp:350
CBlast4Field::GetStrandType
EBlast4_strand_type GetStrandType(const CBlast4_parameter &p) const
Verify parameter name and type, and get strand_type value.
Definition: names.cpp:431
CBlast4Field::m_Fields
static TFieldMap m_Fields
Map of all blast4 field objects.
Definition: names.hpp:227
CBlast4Field::GetBig_integer
Int8 GetBig_integer(const CBlast4_parameter &p) const
Verify parameter name and type, and get big integer value.
Definition: names.cpp:385
CBlast4Field::GetMatrix
CConstRef< CPssmWithParameters > GetMatrix(const CBlast4_parameter &p) const
Verify parameter name and type, and get matrix (pssm) value.
Definition: names.cpp:411
CBlast4Field::GetCutoff
CConstRef< CBlast4_cutoff > GetCutoff(const CBlast4_parameter &p) const
Verify parameter name and type, and get cutoff value.
Definition: names.cpp:392
CBlast4Field::CBlast4Field
CBlast4Field()
Default constructor (for STL)
Definition: names.hpp:167
CBlast4Field::Match
bool Match(const CBlast4_parameter &p) const
Match field name and type to parameter.
Definition: names.cpp:365
CBlast4Field::GetReal
double GetReal(const CBlast4_parameter &p) const
Verify parameter name and type, and get real value.
Definition: names.cpp:424
CBlast4Field::GetIntegerList
list< int > GetIntegerList(const CBlast4_parameter &p) const
Verify parameter name and type, and get integer list value.
Definition: names.cpp:404
CBlast4Field::GetString
string GetString(const CBlast4_parameter &p) const
Verify parameter name and type, and get string value.
Definition: names.cpp:373
CBlast4Field::GetInteger
int GetInteger(const CBlast4_parameter &p) const
Verify parameter name and type, and get integer value.
Definition: names.cpp:398
CBlast4Field::GetType
CBlast4_value::E_Choice GetType() const
Get field type.
Definition: names.cpp:360
CBlast4Field::m_Type
CBlast4_value::E_Choice m_Type
Field value type as used in Blast4_parameter objects.
Definition: names.hpp:221
CBlast4Field::GetName
const string & GetName() const
Get field name (key).
Definition: names.cpp:355
CBlast4Field::Get
static CBlast4Field & Get(EBlastOptIdx opt)
Definition: names.cpp:44
CBlast4Field::GetQueryMask
CConstRef< CBlast4_mask > GetQueryMask(const CBlast4_parameter &p) const
Verify parameter name and type, and get query mask value.
Definition: names.cpp:418
CBlast4_parameter
CBlast4_parameter –.
Definition: Blast4_parameter.hpp:66
CConstRef
CConstRef –.
Definition: ncbiobj.hpp:1266
map
Definition: map.hpp:338
value
char value[7]
Definition: config.c:431
string
string
Definition: cgiapp.hpp:687
ERR_POST
#define ERR_POST(message)
Error posting with file, line number information but without error codes.
Definition: ncbidiag.hpp:186
Warning
void Warning(CExceptionArgs_Base &args)
Definition: ncbiexpt.hpp:1191
Int8
int64_t Int8
8-byte (64-bit) signed integer
Definition: ncbitype.h:104
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
DEFINE_STATIC_MUTEX
#define DEFINE_STATIC_MUTEX(id)
Define static mutex and initialize it.
Definition: ncbimtx.hpp:512
CBlast4_value_Base::GetBig_integer
TBig_integer GetBig_integer(void) const
Get the variant data.
Definition: Blast4_value_.hpp:942
CBlast4_value_Base::GetCutoff
const TCutoff & GetCutoff(void) const
Get the variant data.
Definition: Blast4_value_.cpp:277
CBlast4_parameter_Base::GetName
const TName & GetName(void) const
Get the Name member data.
Definition: Blast4_parameter_.hpp:215
CBlast4_value_Base::GetInteger
TInteger GetInteger(void) const
Get the variant data.
Definition: Blast4_value_.hpp:1008
CBlast4_parameter_Base::GetValue
const TValue & GetValue(void) const
Get the Value member data.
Definition: Blast4_parameter_.hpp:262
CBlast4_value_Base::GetBoolean
TBoolean GetBoolean(void) const
Get the variant data.
Definition: Blast4_value_.hpp:975
CBlast4_value_Base::GetMatrix
const TMatrix & GetMatrix(void) const
Get the variant data.
Definition: Blast4_value_.cpp:299
CBlast4_value_Base::Which
E_Choice Which(void) const
Which variant is currently selected.
Definition: Blast4_value_.hpp:907
CBlast4_value_Base::GetString
const TString & GetString(void) const
Get the variant data.
Definition: Blast4_value_.hpp:1113
CBlast4_value_Base::GetReal
TReal GetReal(void) const
Get the variant data.
Definition: Blast4_value_.hpp:1041
CBlast4_value_Base::GetInteger_list
const TInteger_list & GetInteger_list(void) const
Get the variant data.
Definition: Blast4_value_.hpp:1213
CBlast4_value_Base::GetQuery_mask
const TQuery_mask & GetQuery_mask(void) const
Get the variant data.
Definition: Blast4_value_.cpp:437
CBlast4_parameter_Base::CanGetValue
bool CanGetValue(void) const
Check if it is safe to call GetValue method.
Definition: Blast4_parameter_.hpp:256
CBlast4_value_Base::E_Choice
E_Choice
Choice variants.
Definition: Blast4_value_.hpp:100
CBlast4_value_Base::GetStrand_type
TStrand_type GetStrand_type(void) const
Get the variant data.
Definition: Blast4_value_.hpp:1086
EBlast4_strand_type
EBlast4_strand_type
Access to EBlast4_strand_type's attributes (values, names) as defined in spec.
Definition: Blast4_strand_type_.hpp:63
CBlast4_parameter_Base::CanGetName
bool CanGetName(void) const
Check if it is safe to call GetName method.
Definition: Blast4_parameter_.hpp:209
CBlast4_value_Base::e_Boolean
@ e_Boolean
Definition: Blast4_value_.hpp:104
CBlast4_value_Base::e_Integer
@ e_Integer
Definition: Blast4_value_.hpp:106
CBlast4_value_Base::e_Query_mask
@ e_Query_mask
Intended to represent user-provided masking locations for a single query sequence (name field in Blas...
Definition: Blast4_value_.hpp:128
CBlast4_value_Base::e_Matrix
@ e_Matrix
Definition: Blast4_value_.hpp:107
CBlast4_value_Base::e_not_set
@ e_not_set
No variant selected.
Definition: Blast4_value_.hpp:101
CBlast4_value_Base::e_Real
@ e_Real
Definition: Blast4_value_.hpp:108
CBlast4_value_Base::e_Cutoff
@ e_Cutoff
Definition: Blast4_value_.hpp:105
CBlast4_value_Base::e_String
@ e_String
Definition: Blast4_value_.hpp:113
CBlast4_value_Base::e_Big_integer
@ e_Big_integer
scalar types
Definition: Blast4_value_.hpp:102
CBlast4_value_Base::e_Integer_list
@ e_Integer_list
Definition: Blast4_value_.hpp:118
CBlast4_value_Base::e_Strand_type
@ e_Strand_type
Definition: Blast4_value_.hpp:112
kBlast4SearchInfoReqValue_Status
const char * kBlast4SearchInfoReqValue_Status("status")
kBlast4SearchInfoReqValue_PsiIterationNum
const char * kBlast4SearchInfoReqValue_PsiIterationNum("psi_iteration_number")
kBlast4SearchInfoReqValue_Title
const char * kBlast4SearchInfoReqValue_Title("title")
Blast4SearchInfo_BuildReplyName
string Blast4SearchInfo_BuildReplyName(const string &name, const string &value)
Auxiliary function to consistently build the Blast4-get-search-info-reply names.
Definition: names.cpp:446
kBlast4SearchInfoReqName_Alignment
const char * kBlast4SearchInfoReqName_Alignment("alignment")
kBlast4SearchInfoReqName_Search
const char * kBlast4SearchInfoReqName_Search("search")
kBlast4SearchInfoReqValue_Subjects
const char * kBlast4SearchInfoReqValue_Subjects("subjects")
names.hpp
Names used in blast4 network communications.
EBlastOptIdx
EBlastOptIdx
Index of remote BLAST options.
Definition: names.hpp:55
eBlastOpt_Web_DBInput
@ eBlastOpt_Web_DBInput
Definition: names.hpp:153
eBlastOpt_WordThreshold
@ eBlastOpt_WordThreshold
Definition: names.hpp:57
eBlastOpt_EntrezQuery
@ eBlastOpt_EntrezQuery
Definition: names.hpp:128
eBlastOpt_ComplexityAdjMode
@ eBlastOpt_ComplexityAdjMode
Definition: names.hpp:96
eBlastOpt_MismatchPenalty
@ eBlastOpt_MismatchPenalty
Definition: names.hpp:101
eBlastOpt_MaskLevel
@ eBlastOpt_MaskLevel
Definition: names.hpp:97
eBlastOpt_Web_StepNumber
@ eBlastOpt_Web_StepNumber
Definition: names.hpp:152
eBlastOpt_CompositionBasedStats
@ eBlastOpt_CompositionBasedStats
Definition: names.hpp:114
eBlastOpt_SubjectBestHit
@ eBlastOpt_SubjectBestHit
Definition: names.hpp:127
eBlastOpt_Web_NewWindow
@ eBlastOpt_Web_NewWindow
Definition: names.hpp:148
eBlastOpt_NegativeTaxidList
@ eBlastOpt_NegativeTaxidList
Definition: names.hpp:143
eBlastOpt_QueryGeneticCode
@ eBlastOpt_QueryGeneticCode
Definition: names.hpp:76
eBlastOpt_DbLength
@ eBlastOpt_DbLength
Definition: names.hpp:106
eBlastOpt_WordSize
@ eBlastOpt_WordSize
Definition: names.hpp:59
eBlastOpt_SegFilteringHicut
@ eBlastOpt_SegFilteringHicut
Definition: names.hpp:72
eBlastOpt_HitlistSize
@ eBlastOpt_HitlistSize
Definition: names.hpp:85
eBlastOpt_FilterString
@ eBlastOpt_FilterString
Definition: names.hpp:63
eBlastOpt_StrandOption
@ eBlastOpt_StrandOption
Definition: names.hpp:75
eBlastOpt_RequiredEnd
@ eBlastOpt_RequiredEnd
Definition: names.hpp:139
eBlastOpt_QueryCovHspPerc
@ eBlastOpt_QueryCovHspPerc
Definition: names.hpp:92
eBlastOpt_GapXDropoffFinal
@ eBlastOpt_GapXDropoffFinal
Definition: names.hpp:82
eBlastOpt_DustFilteringLevel
@ eBlastOpt_DustFilteringLevel
Definition: names.hpp:66
eBlastOpt_OutOfFrameMode
@ eBlastOpt_OutOfFrameMode
Definition: names.hpp:105
eBlastOpt_MBTemplateLength
@ eBlastOpt_MBTemplateLength
Definition: names.hpp:61
eBlastOpt_BestHitOverhang
@ eBlastOpt_BestHitOverhang
Definition: names.hpp:122
eBlastOpt_CullingLimit
@ eBlastOpt_CullingLimit
Definition: names.hpp:88
eBlastOpt_TaxidList
@ eBlastOpt_TaxidList
Definition: names.hpp:142
eBlastOpt_PercentIdentity
@ eBlastOpt_PercentIdentity
Definition: names.hpp:91
eBlastOpt_SegFilteringWindow
@ eBlastOpt_SegFilteringWindow
Definition: names.hpp:70
eBlastOpt_UseRealDbSize
@ eBlastOpt_UseRealDbSize
Definition: names.hpp:141
eBlastOpt_IgnoreMsaMaster
@ eBlastOpt_IgnoreMsaMaster
Definition: names.hpp:123
eBlastOpt_Culling
@ eBlastOpt_Culling
Definition: names.hpp:126
eBlastOpt_WindowMaskerTaxId
@ eBlastOpt_WindowMaskerTaxId
Definition: names.hpp:118
eBlastOpt_GapExtensionCost
@ eBlastOpt_GapExtensionCost
Definition: names.hpp:103
eBlastOpt_Web_EntrezQuery
@ eBlastOpt_Web_EntrezQuery
Definition: names.hpp:146
eBlastOpt_GapOpeningCost
@ eBlastOpt_GapOpeningCost
Definition: names.hpp:102
eBlastOpt_DbFilteringAlgorithmKey
@ eBlastOpt_DbFilteringAlgorithmKey
Definition: names.hpp:133
eBlastOpt_Web_DBGroup
@ eBlastOpt_Web_DBGroup
Definition: names.hpp:154
eBlastOpt_WindowSize
@ eBlastOpt_WindowSize
Definition: names.hpp:77
eBlastOpt_MatchReward
@ eBlastOpt_MatchReward
Definition: names.hpp:100
eBlastOpt_MaskAtHash
@ eBlastOpt_MaskAtHash
Definition: names.hpp:64
eBlastOpt_MaxHspsPerSubject
@ eBlastOpt_MaxHspsPerSubject
Definition: names.hpp:87
eBlastOpt_SmithWatermanMode
@ eBlastOpt_SmithWatermanMode
Definition: names.hpp:115
eBlastOpt_SegFiltering
@ eBlastOpt_SegFiltering
Definition: names.hpp:69
eBlastOpt_GapExtnAlgorithm
@ eBlastOpt_GapExtnAlgorithm
Definition: names.hpp:84
eBlastOpt_EvalueThreshold
@ eBlastOpt_EvalueThreshold
Definition: names.hpp:89
eBlastOpt_MatrixTable
@ eBlastOpt_MatrixTable
Definition: names.hpp:137
eBlastOpt_Web_OrganismName
@ eBlastOpt_Web_OrganismName
Definition: names.hpp:149
eBlastOpt_Web_BlastSpecialPage
@ eBlastOpt_Web_BlastSpecialPage
Definition: names.hpp:145
eBlastOpt_RepeatFilteringDB
@ eBlastOpt_RepeatFilteringDB
Definition: names.hpp:74
eBlastOpt_LCaseMask
@ eBlastOpt_LCaseMask
Definition: names.hpp:136
eBlastOpt_MatrixName
@ eBlastOpt_MatrixName
Definition: names.hpp:98
eBlastOpt_Web_RunPsiBlast
@ eBlastOpt_Web_RunPsiBlast
Definition: names.hpp:150
eBlastOpt_NegativeGiList
@ eBlastOpt_NegativeGiList
Definition: names.hpp:138
eBlastOpt_Web_ExclSeqUncult
@ eBlastOpt_Web_ExclSeqUncult
Definition: names.hpp:158
eBlastOpt_DomainInclusionThreshold
@ eBlastOpt_DomainInclusionThreshold
Definition: names.hpp:124
eBlastOpt_BestHitScoreEdge
@ eBlastOpt_BestHitScoreEdge
Definition: names.hpp:121
eBlastOpt_LongestIntronLength
@ eBlastOpt_LongestIntronLength
Definition: names.hpp:94
eBlastOpt_HspRangeMax
@ eBlastOpt_HspRangeMax
Definition: names.hpp:135
eBlastOpt_DustFilteringLinker
@ eBlastOpt_DustFilteringLinker
Definition: names.hpp:68
eBlastOpt_ForceMbIndex
@ eBlastOpt_ForceMbIndex
Definition: names.hpp:119
eBlastOpt_Web_ExclModels
@ eBlastOpt_Web_ExclModels
Definition: names.hpp:157
eBlastOpt_GapTrigger
@ eBlastOpt_GapTrigger
Definition: names.hpp:83
eBlastOpt_DbFilteringAlgorithmId
@ eBlastOpt_DbFilteringAlgorithmId
Definition: names.hpp:132
eBlastOpt_FinalDbSeq
@ eBlastOpt_FinalDbSeq
Definition: names.hpp:129
eBlastOpt_DustFiltering
@ eBlastOpt_DustFiltering
Definition: names.hpp:65
eBlastOpt_DbGeneticCode
@ eBlastOpt_DbGeneticCode
Definition: names.hpp:109
eBlastOpt_FirstDbSeq
@ eBlastOpt_FirstDbSeq
Definition: names.hpp:130
eBlastOpt_RepeatFiltering
@ eBlastOpt_RepeatFiltering
Definition: names.hpp:73
eBlastOpt_SegFilteringLocut
@ eBlastOpt_SegFilteringLocut
Definition: names.hpp:71
eBlastOpt_MBTemplateType
@ eBlastOpt_MBTemplateType
Definition: names.hpp:62
eBlastOpt_Web_ShortQueryAdjust
@ eBlastOpt_Web_ShortQueryAdjust
Definition: names.hpp:151
eBlastOpt_GapXDropoff
@ eBlastOpt_GapXDropoff
Definition: names.hpp:81
eBlastOpt_GiList
@ eBlastOpt_GiList
Definition: names.hpp:131
eBlastOpt_GappedMode
@ eBlastOpt_GappedMode
Definition: names.hpp:95
eBlastOpt_PseudoCount
@ eBlastOpt_PseudoCount
Definition: names.hpp:112
eBlastOpt_WindowMaskerDatabase
@ eBlastOpt_WindowMaskerDatabase
Definition: names.hpp:117
eBlastOpt_EffectiveSearchSpace
@ eBlastOpt_EffectiveSearchSpace
Definition: names.hpp:108
eBlastOpt_SumStatisticsMode
@ eBlastOpt_SumStatisticsMode
Definition: names.hpp:93
eBlastOpt_RequiredStart
@ eBlastOpt_RequiredStart
Definition: names.hpp:140
eBlastOpt_PHIPattern
@ eBlastOpt_PHIPattern
Definition: names.hpp:110
eBlastOpt_Web_DBSubgroup
@ eBlastOpt_Web_DBSubgroup
Definition: names.hpp:156
eBlastOpt_MbIndexName
@ eBlastOpt_MbIndexName
Definition: names.hpp:120
eBlastOpt_Web_JobTitle
@ eBlastOpt_Web_JobTitle
Definition: names.hpp:147
eBlastOpt_GapTracebackAlgorithm
@ eBlastOpt_GapTracebackAlgorithm
Definition: names.hpp:113
eBlastOpt_SubjectMaskingType
@ eBlastOpt_SubjectMaskingType
Definition: names.hpp:134
eBlastOpt_Web_DBSubgroupName
@ eBlastOpt_Web_DBSubgroupName
Definition: names.hpp:155
eBlastOpt_DustFilteringWindow
@ eBlastOpt_DustFilteringWindow
Definition: names.hpp:67
eBlastOpt_CutoffScore
@ eBlastOpt_CutoffScore
Definition: names.hpp:90
eBlastOpt_InclusionThreshold
@ eBlastOpt_InclusionThreshold
Definition: names.hpp:111
eBlastOpt_UnifiedP
@ eBlastOpt_UnifiedP
Definition: names.hpp:116
ncbi_pch.hpp
ncbimtx.hpp
Multi-threading – mutexes; rw-locks; semaphore.
scoremat__.hpp
_ASSERT
#define _ASSERT
Definition: test_assert_impl.h:173
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