NCBI C++ ToolKit
seqfeatdata_unit_test.cpp
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1 /* $Id: seqfeatdata_unit_test.cpp 99326 2023-03-09 19:16:38Z foleyjp $
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: Michael Kornbluh, NCBI
27  *
28  * File Description:
29  * Unit test for CSeqFeatData and some closely related code
30  *
31  * ===========================================================================
32  */
33 
34 #include <ncbi_pch.hpp>
35 
36 #include <objects/general/Name_std.hpp>
37 #include <objects/general/Person_id.hpp>
38 #include <objects/general/User_object.hpp>
39 #include <objects/general/User_field.hpp>
40 #include <objects/general/Object_id.hpp>
41 #include <objects/seqfeat/SeqFeatData.hpp>
42 #include <objects/seqfeat/RNA_ref.hpp>
43 #include <objects/seqfeat/RNA_gen.hpp>
44 #include <objects/seqfeat/Trna_ext.hpp>
45 #include <objects/seqfeat/OrgMod.hpp>
46 #include <objects/seqfeat/SubSource.hpp>
47 #include <objects/seqfeat/BioSource.hpp>
48 #include <objects/seqfeat/OrgName.hpp>
49 #include <objects/seqfeat/Org_ref.hpp>
50 #include <objects/seqfeat/Gb_qual.hpp>
51 #include <objects/seqfeat/Prot_ref.hpp>
52 #include <objects/seqloc/Seq_id.hpp>
53 #include <objects/pub/Pub.hpp>
54 #include <objects/pub/Pub_equiv.hpp>
55 #include <objects/biblio/Cit_art.hpp>
56 #include <objects/biblio/Imprint.hpp>
57 #include <objects/biblio/Cit_gen.hpp>
58 #include <objects/biblio/Cit_jour.hpp>
59 #include <objects/biblio/Cit_book.hpp>
60 #include <objects/biblio/Cit_proc.hpp>
61 #include <objects/biblio/Cit_let.hpp>
62 #include <objects/biblio/Cit_sub.hpp>
63 #include <objects/biblio/Author.hpp>
64 #include <objects/biblio/Auth_list.hpp>
65 #include <objects/biblio/Affil.hpp>
66 #include <corelib/ncbimisc.hpp>
67 #include <corelib/ncbiapp.hpp>
68 #include <corelib/test_boost.hpp>
69 
70 #include <boost/test/parameterized_test.hpp>
71 #include <util/util_exception.hpp>
72 #include <util/util_misc.hpp>
73 #include <util/random_gen.hpp>
74 
75 #include <common/test_assert.h> /* This header must go last */
76 
77 USING_NCBI_SCOPE;
78 USING_SCOPE(objects);
79 
80 static void SetSubSource (objects::CBioSource& src, objects::CSubSource::TSubtype subtype, string val)
81 {
82  if (NStr::IsBlank(val)) {
83  if (src.IsSetSubtype()) {
84  objects::CBioSource::TSubtype::iterator it = src.SetSubtype().begin();
85  while (it != src.SetSubtype().end()) {
86  if ((*it)->IsSetSubtype() && (*it)->GetSubtype() == subtype) {
87  it = src.SetSubtype().erase(it);
88  } else {
89  ++it;
90  }
91  }
92  }
93  } else {
94  CRef<objects::CSubSource> sub(new objects::CSubSource(subtype, val));
95  if (NStr::EqualNocase(val, "true")) {
96  sub->SetName("");
97  }
98  src.SetSubtype().push_back(sub);
99  }
100 }
101 
102 namespace {
103  bool s_TestSubtype(CSeqFeatData::ESubtype eSubtype) {
104  string sNameOfSubtype =
105  CSeqFeatData::SubtypeValueToName(eSubtype);
106  if( sNameOfSubtype.empty() ) {
107  return false;
108  }
109  // make sure it goes in the other direction, too
110  const CSeqFeatData::ESubtype eReverseSubtype =
111  CSeqFeatData::SubtypeNameToValue(sNameOfSubtype);
112  BOOST_CHECK( eReverseSubtype != CSeqFeatData::eSubtype_bad );
113  BOOST_CHECK_EQUAL(eSubtype, eReverseSubtype);
114  return true;
115  }
116 }
117 
118 BOOST_AUTO_TEST_CASE(s_TestSubtypeMaps)
119 {
120  typedef set<CSeqFeatData::ESubtype> TSubtypeSet;
121  // this set holds the subtypes where we expect it to fail
122  // when we try to convert to string
123  TSubtypeSet subtypesExpectedToFail;
124 
125 #ifdef ESUBTYPE_SHOULD_FAIL
126 # error ESUBTYPE_SHOULD_FAIL already defined
127 #endif
128 
129 #define ESUBTYPE_SHOULD_FAIL(name) \
130  subtypesExpectedToFail.insert(CSeqFeatData::eSubtype_##name);
131 
132  // this list seems kind of long. Maybe some of these
133  // should be added to the lookup maps so they
134  // do become valid.
135  ESUBTYPE_SHOULD_FAIL(bad);
136  ESUBTYPE_SHOULD_FAIL(EC_number);
137  ESUBTYPE_SHOULD_FAIL(Imp_CDS);
138  ESUBTYPE_SHOULD_FAIL(allele);
139  ESUBTYPE_SHOULD_FAIL(imp);
140  ESUBTYPE_SHOULD_FAIL(misc_RNA);
141  ESUBTYPE_SHOULD_FAIL(mutation);
142  ESUBTYPE_SHOULD_FAIL(org);
143  ESUBTYPE_SHOULD_FAIL(precursor_RNA);
144  ESUBTYPE_SHOULD_FAIL(source);
145  ESUBTYPE_SHOULD_FAIL(max);
146 
147 #undef ESUBTYPE_SHOULD_FAIL
148 
149  ITERATE_0_IDX(iSubtypeAsInteger, CSeqFeatData::eSubtype_max)
150  {
151  CSeqFeatData::ESubtype eSubtype =
152  static_cast<CSeqFeatData::ESubtype>(iSubtypeAsInteger);
153 
154  // subtypesExpectedToFail tells us which ones are
155  // expected to fail. Others are expected to succeed
156  if( subtypesExpectedToFail.find(eSubtype) ==
157  subtypesExpectedToFail.end() )
158  {
159  NCBITEST_CHECK(s_TestSubtype(eSubtype));
160  } else {
161  NCBITEST_CHECK( ! s_TestSubtype(eSubtype) );
162  }
163  }
164 
165  // a couple values we haven't covered that should
166  // also be tested.
167  NCBITEST_CHECK( ! s_TestSubtype(CSeqFeatData::eSubtype_max) );
168  NCBITEST_CHECK( ! s_TestSubtype(CSeqFeatData::eSubtype_any) );
169 
170  BOOST_CHECK_EQUAL( CSeqFeatData::SubtypeNameToValue("Gene"), CSeqFeatData::eSubtype_gene);
171 }
172 
173 
174 BOOST_AUTO_TEST_CASE(Test_CapitalizationFix)
175 {
176 
177  BOOST_CHECK_EQUAL(COrgMod::FixHostCapitalization("SQUASH"), "squash");
178  BOOST_CHECK_EQUAL(COrgMod::FixHostCapitalization("SOUR cherry"), "sour cherry");
179  CRef<COrgMod> m(new COrgMod());
180  m->SetSubtype(COrgMod::eSubtype_nat_host);
181  m->SetSubname("Turkey");
182  m->FixCapitalization();
183  BOOST_CHECK_EQUAL(m->GetSubname(), "turkey");
184 
185  CRef<CSubSource> s(new CSubSource());
186  s->SetSubtype(CSubSource::eSubtype_sex);
187  s->SetName("Dioecious");
188  s->FixCapitalization();
189  BOOST_CHECK_EQUAL(s->GetName(), "dioecious");
190 
191 
192 }
193 
194 BOOST_AUTO_TEST_CASE(Test_OrgMod_FixHost)
195 {
196  BOOST_CHECK_EQUAL(COrgMod::FixHost("No"),"missing");
197  BOOST_CHECK_EQUAL(COrgMod::FixHost("no"),"missing");
198  BOOST_CHECK_EQUAL(COrgMod::FixHost("NO"),"missing");
199  BOOST_CHECK_EQUAL(COrgMod::FixHost("None"),"missing");
200  BOOST_CHECK_EQUAL(COrgMod::FixHost("none"),"missing");
201  BOOST_CHECK_EQUAL(COrgMod::FixHost("nonE"),"missing");
202  BOOST_CHECK_EQUAL(COrgMod::FixHost("misc"),"missing");
203  BOOST_CHECK_EQUAL(COrgMod::FixHost("obscured"),"obscured");
204  BOOST_CHECK_EQUAL(COrgMod::FixHost("homo sapiens"), "Homo sapiens");
205  BOOST_CHECK_EQUAL(COrgMod::FixHost("HUMAN"), "Homo sapiens");
206  BOOST_CHECK_EQUAL(COrgMod::FixHost("Not Determined"), "unknown");
207 }
208 
209 
210 BOOST_AUTO_TEST_CASE(Test_FixLatLonFormat)
211 {
212  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 degrees 51 degrees 56' 51 ''", true), "51.9475 N 114 E");
213  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 14' 51", true), "51 N 114.23 E");
214  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 degrees, 51 degrees 56' 51 ''", true), "51.9475 N 114 E");
215  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 degrees 14' 42'' 51 degrees 56' 51 ''", true), "51.9475 N 114.2450 E");
216  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 degrees 14' 51 degrees 56' 51 ''", true), "51.9475 N 114.23 E");
217  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 degrees 14' 42'', 51 degrees 56' 51 ''", true), "51.9475 N 114.2450 E");
218  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 degrees 14', 51 degrees 56' 51 ''", true), "51.9475 N 114.23 E");
219  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 14' 42'' 51 56' 51''", true), "51.9475 N 114.2450 E");
220  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 14' 42'' 51 56'", true), "51.93 N 114.2450 E");
221  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 14' 42'' 51", true), "51 N 114.2450 E");
222  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 51", true), "51 N 114 E");
223  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 14' 51 56'", true), "51.93 N 114.23 E");
224  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 14' 42'' 51 56'", true), "51.93 N 114.2450 E");
225  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("114 42'' 51 56'", true), "51.93 N 114.0117 E");
226 
227  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("+60.500280-145.866244", true), "60.500280 N 145.866244 W");
228  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("-60.500280+145.866244", true), "60.500280 S 145.866244 E");
229  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("-60.500280-145.866244", true), "60.500280 S 145.866244 W");
230  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("+60.500280+145.866244", true), "60.500280 N 145.866244 E");
231  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("\"36.222459,139.636522\"", true), "36.222459 N 139.636522 E");
232  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("35 57' 18'' N 79 43' 34\" W", true), "35.9550 N 79.7261 W");
233  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("35 57' 18'' N 79 43' 34' W", true), "35.9550 N 79.7261 W");
234  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("37:22N 005:59W", true), "37.37 N 5.98 W");
235  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("60.42.726'N, 05.05.595E", true), "");
236  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("15.48 N -90.23 W", true), "15.48 N 90.23 W");
237  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("25 . 46 N 108 . 59 W", false), "25.46 N 108.59 W");
238  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("30.1.49N31.11.44E", false), "30.0303 N 31.1956 E");
239  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("27 degrees 22'50'' N 88 degrees 13'16'' E", false), "27.3806 N 88.2211 E");
240  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("27 degrees 22 50 N 88 degrees 13 16 E", false), "27.3806 N 88.2211 E");
241  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("27 degrees 22'50 N 88 degrees 13'16 E", false), "27.3806 N 88.2211 E");
242  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("34 deg 00.465 N 77 deg 41.514 E", false), "34.00775 N 77.69190 E");
243 
244  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("-50.4498 N - 59 74.8912 E", true), "");
245  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("50.4498 N 59 74.8912 E", true), "");
246  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("9.93N\xC2\xB0 and 78.12\xC2\xB0\x45", true), "9.93 N 78.12 E");
247  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("N03'00'12.1 E101'39'33'1", true), "");
248  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("43.098333, -89.405278", true), "43.098333 N 89.405278 W");
249  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("43.098333, -91.00231", true), "43.098333 N 91.00231 W");
250  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("14.60085 and 144.77629", true), "14.60085 N 144.77629 E");
251  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("53.43.20 N 7.43.20 E", true), "53.7222 N 7.7222 E");
252  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("53.43.20.30 N 7.43.20.6 E", true), "");
253  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("91.00 N 5.00 E", true), "");
254  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("83.00 N 181.00 E", true), "");
255  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("91.00 S 5.00 E", true), "");
256  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("83.00 S 181.00 W", true), "");
257 
258  string degree = "\xB0";
259  string to_fix = "9.93" + degree + "N and 78.12" + degree + "E";
260  string fixed = CSubSource::FixLatLonFormat(to_fix, true);
261  BOOST_CHECK_EQUAL(fixed, "9.93 N 78.12 E");
262 
263  to_fix = "Lattitude: 25.790544; longitude: -80.214930";
264  fixed = CSubSource::FixLatLonFormat(to_fix, true);
265  BOOST_CHECK_EQUAL(fixed, "25.790544 N 80.214930 W");
266 
267  to_fix = "34.1030555556 , -118.357777778 34 degrees 6' 11'' North , 118 degrees 21' 28'' West";
268  fixed = CSubSource::FixLatLonFormat(to_fix, true);
269  BOOST_CHECK_EQUAL(fixed, "");
270 
271  to_fix = "0031.02 N 00.01E";
272  fixed = CSubSource::FixLatLonFormat(to_fix, true);
273  BOOST_CHECK_EQUAL(fixed, "31.02 N 0.01 E");
274 
275  to_fix = "000.00 N 0.12 E";
276  fixed = CSubSource::FixLatLonFormat(to_fix, true);
277  BOOST_CHECK_EQUAL(fixed, "0.00 N 0.12 E");
278 
279  to_fix = "0.0023 N 0 E";
280  fixed = CSubSource::FixLatLonFormat(to_fix, true);
281  BOOST_CHECK_EQUAL(fixed, "0.0023 N 0 E");
282 
283  to_fix = "78.32 -0092.25";
284  fixed = CSubSource::FixLatLonFormat(to_fix, true);
285  BOOST_CHECK_EQUAL(fixed, "78.32 N 92.25 W");
286 
287  to_fix = "-0008.34 0.85";
288  fixed = CSubSource::FixLatLonFormat(to_fix, true);
289  BOOST_CHECK_EQUAL(fixed, "8.34 S 0.85 E");
290 
291  to_fix = "0.067682S_76.39885W";
292  fixed = CSubSource::FixLatLonFormat(to_fix, true);
293  BOOST_CHECK_EQUAL(fixed, "0.067682 S 76.39885 W");
294 
295  to_fix = "34degrees 20' 13'' N,47degrees 03' 24''E";
296  fixed = CSubSource::FixLatLonFormat(to_fix, true);
297  BOOST_CHECK_EQUAL(fixed, "34.3369 N 47.0567 E");
298 
299  to_fix = "34degrees 20' 13' N,47deg 03' 24' E";
300  fixed = CSubSource::FixLatLonFormat(to_fix, true);
301  BOOST_CHECK_EQUAL(fixed, "34.3369 N 47.0567 E");
302 
303  to_fix = "8 degrees 28 'N & 77 degrees 41 'E";
304  fixed = CSubSource::FixLatLonFormat(to_fix, true);
305  BOOST_CHECK_EQUAL(fixed, "8.47 N 77.68 E");
306 
307  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 08 36.0S 63 49 00.0W", true), "0.14333 S 63.81667 W");
308  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 08 36.1S 63 49 00.1W", true), "0.14336 S 63.81669 W");
309  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 12 45.5N 50 58 21.7W", true), "0.21264 N 50.97269 W");
310  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 17 28.4N 50 54 07.2W", true), "0.29122 N 50.90200 W");
311  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 4 60.0S 63 07 60.0W", true), "");
312  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 46 56.6S 60 03 37.7W", true), "0.78239 S 60.06047 W");
313  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 50 08.0N 51 12 31.4W", true), "0.83556 N 51.20872 W");
314  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 53 38.85N 52 0 40.37W", true), "0.894125 N 52.011214 W");
315  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("1 00 07.2S 57 07 35.6W", true), "1.00200 S 57.12656 W");
316  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("1 30 59.1N 50 55 01.7W", true), "1.51642 N 50.91714 W");
317  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("1 46 56.6S 60 03 37.7W", true), "1.78239 S 60.06047 W");
318  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("10 0 30.21S 67 50 46.22W", true), "10.008392 S 67.846172 W");
319  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("10 14 14.05S 67 48 42.93W", true), "10.237236 S 67.811925 W");
320  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("2 46 56.6S 60 03 37.7W", true), "2.78239 S 60.06047 W");
321  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("3 53 07.9S 59 04 41.7W", true), "3.88553 S 59.07825 W");
322  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("7 39 52.3S 65 04 11.1W", true), "7.66453 S 65.06975 W");
323  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("8 43 5.46S 63 51 24.49W", true), "8.718183 S 63.856803 W");
324  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("9 30 3.81S 68 53 46.38W", true), "9.501058 S 68.896217 W");
325  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("23.3600 degree N, 92.0000 degree E", true), "23.3600 N 92.0000 E");
326 
327  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("42:43:13N 01:0015W", true), "42.7203 N 1.25 W");
328  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("42:24:37.9 N 85:22:11.7 W", true), "42.41053 N 85.36992 W");
329  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("41deg30'' S 145deg37' E", true), "41.0083 S 145.62 E");
330  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("38 11 44.66 North 0 35 01.93 West", true), "38.195739 N 0.583869 W");
331  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("37deg27N 121deg52'W", true), "37.45 N 121.87 W");
332  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("01deg31'25''N 66''33'31''W", true), "");
333  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("07deg33'30''N 69deg20'W", true), "7.5583 N 69.33 W");
334  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("10.8439,-85.6138", true), "10.8439 N 85.6138 W");
335  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("11.03,-85.527", true), "11.03 N 85.527 W");
336  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("35deg48'50'' N; 82deg5658'' W", true), "");
337  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("45deg34.18''N, 122deg12.00 'W", true), "45.009494 N 122.2000 W");
338  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("37deg27N, 121deg52'W", true), "37.45 N 121.87 W");
339  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("02 deg 28' 29# S, 56 deg 6' 31# W", true), "2.4747 S 56.1086 W");
340  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("86 deg. 30'S, 147 deg. W", true), "86.50 S 147 W");
341  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("E148deg44.8',N19deg24.1", true), "19.402 N 148.747 E");
342  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("-0.000 N 2.415 W", true), "0.000 N 2.415 W");
343  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("N 22.122 E 106.733", true), "22.122 N 106.733 E");
344  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("45#42'N 13#42'E", true), "45.70 N 13.70 E");
345 
346  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("lat 48 deg 32'N, long 58 deg 33'W", true), "48.53 N 58.55 W");
347  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("N 42deg 23.31'; W 111deg 35.12'", true), "42.3885 N 111.5853 W");
348  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("37.9 N lat, 85.8 W long", true), "37.9 N 85.8 W");
349  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("37.918 degrees N latitude, 119.258 degrees W longitude", true), "37.918 N 119.258 W");
350  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("02 37'S, 38 09'E", true), "2.62 S 38.15 E");
351  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("53 deg 23'N 167 deg 50W", true), "53.38 N 167.83 W");
352  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("E148deg44.8',N19deg24.1'", true), "19.402 N 148.747 E");
353  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("N 22 14; W 60 29 28", true), "22.23 N 60.4911 W");
354 
355  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("35 degrees 29'N; 120 degrees 49-51'W", true), "");
356  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("44 deg N 71 deg 30'W", true), "44 N 71.50 W");
357  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("64 deg 41-43'N 165 deg 45'W", true), "");
358  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("N 38deg 25.93'; Wdeg 123 04.88'", true), "38.4322 N 123.0813 W");
359 
360  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("51 56' 51'' -114 14' 42''", true), "51.9475 N 114.2450 W");
361  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("-51 56' 51'' 114 14' 42''", true), "51.9475 S 114.2450 E");
362  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("51 -56' 51'' 114 14' 42''", true), "");
363  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0 56' 51'' -114 14' 42''", true), "0.9475 N 114.2450 W");
364  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("-0 56' 51'' -114 14' 42''", true), "0.9475 S 114.2450 W");
365 
366  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("0.000 S 2.417 W", true), "0.000 N 2.417 W");
367  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("N 16 degree 46 min 57 sec; E 99 degree 01 min 08 sec", true), "16.7825 N 99.0189 E");
368  BOOST_CHECK_EQUAL(CSubSource::FixLatLonFormat("N 16 degree 30 min 16 sec, E 99 degree 09 min 40 sec", true), "16.5044 N 99.1611 E");
369 
370 }
371 
372 
373 CRef<CAuth_list> s_MakeAuthList()
374 {
375  CRef<CAuth_list> auth_list(new CAuth_list());
376 
377  auth_list->SetAffil().SetStd().SetAffil("Murdoch University");
378  auth_list->SetAffil().SetStd().SetDiv("School of Veterinary and Life Sciences");
379  auth_list->SetAffil().SetStd().SetCity("Murdoch");
380  auth_list->SetAffil().SetStd().SetSub("Western Australia");
381  auth_list->SetAffil().SetStd().SetCountry("Australia");
382  auth_list->SetAffil().SetStd().SetStreet("90 South Street");
383  auth_list->SetAffil().SetStd().SetPostal_code("6150");
384  CRef<CAuthor> auth1(new CAuthor());
385  auth1->SetName().SetName().SetLast("Yang");
386  auth1->SetName().SetName().SetFirst("Rongchang");
387  auth1->SetName().SetName().SetInitials("R.");
388  auth_list->SetNames().SetStd().push_back(auth1);
389  CRef<CAuthor> auth2(new CAuthor());
390  auth2->SetName().SetName().SetLast("Ryan");
391  auth2->SetName().SetName().SetFirst("Una");
392  auth2->SetName().SetName().SetInitials("U.");
393  auth_list->SetNames().SetStd().push_back(auth2);
394 
395  return auth_list;
396 }
397 
398 void s_ChangeAuthorFirstName(CAuth_list& auth_list)
399 {
400  if (auth_list.SetNames().SetStd().size() == 0) {
401  CRef<CAuthor> auth(new CAuthor());
402  auth->SetName().SetName().SetLast("Last");
403  auth_list.SetNames().SetStd().push_back(auth);
404  }
405  auth_list.SetNames().SetStd().back()->SetName().SetName().SetFirst("Uan");
406 }
407 
408 
409 void s_ChangeAuthorLastName(CAuth_list& auth_list)
410 {
411  if (auth_list.SetNames().SetStd().size() == 0) {
412  CRef<CAuthor> auth(new CAuthor());
413  auth->SetName().SetName().SetLast("Last");
414  auth_list.SetNames().SetStd().push_back(auth);
415  }
416  auth_list.SetNames().SetStd().back()->SetName().SetName().SetLast("Nyar");
417 }
418 
419 
420 CRef<CAuth_list> s_SetAuthList(CPub& pub)
421 {
422  CRef<CAuth_list> rval(NULL);
423  switch (pub.Which()) {
424  case CPub::e_Article:
425  rval.Reset(&(pub.SetArticle().SetAuthors()));
426  break;
427  case CPub::e_Gen:
428  rval.Reset(&(pub.SetGen().SetAuthors()));
429  break;
430  case CPub::e_Sub:
431  rval.Reset(&(pub.SetSub().SetAuthors()));
432  break;
433  case CPub::e_Book:
434  rval.Reset(&(pub.SetBook().SetAuthors()));
435  break;
436  case CPub::e_Proc:
437  rval.Reset(&(pub.SetProc().SetBook().SetAuthors()));
438  break;
439  case CPub::e_Man:
440  rval.Reset(&(pub.SetMan().SetCit().SetAuthors()));
441  break;
442  default:
443  rval = null;
444  break;
445  }
446  return rval;
447 }
448 
449 
450 bool s_ChangeAuthorFirstName(CPub& pub)
451 {
452  bool rval = false;
453  CRef<CAuth_list> auth_list = s_SetAuthList(pub);
454  if (auth_list) {
455  s_ChangeAuthorFirstName(*auth_list);
456  rval = true;
457  }
458  return rval;
459 }
460 
461 
462 bool s_ChangeAuthorLastName(CPub& pub)
463 {
464  bool rval = true;
465  CRef<CAuth_list> auth_list = s_SetAuthList(pub);
466  if (auth_list) {
467  s_ChangeAuthorLastName(*auth_list);
468  rval = true;
469  }
470  return rval;
471 }
472 
473 
474 CRef<CImprint> s_MakeImprint()
475 {
476  CRef<CImprint> imp(new CImprint());
477  imp->SetDate().SetStr("?");
478  imp->SetPrepub(CImprint::ePrepub_in_press);
479  return imp;
480 }
481 
482 
483 CRef<CImprint> s_SetImprint(CPub& pub)
484 {
485  CRef<CImprint> imp(NULL);
486  switch (pub.Which()) {
487  case CPub::e_Article:
488  if (pub.GetArticle().IsSetFrom()) {
489  if (pub.GetArticle().GetFrom().IsJournal()) {
490  imp.Reset(&(pub.SetArticle().SetFrom().SetJournal().SetImp()));
491  } else if (pub.GetArticle().GetFrom().IsBook()) {
492  imp.Reset(&(pub.SetArticle().SetFrom().SetBook().SetImp()));
493  }
494  }
495  break;
496  case CPub::e_Sub:
497  imp.Reset(&(pub.SetSub().SetImp()));
498  break;
499  case CPub::e_Book:
500  imp.Reset(&(pub.SetBook().SetImp()));
501  break;
502  case CPub::e_Journal:
503  imp.Reset(&(pub.SetJournal().SetImp()));
504  break;
505  case CPub::e_Proc:
506  imp.Reset(&(pub.SetProc().SetBook().SetImp()));
507  break;
508  case CPub::e_Man:
509  imp.Reset(&(pub.SetMan().SetCit().SetImp()));
510  break;
511  default:
512  break;
513  }
514 
515  return imp;
516 }
517 
518 
519 void s_AddNameTitle(CTitle& title)
520 {
521  CRef<CTitle::C_E> t(new CTitle::C_E());
522  t->SetName("a random title");
523  title.Set().push_back(t);
524 }
525 
526 
527 void s_ChangeNameTitle(CTitle& title)
528 {
529  if (title.Set().size() == 0) {
530  s_AddNameTitle(title);
531  }
532  title.Set().front()->SetName() += " plus";
533 }
534 
535 
536 void s_AddJTATitle(CTitle& title)
537 {
538  CRef<CTitle::C_E> t(new CTitle::C_E());
539  t->SetJta("a random title");
540  title.Set().push_back(t);
541 }
542 
543 
544 void s_ChangeJTATitle(CTitle& title)
545 {
546  if (title.Set().size() == 0) {
547  s_AddJTATitle(title);
548  }
549  title.Set().front()->SetJta() += " plus";
550 }
551 
552 void s_ChangeTitle(CPub& pub)
553 {
554  switch (pub.Which()) {
555  case CPub::e_Article:
556  s_ChangeNameTitle(pub.SetArticle().SetTitle());
557  break;
558  case CPub::e_Book:
559  s_ChangeNameTitle(pub.SetBook().SetTitle());
560  break;
561  case CPub::e_Journal:
562  s_ChangeJTATitle(pub.SetJournal().SetTitle());
563  break;
564  case CPub::e_Proc:
565  s_ChangeNameTitle(pub.SetProc().SetBook().SetTitle());
566  break;
567  case CPub::e_Man:
568  s_ChangeNameTitle(pub.SetMan().SetCit().SetTitle());
569  break;
570  case CPub::e_Gen:
571  pub.SetGen().SetCit() += " plus";
572  break;
573  default:
574  break;
575  }
576 }
577 
578 
579 void s_ChangeDate(CDate& date)
580 {
581  date.SetStd().SetYear(2014);
582 }
583 
584 
585 void s_ChangeImprintNoMatch(CImprint& imp, int change_no)
586 {
587  switch (change_no) {
588  case 0:
589  s_ChangeDate(imp.SetDate());
590  break;
591  case 1:
592  imp.SetVolume("123");
593  break;
594  default:
595  break;
596  }
597 }
598 
599 
600 void s_ChangeImprintMatch(CImprint& imp, int change_no)
601 {
602  switch (change_no) {
603  case 0:
604  imp.SetPrepub(CImprint::ePrepub_submitted);
605  break;
606  case 1:
607  imp.SetPub().SetStr("Publisher");
608  break;
609  default:
610  break;
611  }
612 }
613 
614 
615 bool s_ChangeImprintNoMatch(CPub& pub, int change_no)
616 {
617  bool rval = false;
618  CRef<CImprint> imp = s_SetImprint(pub);
619  if (imp) {
620  s_ChangeImprintNoMatch(*imp, change_no);
621  rval = true;
622  }
623  return rval;
624 }
625 
626 
627 bool s_ChangeImprintMatch(CPub& pub, int change_no)
628 {
629  bool rval = false;
630  CRef<CImprint> imp = s_SetImprint(pub);
631  if (imp) {
632  s_ChangeImprintMatch(*imp, change_no);
633  rval = true;
634  }
635  return rval;
636 }
637 
638 
639 BOOST_AUTO_TEST_CASE(Test_AuthList_SameCitation)
640 {
641  CRef<CAuth_list> auth_list1 = s_MakeAuthList();
642  CRef<CAuth_list> auth_list2(new CAuth_list());
643  auth_list2->Assign(*auth_list1);
644 
645  // should match if identical
646  BOOST_CHECK_EQUAL(auth_list1->SameCitation(*auth_list2), true);
647 
648  // should match if only difference is author first name
649  s_ChangeAuthorFirstName(*auth_list2);
650  BOOST_CHECK_EQUAL(auth_list1->SameCitation(*auth_list2), true);
651 
652  // should not match if different last name
653  s_ChangeAuthorLastName(*auth_list2);
654  BOOST_CHECK_EQUAL(auth_list1->SameCitation(*auth_list2), false);
655 }
656 
657 
658 CRef<CCit_jour> s_MakeJournal()
659 {
660  CRef<CCit_jour> jour(new CCit_jour());
661 
662  CRef<CTitle::C_E> j_title(new CTitle::C_E());
663  j_title->SetJta("Experimental Parasitology");
664  jour->SetTitle().Set().push_back(j_title);
665  jour->SetImp().Assign(*s_MakeImprint());
666 
667  return jour;
668 }
669 
670 
671 CRef<CPub> s_MakeJournalArticlePub()
672 {
673  CRef<CPub> pub(new CPub());
674  CRef<CTitle::C_E> title(new CTitle::C_E());
675  title->SetName("Isospora streperae n. sp. (Apicomplexa: Eimeriidae) from a Grey Currawong (Strepera versicolour plumbea) (Passeriformes: Artamidae) in Western Australia");
676  pub->SetArticle().SetTitle().Set().push_back(title);
677  pub->SetArticle().SetFrom().SetJournal().Assign(*s_MakeJournal());
678  pub->SetArticle().SetAuthors().Assign(*s_MakeAuthList());
679  return pub;
680 }
681 
682 
683 CRef<CCit_book> s_MakeBook()
684 {
685  CRef<CCit_book> book(new CCit_book());
686  CRef<CTitle::C_E> b_title(new CTitle::C_E());
687  b_title->SetName("Book Title");
688  book->SetTitle().Set().push_back(b_title);
689  book->SetImp().Assign(*s_MakeImprint());
690  book->SetAuthors().Assign(*s_MakeAuthList());
691 
692  return book;
693 }
694 
695 
696 CRef<CPub> s_MakeBookChapterPub()
697 {
698  CRef<CPub> pub(new CPub());
699  CRef<CTitle::C_E> title(new CTitle::C_E());
700  title->SetName("Isospora streperae n. sp. (Apicomplexa: Eimeriidae) from a Grey Currawong (Strepera versicolour plumbea) (Passeriformes: Artamidae) in Western Australia");
701  pub->SetArticle().SetTitle().Set().push_back(title);
702  pub->SetArticle().SetFrom().SetBook().Assign(*s_MakeBook());
703  pub->SetArticle().SetAuthors().Assign(*s_MakeAuthList());
704  return pub;
705 }
706 
707 
708 void s_TestAuthorChanges(CPub& pub)
709 {
710  CRef<CPub> other(new CPub());
711  other->Assign(pub);
712  // should match if only difference is author first name
713  s_ChangeAuthorFirstName(*other);
714  BOOST_CHECK_EQUAL(pub.SameCitation(*other), true);
715 
716  // should not match if difference in last name
717  other->Assign(pub);
718  s_ChangeAuthorLastName(*other);
719  BOOST_CHECK_EQUAL(pub.SameCitation(*other), false);
720 }
721 
722 
723 void s_TestImprintChanges(CPub& pub)
724 {
725  CRef<CPub> other(new CPub());
726  other->Assign(pub);
727 
728  if (!s_SetImprint(pub)) {
729  if (pub.IsGen()) {
730  // test dates
731  s_ChangeDate(other->SetGen().SetDate());
732  BOOST_CHECK_EQUAL(pub.SameCitation(*other), false);
733  }
734  return;
735  }
736 
737 
738  // should match if noncritical Imprint change
739  s_ChangeImprintMatch(*other, 0);
740  BOOST_CHECK_EQUAL(pub.SameCitation(*other), true);
741  other->Assign(pub);
742  s_ChangeImprintMatch(*other, 1);
743  BOOST_CHECK_EQUAL(pub.SameCitation(*other), true);
744 
745  // should not match if cricital Imprint change
746  other->Assign(pub);
747  s_ChangeImprintNoMatch(*other, 0);
748  BOOST_CHECK_EQUAL(pub.SameCitation(*other), false);
749  other->Assign(pub);
750  s_ChangeImprintNoMatch(*other, 1);
751  BOOST_CHECK_EQUAL(pub.SameCitation(*other), false);
752 
753 }
754 
755 
756 void s_TestTitleChange(CPub& pub)
757 {
758  // should not match if extra text in article title
759  CRef<CPub> other(new CPub());
760  other->Assign(pub);
761  s_ChangeTitle(*other);
762  BOOST_CHECK_EQUAL(pub.SameCitation(*other), false);
763 }
764 
765 
766 BOOST_AUTO_TEST_CASE(Test_Pub_SameCitation)
767 {
768  CRef<CPub> pub1 = s_MakeJournalArticlePub();
769  CRef<CPub> pub2(new CPub());
770  pub2->Assign(*pub1);
771 
772  // journal article
773  // should match if identical
774  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
775 
776  // change journal title
777  s_ChangeJTATitle(pub2->SetArticle().SetFrom().SetJournal().SetTitle());
778  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
779 
780  s_TestAuthorChanges(*pub1);
781  s_TestImprintChanges(*pub1);
782  s_TestTitleChange(*pub1);
783 
784  // journal pub
785  pub1->SetJournal().Assign(*s_MakeJournal());
786  pub2->Assign(*pub1);
787 
788  // should match if identical
789  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
790 
791  s_TestImprintChanges(*pub1);
792  s_TestTitleChange(*pub1);
793 
794  // book chapter
795  pub1 = s_MakeBookChapterPub();
796  pub2->Assign(*pub1);
797 
798  // should match if identical
799  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
800 
801  // change book title
802  s_ChangeNameTitle(pub2->SetArticle().SetFrom().SetBook().SetTitle());
803  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
804 
805  s_TestAuthorChanges(*pub1);
806  s_TestImprintChanges(*pub1);
807  s_TestTitleChange(*pub1);
808 
809  // Book
810  pub1->SetBook().Assign(*s_MakeBook());
811  pub2->Assign(*pub1);
812 
813  // should match if identical
814  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
815 
816  s_TestAuthorChanges(*pub1);
817  s_TestImprintChanges(*pub1);
818  s_TestTitleChange(*pub1);
819 
820  // Proc
821  pub1->SetProc().SetBook().Assign(*s_MakeBook());
822  pub2->Assign(*pub1);
823 
824  // should match if identical
825  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
826 
827  s_TestAuthorChanges(*pub1);
828  s_TestImprintChanges(*pub1);
829  s_TestTitleChange(*pub1);
830 
831  // Man
832  pub1->SetMan().SetCit().Assign(*s_MakeBook());
833  pub2->Assign(*pub1);
834 
835  // should match if identical
836  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
837 
838  s_TestAuthorChanges(*pub1);
839  s_TestImprintChanges(*pub1);
840  s_TestTitleChange(*pub1);
841 
842 
843  // Gen
844  pub1->SetGen().SetCit("citation title");
845  pub1->SetGen().SetVolume("volume");
846  pub1->SetGen().SetIssue("issue");
847  pub1->SetGen().SetPages("pages");
848  pub1->SetGen().SetTitle("title");
849 
850  pub1->SetGen().SetAuthors().Assign(*s_MakeAuthList());
851  pub2->Assign(*pub1);
852 
853  // should match if identical
854  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
855 
856  // change other fields
857  // volume
858  pub2->SetGen().SetVolume("x");
859  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
860  pub1->SetGen().SetVolume("y");
861  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
862  pub2->Assign(*pub1);
863  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
864  // issue
865  pub2->SetGen().SetIssue("x");
866  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
867  pub1->SetGen().SetIssue("y");
868  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
869  pub2->Assign(*pub1);
870  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
871  // pages
872  pub2->SetGen().SetPages("x");
873  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
874  pub1->SetGen().SetPages("y");
875  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
876  pub2->Assign(*pub1);
877  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
878  // title
879  pub2->SetGen().SetTitle("x");
880  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
881  pub1->SetGen().SetTitle("y");
882  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
883  pub2->Assign(*pub1);
884  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
885  // muid
886  pub2->SetGen().SetMuid(ENTREZ_ID_FROM(TIntId, 40));
887  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
888  pub2->Assign(*pub1);
889  pub1->SetGen().SetMuid(ENTREZ_ID_FROM(TIntId, 42));
890  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
891  pub2->Assign(*pub1);
892  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
893  // serial number
894  pub2->SetGen().SetSerial_number(40);
895  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
896  pub1->SetGen().SetSerial_number(42);
897  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
898  pub2->Assign(*pub1);
899  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
900 
901  // journal
902  s_AddNameTitle(pub2->SetGen().SetJournal());
903  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
904  // should still be false if title types are different
905  s_AddJTATitle(pub1->SetGen().SetJournal());
906  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), false);
907  // but ok now
908  s_AddJTATitle(pub2->SetGen().SetJournal());
909  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
910 
911  s_TestAuthorChanges(*pub1);
912  s_TestImprintChanges(*pub1);
913  s_TestTitleChange(*pub1);
914 
915  // sub
916  pub1->SetSub().SetAuthors().Assign(*s_MakeAuthList());
917  pub1->SetSub().SetImp().Assign(*s_MakeImprint());
918  pub2->Assign(*pub1);
919 
920  // should match if identical
921  BOOST_CHECK_EQUAL(pub1->SameCitation(*pub2), true);
922 
923  s_TestAuthorChanges(*pub1);
924  s_TestImprintChanges(*pub1);
925 
926 }
927 
928 
929 BOOST_AUTO_TEST_CASE(Test_PubEquiv_SameCitation)
930 {
931  CRef<CPub_equiv> eq1(new CPub_equiv());
932 
933  CRef<CPub> pub = s_MakeJournalArticlePub();
934  eq1->Set().push_back(pub);
935 
936  CRef<CPub_equiv> eq2(new CPub_equiv());
937  eq2->Assign(*eq1);
938 
939  // should match if identical
940  BOOST_CHECK_EQUAL(eq1->SameCitation(*eq2), true);
941 
942  // should match if second also has PubMed ID (but first does not)
943  CRef<CPub> pmid2(new CPub());
944  pmid2->SetPmid().Set(ENTREZ_ID_FROM(TIntId, 4));
945  eq2->Set().push_back(pmid2);
946  BOOST_CHECK_EQUAL(eq1->SameCitation(*eq2), true);
947 
948  // but not if first has different article
949  s_ChangeAuthorLastName(eq1->Set().front()->SetArticle().SetAuthors());
950  BOOST_CHECK_EQUAL(eq1->SameCitation(*eq2), false);
951 
952  // won't match even if PubMed IDs match
953  CRef<CPub> pmid1(new CPub());
954  pmid1->SetPmid().Set(ENTREZ_ID_FROM(TIntId, 4));
955  eq1->Set().push_back(pmid1);
956  BOOST_CHECK_EQUAL(eq1->SameCitation(*eq2), false);
957 }
958 
959 
960 #define CHECK_COMMON_FIELD(o1,o2,c,Field,val1,val2) \
961  o1->Set##Field(val1); \
962  o2->Reset##Field(); \
963  c = o1->MakeCommon(*o2); \
964  BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \
965  o2->Set##Field(val2); \
966  c = o1->MakeCommon(*o2); \
967  BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \
968  o2->Set##Field(val1); \
969  c = o1->MakeCommon(*o2); \
970  BOOST_CHECK_EQUAL(c->IsSet##Field(), true); \
971  BOOST_CHECK_EQUAL(c->Get##Field(), o1->Get##Field());
972 
973 
974 BOOST_AUTO_TEST_CASE(Test_OrgName_MakeCommon)
975 {
976  CRef<COrgName> on1(new COrgName());
977  CRef<COrgName> on2(new COrgName());
978  CRef<COrgName> common = on1->MakeCommon(*on2);
979  if (common) {
980  BOOST_ASSERT("common OrgName should not have been created");
981  }
982 
983  on1->SetDiv("bacteria");
984  common = on1->MakeCommon(*on2);
985  if (common) {
986  BOOST_ASSERT("common OrgName should not have been created");
987  }
988  on2->SetDiv("archaea");
989  common = on1->MakeCommon(*on2);
990  if (common) {
991  BOOST_ASSERT("common OrgName should not have been created");
992  }
993  on2->SetDiv("bacteria");
994  common = on1->MakeCommon(*on2);
995  BOOST_CHECK_EQUAL(common->GetDiv(), "bacteria");
996 
997  // one orgmod on 1, no orgmods on 2, should not add orgmods to common
998  CRef<COrgMod> m1(new COrgMod());
999  m1->SetSubtype(COrgMod::eSubtype_acronym);
1000  m1->SetSubname("x");
1001  on1->SetMod().push_back(m1);
1002  common = on1->MakeCommon(*on2);
1003  BOOST_CHECK_EQUAL(common->IsSetMod(), false);
1004  // one orgmod on 1, one orgmods on 2 of different type, should not add orgmods to common
1005  CRef<COrgMod> m2(new COrgMod());
1006  m2->SetSubtype(COrgMod::eSubtype_anamorph);
1007  m2->SetSubname("x");
1008  on2->SetMod().push_back(m2);
1009 
1010  common = on1->MakeCommon(*on2);
1011  BOOST_CHECK_EQUAL(common->IsSetMod(), false);
1012  // same orgmod on both, should add
1013  m2->SetSubtype(COrgMod::eSubtype_acronym);
1014  common = on1->MakeCommon(*on2);
1015  BOOST_CHECK_EQUAL(common->IsSetMod(), true);
1016  BOOST_CHECK_EQUAL(common->GetMod().size(), 1);
1017  BOOST_CHECK_EQUAL(common->GetMod().front()->Equals(*m2), true);
1018 
1019  CHECK_COMMON_FIELD(on1,on2,common,Attrib,"x","y");
1020  CHECK_COMMON_FIELD(on1,on2,common,Lineage,"x","y");
1021  CHECK_COMMON_FIELD(on1,on2,common,Gcode,1,2);
1022  CHECK_COMMON_FIELD(on1,on2,common,Mgcode,3,4);
1023  CHECK_COMMON_FIELD(on1,on2,common,Pgcode,5,6);
1024 
1025 }
1026 
1027 
1028 #define CHECK_COMMON_STRING_LIST(o1,o2,c,Field,val1,val2) \
1029  o1->Set##Field().push_back(val1); \
1030  c = o1->MakeCommon(*o2); \
1031  BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \
1032  o2->Set##Field().push_back(val2); \
1033  c = o1->MakeCommon(*o2); \
1034  BOOST_CHECK_EQUAL(c->IsSet##Field(), false); \
1035  o2->Set##Field().push_back(val1); \
1036  c = o1->MakeCommon(*o2); \
1037  BOOST_CHECK_EQUAL(c->IsSet##Field(), true); \
1038  BOOST_CHECK_EQUAL(c->Get##Field().size(), 1); \
1039  BOOST_CHECK_EQUAL(c->Get##Field().front(), val1);
1040 
1041 BOOST_AUTO_TEST_CASE(Test_OrgRef_MakeCommon)
1042 {
1043  CRef<COrg_ref> org1(new COrg_ref());
1044  CRef<COrg_ref> org2(new COrg_ref());
1045  CRef<COrg_ref> common = org1->MakeCommon(*org2);
1046  if (common) {
1047  BOOST_ASSERT("common OrgRef should not have been created");
1048  }
1049  org1->SetTaxId(TAX_ID_CONST(1));
1050  org2->SetTaxId(TAX_ID_CONST(2));
1051  common = org1->MakeCommon(*org2);
1052  if (common) {
1053  BOOST_ASSERT("common OrgRef should not have been created");
1054  }
1055 
1056  org2->SetTaxId(TAX_ID_CONST(1));
1057  common = org1->MakeCommon(*org2);
1058  BOOST_CHECK_EQUAL(common->GetTaxId(), TAX_ID_CONST(1));
1059  BOOST_CHECK_EQUAL(common->IsSetTaxname(), false);
1060 
1061  CHECK_COMMON_FIELD(org1,org2,common,Taxname,"A","B");
1062  CHECK_COMMON_FIELD(org1,org2,common,Common,"A","B");
1063 
1064  CHECK_COMMON_STRING_LIST(org1,org2,common,Mod,"a","b");
1065  CHECK_COMMON_STRING_LIST(org1,org2,common,Syn,"a","b");
1066 
1067 }
1068 
1069 
1070 BOOST_AUTO_TEST_CASE(Test_BioSource_MakeCommon)
1071 {
1072  CRef<CBioSource> src1(new CBioSource());
1073  CRef<CBioSource> src2(new CBioSource());
1074  CRef<CBioSource> common = src1->MakeCommon(*src2);
1075  if (common) {
1076  BOOST_ASSERT("common BioSource should not have been created");
1077  }
1078 
1079  src1->SetOrg().SetTaxId(TAX_ID_CONST(1));
1080  src2->SetOrg().SetTaxId(TAX_ID_CONST(1));
1081  common = src1->MakeCommon(*src2);
1082  BOOST_CHECK_EQUAL(common->GetOrg().GetTaxId(), TAX_ID_CONST(1));
1083 
1084  CRef<CSubSource> s1(new CSubSource());
1085  s1->SetSubtype(CSubSource::eSubtype_altitude);
1086  s1->SetName("x");
1087  src1->SetSubtype().push_back(s1);
1088  common = src1->MakeCommon(*src2);
1089  BOOST_CHECK_EQUAL(common->IsSetSubtype(), false);
1090 
1091  CRef<CSubSource> s2(new CSubSource());
1092  s2->SetSubtype(CSubSource::eSubtype_altitude);
1093  s2->SetName("y");
1094  src2->SetSubtype().push_back(s2);
1095  common = src1->MakeCommon(*src2);
1096  BOOST_CHECK_EQUAL(common->IsSetSubtype(), false);
1097 
1098  s2->SetName("x");
1099  common = src1->MakeCommon(*src2);
1100  BOOST_CHECK_EQUAL(common->IsSetSubtype(), true);
1101  BOOST_CHECK_EQUAL(common->GetSubtype().size(), 1);
1102  BOOST_CHECK_EQUAL(common->GetSubtype().front()->Equals(*s2), true);
1103 
1104  CHECK_COMMON_FIELD(src1,src2,common,Genome,CBioSource::eGenome_apicoplast,CBioSource::eGenome_chloroplast);
1105  CHECK_COMMON_FIELD(src1,src2,common,Origin,CBioSource::eOrigin_artificial,CBioSource::eOrigin_mut);
1106 }
1107 
1108 BOOST_AUTO_TEST_CASE(Test_BioSource_GetRepliconName_CXX_10657)
1109 {
1110  CRef<CBioSource> src1(new CBioSource());
1111 
1112  src1->SetOrg().SetTaxId(TAX_ID_CONST(1));
1113 
1114  SetSubSource(*src1,CSubSource::eSubtype_altitude,"X");
1115  BOOST_CHECK_EQUAL(src1->IsSetSubtype(), true);
1116  // chromosome-name
1117  SetSubSource(*src1,CSubSource::eSubtype_chromosome,"X");
1118  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "X");
1119  // remove chromosome setting
1120  src1->ResetSubtype();
1121  // Plasmid-name
1122  SetSubSource(*src1,CSubSource::eSubtype_plasmid_name,"plasmid1");
1123  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "plasmid1");
1124  src1->ResetSubtype();
1125 
1126  // Plastid-name
1127  SetSubSource(*src1,CSubSource::eSubtype_plastid_name,"pltd1");
1128  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "pltd1");
1129  src1->ResetSubtype();
1130 
1131  // endogenous-virus-name
1132  SetSubSource(*src1,CSubSource::eSubtype_endogenous_virus_name,"virus1");
1133  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "virus1");
1134  src1->ResetSubtype();
1135 
1136  // linkage-group
1137  SetSubSource(*src1,CSubSource::eSubtype_linkage_group,"LG2");
1138  src1->SetGenome(CBioSource_Base::eGenome_chromosome);
1139  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "LG2");
1140 
1141  // cleanup for next test
1142  src1->ResetSubtype();
1143  src1->ResetGenome();
1144 
1145  // segment
1146  // {
1147  // subtype segment,
1148  // name "DNA-U1"
1149  // }
1150  src1->SetOrg().SetOrgname().SetLineage("Viruses; ssDNA viruses; Nanoviridae; Nanovirus");
1151  SetSubSource(*src1,CSubSource::eSubtype_segment,"DNA-U1");
1152  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "DNA-U1");
1153  // reset for next tests
1154  src1->ResetSubtype();
1155  src1->ResetGenome();
1156 
1157  src1->SetGenome(CBioSource::eGenome_unknown);
1158  SetSubSource(*src1,CSubSource::eSubtype_insertion_seq_name,"insername");
1159  BOOST_CHECK_EQUAL(NStr::IsBlank(src1->GetRepliconName()), true);
1160  src1->ResetSubtype();
1161  src1->ResetGenome();
1162  //
1163  // default values
1164  //
1165  src1->SetGenome(CBioSource::eGenome_plasmid);
1166  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "unnamed");
1167  src1->SetGenome(CBioSource::eGenome_plasmid_in_mitochondrion);
1168  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "unnamed");
1169  src1->SetGenome(CBioSource::eGenome_plasmid_in_plastid);
1170  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "unnamed");
1171  // chromosome
1172  src1->SetGenome(CBioSource::eGenome_chromosome);
1173  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "ANONYMOUS");
1174  // kinetoplast
1175  src1->SetGenome(CBioSource::eGenome_kinetoplast);
1176  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "kinetoplast");
1177  // plastid
1178  src1->SetGenome(CBioSource::eGenome_plastid);
1179  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "Pltd");
1180  src1->SetGenome(CBioSource::eGenome_chloroplast);
1181  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "Pltd");
1182  src1->SetGenome(CBioSource::eGenome_chromoplast);
1183  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "Pltd");
1184  src1->SetGenome(CBioSource::eGenome_apicoplast);
1185  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "Pltd");
1186  src1->SetGenome(CBioSource::eGenome_leucoplast);
1187  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "Pltd");
1188  src1->SetGenome(CBioSource::eGenome_proplastid);
1189  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "Pltd");
1190  src1->SetGenome(CBioSource::eGenome_chromatophore);
1191  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "Pltd");
1192  //
1193  // mitochondrion
1194  //
1195  src1->SetGenome(CBioSource::eGenome_mitochondrion);
1196  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "MT");
1197  src1->SetGenome(CBioSource::eGenome_hydrogenosome);
1198  BOOST_CHECK_EQUAL(src1->GetRepliconName(), "MT");
1199  // blank
1200  src1->ResetGenome();
1201  BOOST_CHECK_EQUAL(NStr::IsBlank(src1->GetRepliconName()), true);
1202 }
1203 
1204 
1205 BOOST_AUTO_TEST_CASE(Test_Regulatory)
1206 {
1207  BOOST_CHECK_EQUAL(CSeqFeatData::IsRegulatory(CSeqFeatData::eSubtype_attenuator), true);
1208  BOOST_CHECK_EQUAL(CSeqFeatData::IsRegulatory(CSeqFeatData::eSubtype_cdregion), false);
1209  BOOST_CHECK_EQUAL(CSeqFeatData::GetRegulatoryClass(CSeqFeatData::eSubtype_RBS), "ribosome_binding_site");
1210  BOOST_CHECK_EQUAL(CSeqFeatData::GetRegulatoryClass(CSeqFeatData::eSubtype_terminator), "terminator");
1211  BOOST_CHECK_EQUAL(CSeqFeatData::IsRegulatory(CSeqFeatData::eSubtype_LTR), true);
1212 }
1213 
1214 
1215 BOOST_AUTO_TEST_CASE(Test_RmCultureNotes)
1216 {
1217  CRef<CSubSource> ss(new CSubSource());
1218  ss->SetSubtype(CSubSource::eSubtype_other);
1219  ss->SetName("a; [mixed bacterial source]; b");
1220  ss->RemoveCultureNotes();
1221  BOOST_CHECK_EQUAL(ss->GetName(), "a; b");
1222  ss->SetName("[uncultured (using species-specific primers) bacterial source]");
1223  ss->RemoveCultureNotes();
1224  BOOST_CHECK_EQUAL(ss->GetName(), "amplified with species-specific primers");
1225  ss->SetName("[BankIt_uncultured16S_wizard]; [universal primers]; [tgge]");
1226  ss->RemoveCultureNotes();
1227  BOOST_CHECK_EQUAL(ss->IsSetName(), false);
1228  ss->SetName("[BankIt_uncultured16S_wizard]; [species_specific primers]; [dgge]");
1229  ss->RemoveCultureNotes();
1230  BOOST_CHECK_EQUAL(ss->GetName(), "amplified with species-specific primers");
1231 
1232  CRef<CBioSource> src(new CBioSource());
1233  ss->SetName("a; [mixed bacterial source]; b");
1234  src->SetSubtype().push_back(ss);
1235  src->RemoveCultureNotes();
1236  BOOST_CHECK_EQUAL(ss->GetName(), "a; b");
1237  ss->SetName("[BankIt_uncultured16S_wizard]; [universal primers]; [tgge]");
1238  src->RemoveCultureNotes();
1239  BOOST_CHECK_EQUAL(src->IsSetSubtype(), false);
1240 
1241  ss->SetName("[BankIt_uncultured16S_wizard]; [species_specific primers]; [dgge]");
1242  ss->RemoveCultureNotes(false);
1243  BOOST_CHECK_EQUAL(ss->GetName(), "[BankIt_uncultured16S_wizard]; [species_specific primers]; [dgge]");
1244 
1245  ss->SetName("[BankIt_cultured16S_wizard]");
1246  src->RemoveCultureNotes();
1247  BOOST_CHECK_EQUAL(src->IsSetSubtype(), false);
1248 
1249 }
1250 
1251 BOOST_AUTO_TEST_CASE(Test_DiscouragedEnums)
1252 {
1253  // check for enums that pass
1254  //
1255  // make sure to pick subtypes and quals that are
1256  // very unlikely to be deprecated in the future
1257 
1258  // check for discouraged enums
1259  BOOST_CHECK(
1260  CSeqFeatData::IsDiscouragedSubtype(CSeqFeatData::eSubtype_conflict));
1261  BOOST_CHECK(
1262  CSeqFeatData::IsDiscouragedQual(CSeqFeatData::eQual_insertion_seq));
1263 
1264  BOOST_CHECK(
1265  ! CSeqFeatData::IsDiscouragedSubtype(CSeqFeatData::eSubtype_gene));
1266  BOOST_CHECK(
1267  ! CSeqFeatData::IsDiscouragedQual(CSeqFeatData::eQual_host));
1268 }
1269 
1270 
1271 BOOST_AUTO_TEST_CASE(Test_CheckCellLine)
1272 {
1273  string msg = CSubSource::CheckCellLine("222", "Homo sapiens");
1274  BOOST_CHECK_EQUAL(msg, "The International Cell Line Authentication Committee database indicates that 222 from Homo sapiens is known to be contaminated by PA1 from Human. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1275 
1276  msg = CSubSource::CheckCellLine("223", "Homo sapiens");
1277  BOOST_CHECK_EQUAL(msg, "");
1278 
1279  msg = CSubSource::CheckCellLine("222", "Canis familiaris");
1280  BOOST_CHECK_EQUAL(msg, "");
1281 
1282  msg = CSubSource::CheckCellLine("ARO81-1", "Homo sapiens");
1283  BOOST_CHECK_EQUAL(msg, "The International Cell Line Authentication Committee database indicates that ARO81-1 from Homo sapiens is known to be contaminated by HT-29 from Human. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1284 
1285  msg = CSubSource::CheckCellLine("aRO81-1", "Homo sapiens");
1286  BOOST_CHECK_EQUAL(msg, "The International Cell Line Authentication Committee database indicates that aRO81-1 from Homo sapiens is known to be contaminated by HT-29 from Human. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1287 
1288  msg = CSubSource::CheckCellLine("IPRI-OL-7", "Orgyia leucostigma");
1289  BOOST_CHECK_EQUAL(msg, "The International Cell Line Authentication Committee database indicates that IPRI-OL-7 from Orgyia leucostigma is known to be contaminated by IPRI-CF-124 from Choristoneura fumiferana. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1290 }
1291 
1292 
1293 BOOST_AUTO_TEST_CASE(Test_FixStrain)
1294 {
1295  BOOST_CHECK_EQUAL(COrgMod::FixStrain("DSM1235"), "DSM 1235");
1296  BOOST_CHECK_EQUAL(COrgMod::FixStrain("DSM/1235"), "DSM 1235");
1297  BOOST_CHECK_EQUAL(COrgMod::FixStrain("dsm/1235"), "DSM 1235");
1298  BOOST_CHECK_EQUAL(COrgMod::FixStrain("dsm:1235"), "DSM 1235");
1299  BOOST_CHECK_EQUAL(COrgMod::FixStrain("dsm : 1235"), "DSM 1235");
1300  BOOST_CHECK_EQUAL(COrgMod::FixStrain("DSM"), "DSM");
1301 
1302  BOOST_CHECK_EQUAL(COrgMod::FixStrain("ATCC1235"), "ATCC 1235");
1303  BOOST_CHECK_EQUAL(COrgMod::FixStrain("ATCC/1235"), "ATCC 1235");
1304  BOOST_CHECK_EQUAL(COrgMod::FixStrain("atcc/1235"), "ATCC 1235");
1305  BOOST_CHECK_EQUAL(COrgMod::FixStrain("atcc:1235"), "ATCC 1235");
1306  BOOST_CHECK_EQUAL(COrgMod::FixStrain("atcc : 1235"), "ATCC 1235");
1307  BOOST_CHECK_EQUAL(COrgMod::FixStrain("ATCC"), "ATCC");
1308 }
1309 
1310 BOOST_AUTO_TEST_CASE(Test_AllowedFeatureLocation)
1311 {
1312  BOOST_CHECK_EQUAL(CSeqFeatData::AllowedFeatureLocation(CSeqFeatData::eSubtype_gene), CSeqFeatData::eFeatureLocationAllowed_NucOnly);
1313  BOOST_CHECK_EQUAL(CSeqFeatData::AllowedFeatureLocation(CSeqFeatData::eSubtype_mat_peptide_aa), CSeqFeatData::eFeatureLocationAllowed_ProtOnly);
1314  BOOST_CHECK_EQUAL(CSeqFeatData::AllowedFeatureLocation(CSeqFeatData::eSubtype_site), CSeqFeatData::eFeatureLocationAllowed_Any);
1315  BOOST_CHECK_EQUAL(CSeqFeatData::AllowedFeatureLocation(CSeqFeatData::eSubtype_bad), CSeqFeatData::eFeatureLocationAllowed_Error);
1316 }
1317 
1318 
1319 BOOST_AUTO_TEST_CASE(Test_SQD_2180)
1320 {
1321  string msg = CSubSource::CheckCellLine("Yamada", "Canis lupus familiaris");
1322  BOOST_CHECK_EQUAL(msg, "The International Cell Line Authentication Committee database indicates that Yamada from Canis lupus familiaris is known to be contaminated by Unknown from Mouse. Please see http://iclac.org/databases/cross-contaminations/ for more information and references.");
1323 
1324 }
1325 
1326 
1327 BOOST_AUTO_TEST_CASE(Test_SQD_2183)
1328 {
1329  BOOST_CHECK_EQUAL(CSubSource::FixAltitude("100 meters"), "100 m");
1330  BOOST_CHECK_EQUAL(CSubSource::FixAltitude("100 meter"), "100 m");
1331  BOOST_CHECK_EQUAL(CSubSource::FixAltitude("100 m"), "100 m");
1332  BOOST_CHECK_EQUAL(CSubSource::FixAltitude("100 feet"), "30 m");
1333  BOOST_CHECK_EQUAL(CSubSource::FixAltitude("100 foot"), "30 m");
1334 
1335  //for VR-823
1336  BOOST_CHECK_EQUAL(CSubSource::FixAltitude("1,950 m"), "1950 m");
1337 }
1338 
1339 
1340 BOOST_AUTO_TEST_CASE(Test_SQD_2164)
1341 {
1342  BOOST_CHECK_EQUAL(CCountries::CountryFixupItem("Mediterranean, Malvarrosa Beach (Valencia, Spain)", false),
1343  "Spain: Mediterranean, Malvarrosa Beach (Valencia)");
1344 
1345 }
1346 
1347 
1348 BOOST_AUTO_TEST_CASE(Test_GB_4111)
1349 {
1350  BOOST_CHECK_EQUAL(CCountries::CountryFixupItem("China:, Guangdong Province, Guangzhou City, Tianlu Lake Forest Park", false),
1351  "China: Guangdong Province, Guangzhou City, Tianlu Lake Forest Park");
1352 
1353  BOOST_CHECK_EQUAL(CCountries::CountryFixupItem("China", false), "China");
1354  BOOST_CHECK_EQUAL(CCountries::CountryFixupItem("China: ,", false), "China");
1355  BOOST_CHECK_EQUAL(CCountries::CountryFixupItem("China: Guangdong Province", false), "China: Guangdong Province");
1356 }
1357 
1358 
1359 BOOST_AUTO_TEST_CASE(Test_GB_3965)
1360 {
1361  bool ambig = false;
1362  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("06/11/11", true, ambig), "11-Jun-2011");
1363  BOOST_CHECK_EQUAL(ambig, true);
1364  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("06/11/11"), "");
1365 
1366  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("11/8/12"), "");
1367  ambig = false;
1368  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("11/8/12", true, ambig), "08-Nov-2012");
1369  ambig = false;
1370  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("11/8/12", false, ambig), "11-Aug-2012");
1371 
1372  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("Nov/8/12"), "08-Nov-2012");
1373  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("11/Aug/12"), "11-Aug-2012");
1374 }
1375 
1376 
1377 BOOST_AUTO_TEST_CASE(Test_GB_5458)
1378 {
1379  bool ambig = false;
1380  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("15-Jul-13", false, ambig), "15-Jul-2013");
1381  BOOST_CHECK_EQUAL(ambig, false);
1382 }
1383 
1384 BOOST_AUTO_TEST_CASE(Test_SQD_2319)
1385 {
1386  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("2012-01-52"), "");
1387 }
1388 
1389 
1390 BOOST_AUTO_TEST_CASE(Test_GB_5391)
1391 {
1392  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("June2011"), "Jun-2011");
1393 }
1394 
1395 
1396 BOOST_AUTO_TEST_CASE(Test_SQD_3603)
1397 {
1398  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("11-2009"), "Nov-2009");
1399 }
1400 
1401 BOOST_AUTO_TEST_CASE(Test_GB_6371)
1402 {
1403  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("13-Sept-2012"), "13-Sep-2012");
1404  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("13-J-2012"), "");
1405  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("13-Ja-2012"), "");
1406  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("13-May-2012"), "13-May-2012");
1407  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("13.Septemb.2012"), "13-Sep-2012");
1408  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("13-Setp-2012"), "");
1409 }
1410 
1411 struct SCollDateInfo {
1412  const char * date_to_fix;
1413  const char * expected_result;
1414 };
1415 
1416 BOOST_AUTO_TEST_CASE(Test_FixDateFormat_for_BI_2614)
1417 {
1418  // all these formats should be acceptable, according to
1419  // https://intranet.ncbi.nlm.nih.gov/ieb/DIRSUB/FT/
1420  // (as of 10-Nov-2015), except a few which can be fixed by
1421  // CSubSource::FixDateFormat
1422  //
1423  // In most cases CSubSource::FixDateFormat doesn't do anything,
1424  // but there are a few formats which are not normally accepted but
1425  // which CSubSource::FixDateFormat can fix.
1426  static SCollDateInfo kGoodCollectionDates[] = {
1427  // ISO date/times stay the same after CSubSource::FixDateFormat
1428  { "1952", "1952" },
1429  { "1952-10-21T11:43Z", "1952-10-21T11:43Z"},
1430  { "1952-10-21T11Z", "1952-10-21T11Z" },
1431  { "1952-10-21","1952-10-21" },
1432  { "1952-10", "1952-10" },
1433  { "1952/1953", "1952/1953" },
1434  { "1952-10-21/1953-02-15", "1952-10-21/1953-02-15" },
1435  { "1952-10/1953-02", "1952-10/1953-02" },
1436  { "1952-10-21T11:43Z/1952-10-21T17:43Z",
1437  "1952-10-21T11:43Z/1952-10-21T17:43Z"},
1438 
1439  // Dates already in DD-Mmm-YYY format also remain unchanged
1440  // after CSubSource::FixDateFormat
1441  { "21-Oct-1952", "21-Oct-1952" },
1442  { "Oct-1952", "Oct-1952" },
1443  { "21-Oct-1952/15-Feb-1953", "21-Oct-1952/15-Feb-1953" },
1444  { "Oct-1952/Feb-1953", "Oct-1952/Feb-1953" },
1445 
1446  // A few formats can be corrected
1447  { "1-1-1952", "01-Jan-1952" },
1448  { "1-1-1952/2-2-1952", "01-Jan-1952/02-Feb-1952" }
1449  };
1450  ITERATE_0_IDX(idx, ArraySize(kGoodCollectionDates)) {
1451  // check CSubSource::FixDateFormat
1452  const string fixed_date =
1453  CSubSource::FixDateFormat(kGoodCollectionDates[idx].date_to_fix);
1454  const string expected_date(
1455  kGoodCollectionDates[idx].expected_result);
1456  BOOST_CHECK_EQUAL(fixed_date, expected_date);
1457 
1458  // check that fixed dates do pass CSubSource::IsCorrectDateFormat
1459  bool bad_format = false;
1460  bool in_future = false;
1461  CSubSource::IsCorrectDateFormat(
1462  fixed_date, bad_format, in_future);
1463  BOOST_CHECK_MESSAGE( ! bad_format, fixed_date );
1464  BOOST_CHECK_MESSAGE( ! in_future, fixed_date );
1465 
1466  // check that fixed_date also passes
1467  // CSubSource::GetCollectionDateProblem
1468  BOOST_CHECK_MESSAGE(
1469  "" == CSubSource::GetCollectionDateProblem(fixed_date),
1470  fixed_date);
1471 
1472  // divide into pieces for the functions that cannot handle a "/"
1473  vector<string> date_pieces_strs;
1474  NStr::Split(fixed_date, "/", date_pieces_strs);
1475 
1476  ITERATE( vector<string>, date_piece_ci, date_pieces_strs ) {
1477  const string & date_piece_str = *date_piece_ci;
1478 
1479  // make sure fixed dates are acceptable to
1480  // CSubSource::DateFromCollectionDate
1481  BOOST_CHECK_MESSAGE(
1482  CSubSource::DateFromCollectionDate(date_piece_str),
1483  date_piece_str);
1484  BOOST_CHECK_MESSAGE(
1485  CSubSource::DateFromCollectionDate(date_piece_str),
1486  date_piece_str);
1487  }
1488  }
1489 }
1490 
1491 BOOST_AUTO_TEST_CASE(Test_GetRNAProduct)
1492 {
1493  CRef<CRNA_ref> rna(new CRNA_ref());
1494  rna->SetType(CRNA_ref::eType_mRNA);
1495  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), kEmptyStr);
1496 
1497  string product("mRNA product");
1498  rna->SetExt().SetName(product);
1499  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1500 
1501  rna->SetType(CRNA_ref::eType_miscRNA);
1502  CRef<CRNA_gen> rna_gen(new CRNA_gen());
1503  rna->SetExt().SetGen(*rna_gen);
1504  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), kEmptyStr);
1505 
1506  product.assign("miscRNA product");
1507  rna_gen->SetProduct(product);
1508  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1509 
1510  // the type of RNA does not affect the product name
1511  rna->SetType(CRNA_ref::eType_ncRNA);
1512  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1513 
1514  rna->SetType(CRNA_ref::eType_tRNA);
1515  product.assign("tRNA-Ser");
1516  rna->SetExt().SetTRNA().SetAa().SetNcbieaa(83);
1517  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1518 
1519  rna->SetType(CRNA_ref::eType_ncRNA);
1520  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1521 
1522  product.assign("tRNA-Met");
1523  rna->SetType(CRNA_ref::eType_tRNA);
1524  rna->SetExt().SetTRNA().SetAa().SetIupacaa(77);
1525  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1526 
1527  product.assign("tRNA-OTHER");
1528  rna->SetExt().SetTRNA().SetAa().SetIupacaa(88);
1529  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1530 
1531  rna->SetExt().SetTRNA().SetAa().SetNcbieaa(88);
1532  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1533 
1534  product.assign("tRNA-TERM");
1535  rna->SetExt().SetTRNA().SetAa().SetNcbieaa(42);
1536  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1537 
1538  rna->SetExt().SetTRNA().SetAa().SetIupacaa(42);
1539  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1540 
1541  product.clear();
1542  rna->SetExt().SetTRNA().SetAa().SetIupacaa(43);
1543  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), product);
1544 }
1545 
1546 BOOST_AUTO_TEST_CASE(Test_SetRnaProductName)
1547 {
1548  CRef<CRNA_ref> rna(new CRNA_ref());
1549 
1550  string remainder;
1551  string product("mRNA product");
1552  rna->SetType(CRNA_ref::eType_mRNA);
1553  rna->SetRnaProductName(product, remainder);
1554  BOOST_CHECK_EQUAL(rna->IsSetExt(), true);
1555  BOOST_CHECK_EQUAL(rna->GetExt().GetName(), product);
1556  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1557 
1558  product.resize(0);
1559  rna->SetRnaProductName(product, remainder);
1560  BOOST_CHECK_EQUAL(rna->IsSetExt(), false);
1561  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1562 
1563  product.assign("rRNA product");
1564  rna->SetType(CRNA_ref::eType_rRNA);
1565  rna->SetRnaProductName(product, remainder);
1566  BOOST_CHECK_EQUAL(rna->IsSetExt(), true);
1567  BOOST_CHECK_EQUAL(rna->GetExt().GetName(), product);
1568  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1569 
1570  product.resize(0);
1571  rna->SetRnaProductName(product, remainder);
1572  BOOST_CHECK_EQUAL(rna->IsSetExt(), false);
1573  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1574 
1575  product.assign("miscRNA product");
1576  rna->SetType(CRNA_ref::eType_miscRNA);
1577  rna->SetRnaProductName(product, remainder);
1578  BOOST_CHECK_EQUAL(rna->IsSetExt(), true);
1579  BOOST_CHECK_EQUAL(rna->GetExt().GetGen().GetProduct(), product);
1580  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1581 
1582  product.resize(0);
1583  rna->SetRnaProductName(product, remainder);
1584  BOOST_CHECK_EQUAL(rna->IsSetExt(), false);
1585  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1586 
1587  // name containing underscore is not recognized
1588  product.assign("tRNA_Ala");
1589  rna->SetType(CRNA_ref::eType_tRNA);
1590  rna->SetRnaProductName(product, remainder);
1591  BOOST_CHECK_EQUAL(rna->GetExt().IsTRNA(), true);
1592  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().IsSetAa(), false);
1593  BOOST_CHECK_EQUAL(remainder, product);
1594 
1595  // it is also case-sensitive
1596  product.assign("TRNA-Ala");
1597  rna->SetRnaProductName(product, remainder);
1598  BOOST_CHECK_EQUAL(rna->GetExt().IsTRNA(), true);
1599  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().IsSetAa(), false);
1600  BOOST_CHECK_EQUAL(remainder, product);
1601 
1602  product.assign("tRNA-Ala");
1603  rna->SetRnaProductName(product, remainder);
1604  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().IsSetAa(), true);
1605  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 65);
1606  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1607 
1608  product.clear();
1609  rna->SetRnaProductName(product, remainder);
1610  BOOST_CHECK_EQUAL(rna->IsSetExt(), true);
1611  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().IsSetAa(), false);
1612  BOOST_CHECK_EQUAL(rna->GetRnaProductName(), kEmptyStr);
1613  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1614 
1615  product.assign("Ser");
1616  rna->SetRnaProductName(product, remainder);
1617  BOOST_CHECK_EQUAL(rna->GetExt().IsTRNA(), true);
1618  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 83);
1619  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1620 
1621  product.assign("TERM");
1622  rna->SetRnaProductName(product, remainder);
1623  BOOST_CHECK_EQUAL(rna->GetExt().IsTRNA(), true);
1624  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 42);
1625  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1626 
1627  product.assign("tRNA-other");
1628  rna->SetRnaProductName(product, remainder);
1629  BOOST_CHECK_EQUAL(rna->GetExt().IsTRNA(), true);
1630  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 88);
1631  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1632 
1633  // also take single-letter codes
1634  product.assign("tRNA-A(gct)");
1635  rna->SetRnaProductName(product, remainder);
1636  BOOST_CHECK_EQUAL(rna->GetExt().IsTRNA(), true);
1637  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 65);
1638  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1639 
1640  product.assign("tRNA-*(gct)");
1641  rna->SetRnaProductName(product, remainder);
1642  BOOST_CHECK_EQUAL(rna->GetExt().IsTRNA(), true);
1643  BOOST_CHECK_EQUAL(rna->GetExt().GetTRNA().GetAa().GetNcbieaa(), 42);
1644  BOOST_CHECK_EQUAL(remainder, kEmptyStr);
1645 
1646 }
1647 
1648 
1649 BOOST_AUTO_TEST_CASE(Test_IsIllegalQualName)
1650 {
1651  BOOST_CHECK_EQUAL(CGb_qual::IsIllegalQualName("exception"), true);
1652  BOOST_CHECK_EQUAL(CGb_qual::IsIllegalQualName("number"), false);
1653 }
1654 
1655 
1656 BOOST_AUTO_TEST_CASE(Test_IsECNumberSplit)
1657 {
1658  BOOST_CHECK_EQUAL(CProt_ref::IsECNumberSplit("1.1.1.246"), true);
1659  BOOST_CHECK_EQUAL(CProt_ref::IsECNumberSplit("1.1.1.63"), false);
1660  BOOST_CHECK_EQUAL(CProt_ref::IsECNumberSplit("1.1.1.128"), false);
1661 }
1662 
1663 
1664 BOOST_AUTO_TEST_CASE(Test_FileTrack)
1665 {
1666  CRef<CUser_object> obj(new CUser_object());
1667 
1668  obj->SetFileTrackUploadId("7azalbch/brev2_motif_summary.csv");
1669  BOOST_CHECK_EQUAL(obj->GetObjectType(), CUser_object::eObjectType_FileTrack);
1670  BOOST_CHECK_EQUAL(obj->GetData().front()->GetLabel().GetStr(), "BaseModification-FileTrackURL");
1671  BOOST_CHECK_EQUAL(obj->GetData().front()->GetData().GetStr(), "https://submit.ncbi.nlm.nih.gov/ft/byid/7azalbch/brev2_motif_summary.csv");
1672 }
1673 
1674 
1675 BOOST_AUTO_TEST_CASE(Test_EnvSampleCleanup)
1676 {
1677  CRef<CBioSource> src(new CBioSource());
1678 
1679  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), false);
1680  src->SetOrg().SetTaxname("uncultured x");
1681  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), true);
1682  BOOST_CHECK_EQUAL(src->GetSubtype().front()->GetSubtype(), CSubSource::eSubtype_environmental_sample);
1683  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), false);
1684 
1685  src->ResetSubtype();
1686  src->SetOrg().SetTaxname("Homo sapiens");
1687  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), false);
1688  src->SetSubtype().push_back(CRef<CSubSource>(new CSubSource(CSubSource::eSubtype_metagenomic, " ")));
1689  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), true);
1690  BOOST_CHECK_EQUAL(src->GetSubtype().back()->GetSubtype(), CSubSource::eSubtype_environmental_sample);
1691  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), false);
1692 
1693  src->ResetSubtype();
1694  src->SetOrg().SetOrgname().SetDiv("ENV");
1695  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), true);
1696  BOOST_CHECK_EQUAL(src->GetSubtype().front()->GetSubtype(), CSubSource::eSubtype_environmental_sample);
1697  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), false);
1698 
1699  src->ResetSubtype();
1700  src->SetOrg().SetOrgname().ResetDiv();
1701  src->SetOrg().SetOrgname().SetLineage("metagenomes");
1702  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), true);
1703  BOOST_CHECK_EQUAL(src->GetSubtype().front()->GetSubtype(), CSubSource::eSubtype_environmental_sample);
1704  BOOST_CHECK_EQUAL(src->GetSubtype().back()->GetSubtype(), CSubSource::eSubtype_metagenomic);
1705  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), false);
1706 
1707  src->ResetSubtype();
1708  src->SetOrg().SetOrgname().ResetLineage();
1709  src->SetOrg().SetOrgname().SetMod().push_back(CRef<COrgMod>(new COrgMod(COrgMod::eSubtype_metagenome_source, "X")));
1710  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), true);
1711  BOOST_CHECK_EQUAL(src->GetSubtype().front()->GetSubtype(), CSubSource::eSubtype_environmental_sample);
1712  BOOST_CHECK_EQUAL(src->GetSubtype().back()->GetSubtype(), CSubSource::eSubtype_metagenomic);
1713  BOOST_CHECK_EQUAL(src->FixEnvironmentalSample(), false);
1714 
1715 }
1716 
1717 
1718 BOOST_AUTO_TEST_CASE(Test_RemoveNullTerms)
1719 {
1720  CRef<CBioSource> src(new CBioSource());
1721 
1722  src->SetSubtype().push_back(CRef<CSubSource>(new CSubSource(CSubSource::eSubtype_altitude, "N/A")));
1723  src->SetOrg().SetOrgname().SetMod().push_back(CRef<COrgMod>(new COrgMod(COrgMod::eSubtype_acronym, "Missing")));
1724  src->SetOrg().SetOrgname().SetMod().push_back(CRef<COrgMod>(new COrgMod(COrgMod::eSubtype_anamorph, "not Missing")));
1725 
1726  BOOST_CHECK_EQUAL(src->RemoveNullTerms(), true);
1727  BOOST_CHECK_EQUAL(src->IsSetSubtype(), false);
1728  BOOST_CHECK_EQUAL(src->GetOrg().GetOrgname().GetMod().size(), 1);
1729  BOOST_CHECK_EQUAL(src->GetOrg().GetOrgname().GetMod().front()->GetSubtype(), COrgMod::eSubtype_anamorph);
1730 }
1731 
1732 
1733 BOOST_AUTO_TEST_CASE(Test_RemoveAbbreviation)
1734 {
1735  CRef<COrgMod> om(new COrgMod(COrgMod::eSubtype_serovar, "serovar x"));
1736  BOOST_CHECK_EQUAL(om->RemoveAbbreviation(), true);
1737  BOOST_CHECK_EQUAL(om->GetSubname(), "x");
1738 
1739  CRef<COrgMod> om2(new COrgMod(COrgMod::eSubtype_sub_species, "subsp. y"));
1740  BOOST_CHECK_EQUAL(om2->RemoveAbbreviation(), true);
1741  BOOST_CHECK_EQUAL(om2->GetSubname(), "y");
1742 
1743 }
1744 
1745 
1746 BOOST_AUTO_TEST_CASE(Test_FixSexMatingTypeInconsistencies)
1747 {
1748  CRef<CBioSource> src(new CBioSource());
1749 
1750  src->SetOrg().SetOrgname().SetLineage("Viruses; foo");
1751  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), false);
1752  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), false);
1753  src->SetOrg().SetOrgname().SetLineage("Bacteria; foo");
1754  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), false);
1755  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), true);
1756  src->SetOrg().SetOrgname().SetLineage("Archaea; foo");
1757  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), false);
1758  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), true);
1759  src->SetOrg().SetOrgname().SetLineage("Eukaryota; Fungi; foo");
1760  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), false);
1761  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), true);
1762  src->SetOrg().SetOrgname().SetLineage("Eukaryota; Metazoa; foo");
1763  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), true);
1764  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), false);
1765  src->SetOrg().SetOrgname().SetLineage("Eukaryota; Viridiplantae; Streptophyta; Embryophyta; foo");
1766  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), true);
1767  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), false);
1768  src->SetOrg().SetOrgname().SetLineage("Eukaryota; Rhodophyta; foo");
1769  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), true);
1770  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), false);
1771  src->SetOrg().SetOrgname().SetLineage("Eukaryota; stramenopiles; Phaeophyceae; foo");
1772  BOOST_CHECK_EQUAL(src->AllowSexQualifier(), true);
1773  BOOST_CHECK_EQUAL(src->AllowMatingTypeQualifier(), false);
1774 
1775  CRef<CSubSource> s(new CSubSource(CSubSource::eSubtype_sex, "f"));
1776  src->SetSubtype().push_back(s);
1777  BOOST_CHECK_EQUAL(src->FixSexMatingTypeInconsistencies(), false);
1778  BOOST_CHECK_EQUAL(src->GetSubtype().size(), 1);
1779 
1780  s->SetSubtype(CSubSource::eSubtype_mating_type);
1781  BOOST_CHECK_EQUAL(src->FixSexMatingTypeInconsistencies(), true);
1782  BOOST_CHECK_EQUAL(src->GetSubtype().size(), 1);
1783  BOOST_CHECK_EQUAL(src->GetSubtype().front()->GetSubtype(), CSubSource::eSubtype_sex);
1784 
1785  s->SetSubtype(CSubSource::eSubtype_mating_type);
1786  s->SetName("foo");
1787  BOOST_CHECK_EQUAL(src->FixSexMatingTypeInconsistencies(), true);
1788  BOOST_CHECK_EQUAL(src->IsSetSubtype(), false);
1789 
1790  src->SetOrg().SetOrgname().SetLineage("Viruses; foo");
1791  src->SetSubtype().push_back(s);
1792  BOOST_CHECK_EQUAL(src->FixSexMatingTypeInconsistencies(), true);
1793  BOOST_CHECK_EQUAL(src->IsSetSubtype(), false);
1794 
1795  s->SetSubtype(CSubSource::eSubtype_sex);
1796  src->SetSubtype().push_back(s);
1797  BOOST_CHECK_EQUAL(src->FixSexMatingTypeInconsistencies(), true);
1798  BOOST_CHECK_EQUAL(src->IsSetSubtype(), false);
1799 
1800 }
1801 
1802 
1803 BOOST_AUTO_TEST_CASE(Test_RemoveUnexpectedViralQualifiers)
1804 {
1805  CRef<CBioSource> src(new CBioSource());
1806 
1807  src->SetOrg().SetOrgname().SetMod().push_back(CRef<COrgMod>(new COrgMod(COrgMod::eSubtype_breed, "x")));
1808  src->SetOrg().SetOrgname().SetMod().push_back(CRef<COrgMod>(new COrgMod(COrgMod::eSubtype_cultivar, "y")));
1809  src->SetOrg().SetOrgname().SetMod().push_back(CRef<COrgMod>(new COrgMod(COrgMod::eSubtype_specimen_voucher, "z")));
1810  src->SetOrg().SetOrgname().SetMod().push_back(CRef<COrgMod>(new COrgMod(COrgMod::eSubtype_acronym, "a")));
1811 
1812  BOOST_CHECK_EQUAL(src->RemoveUnexpectedViralQualifiers(), false);
1813  BOOST_CHECK_EQUAL(src->GetOrg().GetOrgname().GetMod().size(), 4);
1814  src->SetOrg().SetOrgname().SetLineage("Viruses; foo");
1815  BOOST_CHECK_EQUAL(src->RemoveUnexpectedViralQualifiers(), true);
1816  BOOST_CHECK_EQUAL(src->GetOrg().GetOrgname().GetMod().size(), 1);
1817  BOOST_CHECK_EQUAL(src->GetOrg().GetOrgname().GetMod().front()->GetSubtype(), COrgMod::eSubtype_acronym);
1818 
1819 }
1820 
1821 
1822 BOOST_AUTO_TEST_CASE(Test_FixGenomeForQualifiers)
1823 {
1824  CRef<CBioSource> src(new CBioSource());
1825 
1826  BOOST_CHECK_EQUAL(src->FixGenomeForQualifiers(), false);
1827  src->SetSubtype().push_back(CRef<CSubSource>(new CSubSource(CSubSource::eSubtype_plasmid_name, "X")));
1828  BOOST_CHECK_EQUAL(src->FixGenomeForQualifiers(), true);
1829  BOOST_CHECK_EQUAL(src->GetGenome(), CBioSource::eGenome_plasmid);
1830  BOOST_CHECK_EQUAL(src->FixGenomeForQualifiers(), false);
1831  src->SetGenome(CBioSource::eGenome_apicoplast);
1832  BOOST_CHECK_EQUAL(src->FixGenomeForQualifiers(), false);
1833  BOOST_CHECK_EQUAL(src->GetGenome(), CBioSource::eGenome_apicoplast);
1834  src->SetGenome(CBioSource::eGenome_unknown);
1835  BOOST_CHECK_EQUAL(src->FixGenomeForQualifiers(), true);
1836  BOOST_CHECK_EQUAL(src->GetGenome(), CBioSource::eGenome_plasmid);
1837 }
1838 
1839 
1840 BOOST_AUTO_TEST_CASE(Test_AllowXref)
1841 {
1842  BOOST_CHECK_EQUAL(CSeqFeatData::AllowXref(CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_cdregion), true);
1843  BOOST_CHECK_EQUAL(CSeqFeatData::AllowXref(CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_regulatory), false);
1844  BOOST_CHECK_EQUAL(CSeqFeatData::AllowXref(CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_exon), false);
1845  BOOST_CHECK_EQUAL(CSeqFeatData::ProhibitXref(CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_cdregion), false);
1846  BOOST_CHECK_EQUAL(CSeqFeatData::ProhibitXref(CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_regulatory), true);
1847  BOOST_CHECK_EQUAL(CSeqFeatData::ProhibitXref(CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_exon), true);
1848 }
1849 
1850 BOOST_AUTO_TEST_CASE(Test_recombination_class)
1851 {
1852  BOOST_CHECK_EQUAL(CSeqFeatData::IsLegalQualifier(CSeqFeatData::eSubtype_misc_recomb, CSeqFeatData::eQual_recombination_class), true);
1853  const CGb_qual::TLegalRecombinationClassSet recomb_values = CGb_qual::GetSetOfLegalRecombinationClassValues();
1854  BOOST_ASSERT(recomb_values.find("chromosome_breakpoint") != recomb_values.end());
1855 
1856 
1857  string old_recomb_value("meiotic_recombination");
1858  BOOST_CHECK_EQUAL(CGb_qual::FixRecombinationClassValue(old_recomb_value), true);
1859  BOOST_CHECK_EQUAL(old_recomb_value, "meiotic");
1860 
1861  old_recomb_value = ("other:non_allelic_homologous_recombination");
1862  BOOST_CHECK_EQUAL(CGb_qual::FixRecombinationClassValue(old_recomb_value), true);
1863  BOOST_CHECK_EQUAL(old_recomb_value, "non_allelic_homologous");
1864 
1865  string valid_recomb_value("mitotic");
1866  BOOST_CHECK_EQUAL(CGb_qual::FixRecombinationClassValue(valid_recomb_value), false);
1867  BOOST_CHECK_EQUAL(valid_recomb_value, "mitotic");
1868 }
1869 
1870 
1871 BOOST_AUTO_TEST_CASE(Test_OrgMod_IsDiscouraged)
1872 {
1873  BOOST_CHECK_EQUAL(COrgMod::IsDiscouraged(COrgMod::eSubtype_metagenome_source), true);
1874  BOOST_CHECK_EQUAL(COrgMod::IsDiscouraged(COrgMod::eSubtype_metagenome_source, true), false);
1875 }
1876 
1877 
1878 void CheckViruses(CBioSource& src)
1879 {
1880  src.SetOrg().SetOrgname().SetLineage("viruses");
1881  BOOST_CHECK_EQUAL(src.GetBioprojectType(), "eSegment");
1882  BOOST_CHECK_EQUAL(src.GetBioprojectLocation(), "eVirionPhage");
1883  src.SetOrg().SetOrgname().SetLineage("viroids");
1884  BOOST_CHECK_EQUAL(src.GetBioprojectType(), "eSegment");
1885  BOOST_CHECK_EQUAL(src.GetBioprojectLocation(), "eViroid");
1886  src.SetOrg().SetOrgname().ResetLineage();
1887 }
1888 
1889 
1890 void CheckPlasmid(CBioSource& src)
1891 {
1892  CRef<CSubSource> p(new CSubSource(CSubSource::eSubtype_plasmid_name, "foo"));
1893  src.SetSubtype().push_back(p);
1894  BOOST_CHECK_EQUAL(src.GetBioprojectType(), "ePlasmid");
1895  src.ResetSubtype();
1896 }
1897 
1898 
1899 void CheckBioProjectLocationVals(CBioSource::EGenome genome, const string& bioprojectlocation)
1900 {
1901  CRef<CBioSource> src(new CBioSource());
1902  src->SetGenome(genome);
1903  BOOST_CHECK_EQUAL(src->GetBioprojectType(), "eChromosome");
1904  BOOST_CHECK_EQUAL(src->GetBioprojectLocation(), bioprojectlocation);
1905  CheckViruses(*src);
1906  CheckPlasmid(*src);
1907 }
1908 
1909 
1910 BOOST_AUTO_TEST_CASE(Test_GetBioProjectTypeAndLocation)
1911 {
1912  CRef<CBioSource> src(new CBioSource());
1913  BOOST_CHECK_EQUAL(src->GetBioprojectType(), "eChromosome");
1914  BOOST_CHECK_EQUAL(src->GetBioprojectLocation(), "eNuclearProkaryote");
1915  CheckViruses(*src);
1916 
1917  src->SetGenome(CBioSource::eGenome_unknown);
1918  BOOST_CHECK_EQUAL(src->GetBioprojectType(), "eChromosome");
1919  BOOST_CHECK_EQUAL(src->GetBioprojectLocation(), "eNuclearProkaryote");
1920  CheckViruses(*src);
1921 
1922  src->SetGenome(CBioSource::eGenome_chromosome);
1923  BOOST_CHECK_EQUAL(src->GetBioprojectType(), "eChromosome");
1924  BOOST_CHECK_EQUAL(src->GetBioprojectLocation(), "eNuclearProkaryote");
1925  src->SetSubtype().push_back(CRef<CSubSource>(new CSubSource(CSubSource::eSubtype_linkage_group, "x")));
1926  BOOST_CHECK_EQUAL(src->GetBioprojectType(), "eLinkageGroup");
1927  BOOST_CHECK_EQUAL(src->GetBioprojectLocation(), "eNuclearProkaryote");
1928  src->ResetSubtype();
1929 
1930  src->SetGenome(CBioSource::eGenome_extrachrom);
1931  BOOST_CHECK_EQUAL(src->GetBioprojectType(), "eExtrachrom");
1932  BOOST_CHECK_EQUAL(src->GetBioprojectLocation(), "eNuclearProkaryote");
1933 
1934  CheckBioProjectLocationVals(CBioSource::eGenome_apicoplast, "eApicoplast");
1935  CheckBioProjectLocationVals(CBioSource::eGenome_chloroplast, "eChloroplast");
1936  CheckBioProjectLocationVals(CBioSource::eGenome_chromatophore, "eChromatophore");
1937  CheckBioProjectLocationVals(CBioSource::eGenome_chromoplast, "eChromoplast");
1938  CheckBioProjectLocationVals(CBioSource::eGenome_cyanelle, "eCyanelle");
1939  CheckBioProjectLocationVals(CBioSource::eGenome_hydrogenosome, "eHydrogenosome");
1940  CheckBioProjectLocationVals(CBioSource::eGenome_kinetoplast, "eKinetoplast");
1941  CheckBioProjectLocationVals(CBioSource::eGenome_leucoplast, "eLeucoplast");
1942  CheckBioProjectLocationVals(CBioSource::eGenome_macronuclear, "eMacronuclear");
1943  CheckBioProjectLocationVals(CBioSource::eGenome_mitochondrion, "eMitochondrion");
1944  CheckBioProjectLocationVals(CBioSource::eGenome_nucleomorph, "eNucleomorph");
1945  CheckBioProjectLocationVals(CBioSource::eGenome_plastid, "ePlastid");
1946  CheckBioProjectLocationVals(CBioSource::eGenome_proplastid, "eProplastid");
1947  CheckBioProjectLocationVals(CBioSource::eGenome_proviral, "eProviralProphage");
1948  CheckBioProjectLocationVals(CBioSource::eGenome_endogenous_virus, "eProviralProphage");
1949  CheckBioProjectLocationVals(CBioSource::eGenome_transposon, "eOther");
1950  CheckBioProjectLocationVals(CBioSource::eGenome_insertion_seq, "eOther");
1951 
1952 }
1953 
1954 
1955 BOOST_AUTO_TEST_CASE(Test_OrgRefLookup)
1956 {
1957  string taxname = "Zea mays";
1958 
1959  CConstRef<COrg_ref> lookup = COrg_ref::TableLookup(taxname);
1960  if (! lookup) {
1961  BOOST_CHECK_EQUAL("", taxname);
1962  return;
1963  }
1964  BOOST_CHECK_EQUAL(lookup->GetTaxname(), taxname);
1965  BOOST_CHECK_EQUAL(lookup->GetOrgname().GetDiv(), "PLN");
1966 }
1967 
1968 
1969 BOOST_AUTO_TEST_CASE(Test_CleanupAndRepairInference)
1970 {
1971  BOOST_CHECK_EQUAL(CGb_qual::CleanupAndRepairInference("similar to sequence : UniProtKB : P39748"), "similar to sequence:UniProtKB:P39748");
1972  BOOST_CHECK_EQUAL(CGb_qual::CleanupAndRepairInference("similar to RNA sequence, mRNA: INSDC:AY262280.1"), "similar to RNA sequence, mRNA:INSDC:AY262280.1");
1973  BOOST_CHECK_EQUAL(CGb_qual::CleanupAndRepairInference("similar to AA: UniProtKB : P39748"), "similar to AA sequence:UniProtKB:P39748");
1974  BOOST_CHECK_EQUAL(CGb_qual::CleanupAndRepairInference("similar to AA sequence: UniProtKB : P39748"), "similar to AA sequence:UniProtKB:P39748");
1975 }
1976 
1977 
1978 BOOST_AUTO_TEST_CASE(Test_SQD_4173)
1979 {
1980  BOOST_CHECK_EQUAL(CBioSource::ShouldIgnoreConflict("lat-lon", "12.12345 N 23.123456 W", "12.12 N 23.12 W"), false);
1981 }
1982 
1983 
1984 BOOST_AUTO_TEST_CASE(Test_VR_665)
1985 {
1986  string voucher_type;
1987  bool is_miscapitalized;
1988  string correct_cap;
1989  bool needs_country;
1990  bool erroneous_country;
1991  string inst_code = "ARBH";
1992  BOOST_CHECK_EQUAL(COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country), true);
1993  BOOST_CHECK_EQUAL(voucher_type, "s");
1994  BOOST_CHECK_EQUAL(is_miscapitalized, false);
1995  BOOST_CHECK_EQUAL(correct_cap, "ARBH");
1996  BOOST_CHECK_EQUAL(needs_country, false);
1997  BOOST_CHECK_EQUAL(erroneous_country, false);
1998 
1999  inst_code = "NMNH";
2000  BOOST_CHECK_EQUAL(COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country), true);
2001  BOOST_CHECK_EQUAL(voucher_type, "sb");
2002  BOOST_CHECK_EQUAL(is_miscapitalized, false);
2003  BOOST_CHECK_EQUAL(correct_cap, "NMNH");
2004  BOOST_CHECK_EQUAL(needs_country, false);
2005  BOOST_CHECK_EQUAL(erroneous_country, false);
2006 
2007  inst_code = "ZMM";
2008  BOOST_CHECK_EQUAL(COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country), true);
2009  BOOST_CHECK_EQUAL(voucher_type, "s");
2010  BOOST_CHECK_EQUAL(is_miscapitalized, false);
2011  BOOST_CHECK_EQUAL(correct_cap, "ZMM");
2012  BOOST_CHECK_EQUAL(needs_country, false);
2013  BOOST_CHECK_EQUAL(erroneous_country, false);
2014 
2015  inst_code = "ZMUM";
2016  BOOST_CHECK_EQUAL(COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country), true);
2017  BOOST_CHECK_EQUAL(voucher_type, "s");
2018  BOOST_CHECK_EQUAL(is_miscapitalized, false);
2019  BOOST_CHECK_EQUAL(correct_cap, "ZMUM");
2020  BOOST_CHECK_EQUAL(needs_country, false);
2021  BOOST_CHECK_EQUAL(erroneous_country, false);
2022 }
2023 
2024 
2025 BOOST_AUTO_TEST_CASE(Test_VR_693)
2026 {
2027  BOOST_CHECK_EQUAL(CSubSource::FixDevStageCapitalization("FOO"), "FOO");
2028  BOOST_CHECK_EQUAL(CSubSource::FixDevStageCapitalization("LARVA"), "larva");
2029 
2030  BOOST_CHECK_EQUAL(CSubSource::FixCellTypeCapitalization("FOO"), "FOO");
2031  BOOST_CHECK_EQUAL(CSubSource::FixCellTypeCapitalization("Lymphocyte"), "lymphocyte");
2032 
2033  BOOST_CHECK_EQUAL(CSubSource::FixTissueTypeCapitalization("CLINICAL"), "clinical");
2034 
2035  BOOST_CHECK_EQUAL(CSubSource::FixIsolationSourceCapitalization("Bovine (feces)"), "bovine feces");
2036  BOOST_CHECK_EQUAL(CSubSource::FixIsolationSourceCapitalization("BLOOD"), "blood");
2037 
2038  BOOST_CHECK_EQUAL(CSubSource::FixIsolationSourceCapitalization("Leaf"), "leaf");
2039  BOOST_CHECK_EQUAL(CSubSource::FixIsolationSourceCapitalization("Roots"), "roots");
2040 
2041 }
2042 
2043 
2044 BOOST_AUTO_TEST_CASE(Test_IsLegalClass)
2045 {
2046  BOOST_CHECK_EQUAL(CRNA_gen::IsLegalClass("lncRNA"), true);
2047  BOOST_CHECK_EQUAL(CRNA_gen::IsLegalClass("babble"), false);
2048  BOOST_CHECK_EQUAL(CRNA_gen::GetncRNAClassList().size(), 24);
2049 }
2050 
2051 
2052 BOOST_AUTO_TEST_CASE(Test_LegalMobileElement)
2053 {
2054  BOOST_CHECK_EQUAL(CGb_qual::IsLegalMobileElementValue("foo"), false);
2055  BOOST_CHECK_EQUAL(CGb_qual::IsLegalMobileElementValue("integron"), true);
2056 
2057  string val = "p-element";
2058  BOOST_CHECK_EQUAL(CGb_qual::FixMobileElementValue(val), true);
2059  BOOST_CHECK_EQUAL(val, "P-element");
2060 }
2061 
2062 
2063 BOOST_AUTO_TEST_CASE(Test_FixImportKey)
2064 {
2065  string val = "Exon";
2066  BOOST_CHECK_EQUAL(CSeqFeatData::FixImportKey(val), true);
2067  BOOST_CHECK_EQUAL(val, "exon");
2068  BOOST_CHECK_EQUAL(CSeqFeatData::FixImportKey(val), false);
2069 }
2070 
2071 
2072 BOOST_AUTO_TEST_CASE(Test_IsTypeMaterialValid)
2073 {
2074  BOOST_CHECK_EQUAL(COrgMod::IsValidTypeMaterial("holotype X"), true);
2075  BOOST_CHECK_EQUAL(COrgMod::IsINSDCValidTypeMaterial("holotype X"), true);
2076  BOOST_CHECK_EQUAL(COrgMod::IsValidTypeMaterial("culture from epitype Y"), true);
2077  BOOST_CHECK_EQUAL(COrgMod::IsINSDCValidTypeMaterial("culture from epitype Y"), true);
2078  BOOST_CHECK_EQUAL(COrgMod::IsValidTypeMaterial("ex-syntype Z"), true);
2079  BOOST_CHECK_EQUAL(COrgMod::IsINSDCValidTypeMaterial("ex-syntype Z"), true);
2080 
2081 
2082 }
2083 
2084 
2085 BOOST_AUTO_TEST_CASE(Test_VR_730)
2086 {
2087  int hour, min, sec;
2088  // succeed
2089  BOOST_CHECK_EQUAL(CSubSource::IsISOFormatTime("11:13:00Z", hour, min, sec), true);
2090  BOOST_CHECK_EQUAL(hour, 11);
2091  BOOST_CHECK_EQUAL(min, 13);
2092  BOOST_CHECK_EQUAL(sec, 0);
2093  // fail because no time zone specified
2094  BOOST_CHECK_EQUAL(CSubSource::IsISOFormatTime("11:13:00", hour, min, sec), false);
2095  // succeed because time zone not required
2096  BOOST_CHECK_EQUAL(CSubSource::IsISOFormatTime("11:13:00", hour, min, sec, false), true);
2097  BOOST_CHECK_EQUAL(hour, 11);
2098  BOOST_CHECK_EQUAL(min, 13);
2099  BOOST_CHECK_EQUAL(sec, 0);
2100 
2101  BOOST_CHECK_EQUAL(CSubSource::FixDateFormat("2012-10-26T11:13:00"), "2012-10-26");
2102 }
2103 
2104 
2105 BOOST_AUTO_TEST_CASE(Test_RefGeneTracking)
2106 {
2107  CRef<CUser_object> user(new CUser_object());
2108  user->SetObjectType(CUser_object::eObjectType_RefGeneTracking);
2109  BOOST_CHECK_EQUAL(user->GetType().GetStr(), "RefGeneTracking");
2110  BOOST_CHECK_EQUAL(user->GetObjectType(), CUser_object::eObjectType_RefGeneTracking);
2111  BOOST_CHECK_EQUAL(user->IsRefGeneTracking(), true);
2112 
2113  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_NotSet);
2114  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingStatus(), false);
2115  user->SetRefGeneTrackingStatus(CUser_object::eRefGeneTrackingStatus_PIPELINE);
2116  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingStatus(), true);
2117  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_PIPELINE);
2118  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "Status");
2119  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetStr(), "PIPELINE");
2120  user->SetRefGeneTrackingStatus(CUser_object::eRefGeneTrackingStatus_INFERRED);
2121  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_INFERRED);
2122  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "Status");
2123  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetStr(), "INFERRED");
2124  BOOST_CHECK_EQUAL(user->GetData().size(), 1);
2125 
2126  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingGenomicSource(), false);
2127  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenomicSource(), kEmptyStr);
2128  user->SetRefGeneTrackingGenomicSource("XXX");
2129  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingGenomicSource(), true);
2130  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenomicSource(), "XXX");
2131  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "GenomicSource");
2132  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetStr(), "XXX");
2133  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_INFERRED);
2134  user->SetRefGeneTrackingGenomicSource("XXX2");
2135  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenomicSource(), "XXX2");
2136  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "GenomicSource");
2137  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetStr(), "XXX2");
2138  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_INFERRED);
2139  BOOST_CHECK_EQUAL(user->GetData().size(), 2);
2140 
2141  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingCollaborator(), false);
2142  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaborator(), kEmptyStr);
2143  user->SetRefGeneTrackingCollaborator("YYY");
2144  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingCollaborator(), true);
2145  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaborator(), "YYY");
2146  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "Collaborator");
2147  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetStr(), "YYY");
2148  user->SetRefGeneTrackingCollaborator("YYY2");
2149  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaborator(), "YYY2");
2150  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "Collaborator");
2151  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetStr(), "YYY2");
2152  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_INFERRED);
2153  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenomicSource(), "XXX2");
2154  BOOST_CHECK_EQUAL(user->GetData().size(), 3);
2155 
2156  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingCollaboratorURL(), false);
2157  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaboratorURL(), kEmptyStr);
2158  user->SetRefGeneTrackingCollaboratorURL("ZZZ");
2159  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingCollaboratorURL(), true);
2160  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaboratorURL(), "ZZZ");
2161  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "CollaboratorURL");
2162  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetStr(), "ZZZ");
2163  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_INFERRED);
2164  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenomicSource(), "XXX2");
2165  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaborator(), "YYY2");
2166  BOOST_CHECK_EQUAL(user->GetData().size(), 4);
2167 
2168  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenerated(), false);
2169  user->SetRefGeneTrackingGenerated(true);
2170  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenerated(), true);
2171  BOOST_CHECK_EQUAL(user->GetData().back()->GetLabel().GetStr(), "Generated");
2172  BOOST_CHECK_EQUAL(user->GetData().back()->GetData().GetBool(), true);
2173 
2174  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_INFERRED);
2175  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenomicSource(), "XXX2");
2176  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaborator(), "YYY2");
2177  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaboratorURL(), "ZZZ");
2178  BOOST_CHECK_EQUAL(user->GetData().size(), 5);
2179 
2180  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingIdenticalTo(), false);
2181  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingIdenticalTo(), CConstRef<CUser_object::CRefGeneTrackingAccession>(NULL));
2182  CRef<CUser_object::CRefGeneTrackingAccession> ident(new CUser_object::CRefGeneTrackingAccession("AY12345"));
2183  user->SetRefGeneTrackingIdenticalTo(*ident);
2184  BOOST_CHECK_EQUAL(user->IsSetRefGeneTrackingIdenticalTo(), true);
2185  CConstRef<CUser_object::CRefGeneTrackingAccession> r_ident = user->GetRefGeneTrackingIdenticalTo();
2186  BOOST_CHECK_EQUAL(r_ident->GetAccession(), "AY12345");
2187  BOOST_CHECK_EQUAL(user->GetData().size(), 6);
2188 
2189  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingAssembly().size(), 0);
2190  vector<CConstRef<CUser_object::CRefGeneTrackingAccession> > assembly;
2191  assembly.push_back(CConstRef<CUser_object::CRefGeneTrackingAccession>
2192  (new CUser_object::CRefGeneTrackingAccession
2193  ("XXX", GI_CONST(123), 0, 100, "comment1", "name1")));
2194  assembly.push_back(CConstRef<CUser_object::CRefGeneTrackingAccession>
2195  (new CUser_object::CRefGeneTrackingAccession
2196  ("YYY", GI_CONST(124), 10, 1100, "comment2", "name2")));
2197  user->SetRefGeneTrackingAssembly(assembly);
2198  BOOST_CHECK_EQUAL(user->GetData().size(), 7);
2199 
2200  CUser_object::TRefGeneTrackingAccessions r_assembly = user->GetRefGeneTrackingAssembly();
2201  BOOST_CHECK_EQUAL(r_assembly.size(), 2);
2202  BOOST_CHECK_EQUAL(r_assembly.front()->GetAccession(), "XXX");
2203  BOOST_CHECK_EQUAL(r_assembly.front()->GetGI(), GI_CONST(123));
2204  BOOST_CHECK_EQUAL(r_assembly.front()->GetFrom(), 0);
2205  BOOST_CHECK_EQUAL(r_assembly.front()->GetTo(), 100);
2206  BOOST_CHECK_EQUAL(r_assembly.front()->GetName(), "name1");
2207  BOOST_CHECK_EQUAL(r_assembly.front()->GetComment(), "comment1");
2208  BOOST_CHECK_EQUAL(r_assembly.back()->GetAccession(), "YYY");
2209  BOOST_CHECK_EQUAL(r_assembly.back()->GetGI(), GI_CONST(124));
2210  BOOST_CHECK_EQUAL(r_assembly.back()->GetFrom(), 10);
2211  BOOST_CHECK_EQUAL(r_assembly.back()->GetTo(), 1100);
2212  BOOST_CHECK_EQUAL(r_assembly.back()->GetName(), "name2");
2213  BOOST_CHECK_EQUAL(r_assembly.back()->GetComment(), "comment2");
2214 
2215  user->ResetRefGeneTrackingAssembly();
2216  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingAssembly().size(), 0);
2217  BOOST_CHECK_EQUAL(user->GetData().size(), 6);
2218  user->ResetRefGeneTrackingIdenticalTo();
2219  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingIdenticalTo(), CConstRef<CUser_object::CRefGeneTrackingAccession>(NULL));
2220  BOOST_CHECK_EQUAL(user->GetData().size(), 5);
2221  user->ResetRefGeneTrackingCollaboratorURL();
2222  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaboratorURL(), kEmptyStr);
2223  BOOST_CHECK_EQUAL(user->GetData().size(), 4);
2224  user->ResetRefGeneTrackingCollaborator();
2225  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingCollaborator(), kEmptyStr);
2226  BOOST_CHECK_EQUAL(user->GetData().size(), 3);
2227  user->ResetRefGeneTrackingGenerated();
2228  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenerated(), false);
2229  BOOST_CHECK_EQUAL(user->GetData().size(), 2);
2230  user->ResetRefGeneTrackingGenomicSource();
2231  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingGenomicSource(), kEmptyStr);
2232  BOOST_CHECK_EQUAL(user->GetData().size(), 1);
2233  user->ResetRefGeneTrackingStatus();
2234  BOOST_CHECK_EQUAL(user->GetRefGeneTrackingStatus(), CUser_object::eRefGeneTrackingStatus_NotSet);
2235  BOOST_CHECK_EQUAL(user->GetData().size(), 0);
2236 
2237  BOOST_CHECK_EQUAL(user->GetObjectType(), CUser_object::eObjectType_RefGeneTracking);
2238 }
2239 
2240 
2241 BOOST_AUTO_TEST_CASE(Test_IsValidEcNumberFormat)
2242 {
2243  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("1.1.2.4"), true);
2244  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("1.1.2.-"), true);
2245  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("1.1.2.n"), true);
2246  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("11.22.33.44"), true);
2247  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("11.22.n33.44"), false);
2248  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("1.2.3.10"), true);
2249  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("1"), false);
2250  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("1.2"), false);
2251  BOOST_CHECK_EQUAL(CProt_ref::IsValidECNumberFormat("1.2.3"), false);
2252 
2253 }
2254 
2255 
2256 BOOST_AUTO_TEST_CASE(Test_IsValidLocalID)
2257 {
2258  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID(""), false);
2259  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWXY"), false);
2260  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("ABCDEFGHIJKLMNOPQRSTUVWXYZABCDEFGHIJKLMNOPQRSTUVWX"), true);
2261  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc1"), true);
2262  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc 1"), false);
2263  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc>1"), false);
2264  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc[1"), false);
2265  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc]1"), false);
2266  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc|1"), false);
2267  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc=1"), true);
2268  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc\"1"), false);
2269  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc$1"), true);
2270  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc@1"), true);
2271  BOOST_CHECK_EQUAL(CSeq_id::IsValidLocalID("nuc{1"), true);
2272 }
2273 
2274 
2275 BOOST_AUTO_TEST_CASE(Test_Unverified)
2276 {
2277  CRef<CUser_object> obj(new CUser_object());
2278  BOOST_CHECK_EQUAL(obj->IsUnverified(), false);
2279  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), false);
2280  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), false);
2281  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), false);
2282  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), false);
2283 
2284  obj->SetObjectType(CUser_object::eObjectType_Unverified);
2285  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2286  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), false);
2287  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), false);
2288  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), false);
2289  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), false);
2290 
2291  obj->AddUnverifiedContaminant();
2292  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2293  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), true);
2294  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), false);
2295  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), false);
2296  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), false);
2297 
2298  obj->AddUnverifiedFeature();
2299  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2300  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), true);
2301  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), true);
2302  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), false);
2303  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), false);
2304 
2305  obj->AddUnverifiedMisassembled();
2306  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2307  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), true);
2308  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), true);
2309  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), true);
2310  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), false);
2311 
2312  obj->AddUnverifiedOrganism();
2313  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2314  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), true);
2315  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), true);
2316  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), true);
2317  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), true);
2318 
2319  obj->RemoveUnverifiedContaminant();
2320  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2321  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), false);
2322  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), true);
2323  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), true);
2324  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), true);
2325 
2326  obj->RemoveUnverifiedFeature();
2327  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2328  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), false);
2329  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), false);
2330  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), true);
2331  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), true);
2332 
2333  obj->RemoveUnverifiedMisassembled();
2334  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2335  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), false);
2336  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), false);
2337  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), false);
2338  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), true);
2339 
2340  obj->RemoveUnverifiedOrganism();
2341  BOOST_CHECK_EQUAL(obj->IsUnverified(), true);
2342  BOOST_CHECK_EQUAL(obj->IsUnverifiedContaminant(), false);
2343  BOOST_CHECK_EQUAL(obj->IsUnverifiedFeature(), false);
2344  BOOST_CHECK_EQUAL(obj->IsUnverifiedMisassembled(), false);
2345  BOOST_CHECK_EQUAL(obj->IsUnverifiedOrganism(), false);
2346 
2347 }
2348 
2349 
2350 BOOST_AUTO_TEST_CASE(Test_LegalQualsAny)
2351 {
2352  const size_t numExpectedQuals = 138;
2353  size_t count = 0;
2354  auto all_quals = CSeqFeatData::GetLegalQualifiers(CSeqFeatData::eSubtype_any);
2355  BOOST_CHECK_EQUAL(all_quals.size(), numExpectedQuals);
2356  for (auto b : all_quals)
2357  ++count;
2358  BOOST_CHECK_EQUAL(count, numExpectedQuals);
2359 
2360  auto empty_quals = CSeqFeatData::GetLegalQualifiers(CSeqFeatData::eSubtype_clone);
2361  BOOST_CHECK_EQUAL(empty_quals.size(), 0);
2362  count = 0;
2363  for (auto b : empty_quals)
2364  ++count;
2365  BOOST_CHECK_EQUAL(count, 0);
2366 
2367  auto mandatory = CSeqFeatData::GetMandatoryQualifiers(CSeqFeatData::eSubtype_assembly_gap);
2368 
2369  for (auto rec: mandatory)
2370  {
2371  std::cout << rec << std::endl;
2372  }
2373 }
2374 
2375 BOOST_AUTO_TEST_CASE(Test_GetQualifierTypeAndCheckCase)
2376 {
2377  auto test1 = CSeqFeatData::GetQualifierTypeAndValue("host");
2378  BOOST_CHECK(test1.first == CSeqFeatData::eQual_host);
2379  BOOST_CHECK_EQUAL(test1.second, "host");
2380  auto test2 = CSeqFeatData::GetQualifierTypeAndValue("Host");
2381  BOOST_CHECK(test2.first == CSeqFeatData::eQual_host);
2382  BOOST_CHECK_EQUAL(test2.second, "host");
2383  auto test3 = CSeqFeatData::GetQualifierTypeAndValue("specific_host");
2384  BOOST_CHECK(test3.first == CSeqFeatData::eQual_host);
2385  BOOST_CHECK_EQUAL(test3.second, "specific_host");
2386  auto test4 = CSeqFeatData::GetQualifierTypeAndValue("Specific_host");
2387  BOOST_CHECK(test4.first == CSeqFeatData::eQual_host);
2388  BOOST_CHECK_EQUAL(test4.second, "specific_host");
2389 
2390  auto test5 = CSeqFeatData::GetQualifierAsString(CSeqFeatData::eQual_host);
2391  BOOST_CHECK_EQUAL(test5, "host");
2392 }
2393 BOOST_AUTO_TEST_CASE(Test_x_ExhonerateQualifier)
2394 {
2395  auto& orig = CSeqFeatData::GetMandatoryQualifiers(CSeqFeatData::eSubtype_assembly_gap);
2396  size_t orig_size = orig.size();
2397  BOOST_CHECK(orig_size == 2);
2398  std::vector<CSeqFeatData::EQualifier> mandatory = orig;
2399  CSeqFeatData::EQualifier not_mandatory = CSeqFeatData::eQual_estimated_length;
2400  bool res = false;
2401  ERASE_ITERATE(std::vector<CSeqFeatData::EQualifier>, it, mandatory) {
2402  if (*it == not_mandatory) {
2403  res = true;
2404  VECTOR_ERASE(it, mandatory);
2405  }
2406  }
2407 
2408  BOOST_CHECK(mandatory.size() == 1);
2409 
2410  auto mandatory_copy = orig;
2411  bool res2 = mandatory_copy.reset(not_mandatory);
2412  BOOST_CHECK(res == res2);
2413  BOOST_CHECK(mandatory_copy.size() == 1);
2414 
2415  bool res3 = mandatory_copy.set(not_mandatory);
2416  BOOST_CHECK(res != res3);
2417  BOOST_CHECK(mandatory_copy.size() == 2);
2418 
2419 }
2420 
Auth_list.hpp
Cit_art.hpp
Cit_book.hpp
Cit_gen.hpp
Cit_jour.hpp
Cit_let.hpp
Cit_proc.hpp
Cit_sub.hpp
Gb_qual.hpp
Imprint.hpp
User-defined methods of the data storage class.
Name_std.hpp
Object_id.hpp
Org_ref.hpp
Person_id.hpp
Prot_ref.hpp
Pub_equiv.hpp
RNA_gen.hpp
User-defined methods of the data storage class.
RNA_ref.hpp
Seq_id.hpp
Trna_ext.hpp
User-defined methods of the data storage class.
User_field.hpp
User_object.hpp
lookup
static int lookup(const char *name, const struct lookup_int *table)
Definition: attributes.c:50
CAuth_list
@Auth_list.hpp User-defined methods of the data storage class.
Definition: Auth_list.hpp:57
CAuth_list::SameCitation
bool SameCitation(const CAuth_list &other) const
Definition: Auth_list.cpp:264
CAuthor
CAuthor –.
Definition: Author.hpp:59
CBioSource::FixEnvironmentalSample
bool FixEnvironmentalSample()
Definition: BioSource.cpp:1681
CBioSource::GetRepliconName
string GetRepliconName(void) const
Definition: BioSource.cpp:421
CBioSource::ShouldIgnoreConflict
static bool ShouldIgnoreConflict(const string &label, string src_val, string sample_val, bool is_local_copy=false)
Definition: BioSource.cpp:1033
CBioSource::AllowSexQualifier
static bool AllowSexQualifier(const string &lineage)
Definition: BioSource.cpp:1845
CBioSource::RemoveCultureNotes
void RemoveCultureNotes(bool is_species_level=true)
Definition: BioSource.cpp:1428
CBioSource::GetBioprojectLocation
string GetBioprojectLocation(void) const
Definition: BioSource.cpp:522
CBioSource::FixSexMatingTypeInconsistencies
bool FixSexMatingTypeInconsistencies()
Definition: BioSource.cpp:1910
CBioSource::RemoveNullTerms
bool RemoveNullTerms()
Definition: BioSource.cpp:1772
CBioSource::MakeCommon
CRef< CBioSource > MakeCommon(const CBioSource &other) const
Definition: BioSource.cpp:2022
CBioSource::AllowMatingTypeQualifier
static bool AllowMatingTypeQualifier(const string &lineage)
Definition: BioSource.cpp:1878
CBioSource::FixGenomeForQualifiers
bool FixGenomeForQualifiers()
Definition: BioSource.cpp:1974
CBioSource::GetBioprojectType
string GetBioprojectType(void) const
Definition: BioSource.cpp:482
CBioSource::RemoveUnexpectedViralQualifiers
bool RemoveUnexpectedViralQualifiers()
Definition: BioSource.cpp:1949
CCit_book
Definition: Cit_book.hpp:53
CCit_jour
Definition: Cit_jour.hpp:53
CConstRef
CConstRef –.
Definition: ncbiobj.hpp:1266
CCountries::CountryFixupItem
static string CountryFixupItem(const string &input, bool capitalize_after_colon)
Definition: SubSource.cpp:4765
CDate
Definition: Date.hpp:53
CGb_qual::IsLegalMobileElementValue
static bool IsLegalMobileElementValue(const string &val)
Definition: Gb_qual.cpp:454
CGb_qual::IsIllegalQualName
static bool IsIllegalQualName(const string &val)
Definition: Gb_qual.cpp:508
CGb_qual::FixRecombinationClassValue
static bool FixRecombinationClassValue(string &val)
Definition: Gb_qual.cpp:345
CGb_qual::CleanupAndRepairInference
static string CleanupAndRepairInference(const string &orig_inference)
Definition: Gb_qual.cpp:735
CGb_qual::FixMobileElementValue
static bool FixMobileElementValue(string &val)
Definition: Gb_qual.cpp:469
CGb_qual::GetSetOfLegalRecombinationClassValues
static const TLegalRecombinationClassSet & GetSetOfLegalRecombinationClassValues(void)
Definition: Gb_qual.cpp:329
CImprint
CImprint –.
Definition: Imprint.hpp:66
COrgMod
@OrgMod.hpp User-defined methods of the data storage class.
Definition: OrgMod.hpp:54
COrgMod::FixCapitalization
static string FixCapitalization(TSubtype subtype, const string &value)
Definition: OrgMod.cpp:1012
COrgMod::IsINSDCValidTypeMaterial
static bool IsINSDCValidTypeMaterial(const string &type_material)
Definition: OrgMod.cpp:1214
COrgMod::IsInstitutionCodeValid
static bool IsInstitutionCodeValid(const string &inst_coll, string &voucher_type, bool &is_miscapitalized, string &correct_cap, bool &needs_country, bool &erroneous_country)
Definition: OrgMod.cpp:356
COrgMod::IsDiscouraged
static bool IsDiscouraged(const TSubtype stype, bool indexer=false)
Definition: OrgMod.cpp:159
COrgMod::FixHost
static string FixHost(const string &value)
Definition: OrgMod.cpp:999
COrgMod::RemoveAbbreviation
bool RemoveAbbreviation()
Definition: OrgMod.cpp:1095
COrgMod::IsValidTypeMaterial
static bool IsValidTypeMaterial(const string &type_material)
Definition: OrgMod.cpp:1192
COrgMod::FixHostCapitalization
static string FixHostCapitalization(const string &value)
Definition: OrgMod.cpp:956
COrgMod::FixStrain
static string FixStrain(const string &strain)
Definition: OrgMod.cpp:799
COrgName::MakeCommon
CRef< COrgName > MakeCommon(const COrgName &other) const
Definition: OrgName.cpp:323
COrg_ref
Definition: Org_ref.hpp:51
COrg_ref::GetTaxId
TTaxId GetTaxId() const
Definition: Org_ref.cpp:72
COrg_ref::TableLookup
static CConstRef< COrg_ref > TableLookup(const string &taxname)
Definition: Org_ref.cpp:448
COrg_ref::SetTaxId
TTaxId SetTaxId(TTaxId tax_id)
Definition: Org_ref.cpp:93
COrg_ref::MakeCommon
CRef< COrg_ref > MakeCommon(const COrg_ref &other) const
Definition: Org_ref.cpp:280
CProt_ref::IsECNumberSplit
static bool IsECNumberSplit(const string &old_ecno)
Definition: Prot_ref.cpp:226
CProt_ref::IsValidECNumberFormat
static bool IsValidECNumberFormat(const string &ecno)
Verify correct form of EC number.
Definition: Prot_ref.cpp:257
CPub_equiv
Definition: Pub_equiv.hpp:54
CPub_equiv::SameCitation
bool SameCitation(const CPub_equiv &other) const
Definition: Pub_equiv.cpp:127
CPub
Definition: Pub.hpp:56
CPub::SameCitation
bool SameCitation(const CPub &other) const
Definition: Pub.cpp:733
CRNA_gen
Definition: RNA_gen.hpp:54
CRNA_gen::GetncRNAClassList
static vector< string > GetncRNAClassList()
Definition: RNA_gen.cpp:86
CRNA_gen::IsLegalClass
bool IsLegalClass() const
Definition: RNA_gen.cpp:119
CRNA_ref
@RNA_ref.hpp User-defined methods of the data storage class.
Definition: RNA_ref.hpp:54
CRef
CRef –.
Definition: ncbiobj.hpp:618
CSeqFeatData::GetRegulatoryClass
static const string & GetRegulatoryClass(ESubtype subtype)
Definition: SeqFeatData.cpp:3809
CSeqFeatData::IsLegalQualifier
bool IsLegalQualifier(EQualifier qual) const
Test wheather a certain qualifier is legal for the feature.
Definition: SeqFeatData.hpp:573
CSeqFeatData::IsDiscouragedQual
static bool IsDiscouragedQual(EQualifier qual)
Definition: SeqFeatData.cpp:4006
CSeqFeatData::AllowedFeatureLocation
static EFeatureLocationAllowed AllowedFeatureLocation(ESubtype subtype)
Definition: SeqFeatData.cpp:4453
CSeqFeatData::EQualifier
EQualifier
List of available qualifiers for feature keys.
Definition: SeqFeatData.hpp:326
CSeqFeatData::eQual_recombination_class
@ eQual_recombination_class
Definition: SeqFeatData.hpp:424
CSeqFeatData::eFeatureLocationAllowed_NucOnly
@ eFeatureLocationAllowed_NucOnly
Definition: SeqFeatData.hpp:511
CSeqFeatData::eFeatureLocationAllowed_Error
@ eFeatureLocationAllowed_Error
Definition: SeqFeatData.hpp:510
CSeqFeatData::eFeatureLocationAllowed_ProtOnly
@ eFeatureLocationAllowed_ProtOnly
Definition: SeqFeatData.hpp:512
CSeqFeatData::eFeatureLocationAllowed_Any
@ eFeatureLocationAllowed_Any
Definition: SeqFeatData.hpp:509
CSeqFeatData::ProhibitXref
static bool ProhibitXref(CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)
Definition: SeqFeatData.cpp:3749
CSeqFeatData::GetLegalQualifiers
const TLegalQualifiers & GetLegalQualifiers(void) const
Get a list of all the legal qualifiers for the feature.
Definition: SeqFeatData.hpp:580
CSeqFeatData::GetMandatoryQualifiers
const TQualifiers & GetMandatoryQualifiers(void) const
Get the list of all mandatory qualifiers for the feature.
Definition: SeqFeatData.hpp:587
CSeqFeatData::IsDiscouragedSubtype
static bool IsDiscouragedSubtype(ESubtype subtype)
Definition: SeqFeatData.cpp:3972
CSeqFeatData::GetQualifierTypeAndValue
static std::pair< EQualifier, CTempString > GetQualifierTypeAndValue(CTempString qual)
Definition: SeqFeatData.cpp:3179
CSeqFeatData::FixImportKey
static bool FixImportKey(string &key)
Definition: SeqFeatData.cpp:4664
CSeqFeatData::eSubtype_bad
@ eSubtype_bad
These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.
Definition: SeqFeatData.hpp:131
CSeqFeatData::GetQualifierAsString
static CTempString GetQualifierAsString(EQualifier qual)
Convert a qualifier from an enumerated value to a string representation or empty if not found.
CSeqFeatData::SubtypeNameToValue
static ESubtype SubtypeNameToValue(CTempString sName)
Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum.
CSeqFeatData::SubtypeValueToName
static CTempString SubtypeValueToName(ESubtype eSubtype)
Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...
Definition: SeqFeatData.cpp:513
CSeqFeatData::IsRegulatory
static bool IsRegulatory(ESubtype subtype)
Definition: SeqFeatData.cpp:3800
CSeqFeatData::AllowXref
static bool AllowXref(CSeqFeatData::ESubtype subtype1, CSeqFeatData::ESubtype subtype2)
Definition: SeqFeatData.cpp:3745
CStaticArraySearchBase::find
const_iterator find(const key_type &key) const
Return a const_iterator pointing to the specified element, or to the end if the element is not found.
Definition: static_set.hpp:680
CStaticArraySearchBase::end
const_iterator end() const
Return the end of the controlled sequence.
Definition: static_set.hpp:647
CSubSource::FixCapitalization
static string FixCapitalization(TSubtype subtype, const string &value)
Definition: SubSource.cpp:4969
CSubSource::GetCollectionDateProblem
static string GetCollectionDateProblem(const string &date_string)
CSubSource::FixTissueTypeCapitalization
static string FixTissueTypeCapitalization(const string &value)
Definition: SubSource.cpp:4936
CSubSource::IsISOFormatTime
static bool IsISOFormatTime(const string &orig_time, int &hour, int &min, int &sec, bool require_time_zone=true)
Definition: SubSource.cpp:610
CSubSource::FixLatLonFormat
static string FixLatLonFormat(string orig_lat_lon, bool guess=false)
Definition: SubSource.cpp:1828
CSubSource::FixIsolationSourceCapitalization
static string FixIsolationSourceCapitalization(const string &value)
Definition: SubSource.cpp:4909
CSubSource::FixCellTypeCapitalization
static string FixCellTypeCapitalization(const string &value)
Definition: SubSource.cpp:4829
CSubSource::FixDateFormat
static string FixDateFormat(const string &orig_date)
Attempt to fix the format of the date Returns a blank if the format of the date cannot be determined.
Definition: SubSource.cpp:586
CSubSource::CheckCellLine
static string CheckCellLine(const string &cell_line, const string &organism)
Definition: SubSource.cpp:2921
CSubSource::DateFromCollectionDate
static CRef< CDate > DateFromCollectionDate(const string &str) THROWS((CException))
Definition: SubSource.cpp:253
CSubSource::FixDevStageCapitalization
static string FixDevStageCapitalization(const string &value)
Definition: SubSource.cpp:4808
CSubSource::FixAltitude
static string FixAltitude(const string &value)
Definition: SubSource.cpp:2656
CSubSource::RemoveCultureNotes
static void RemoveCultureNotes(string &value, bool is_species_level=true)
Definition: SubSource.cpp:5145
CSubSource::IsCorrectDateFormat
static void IsCorrectDateFormat(const string &date_string, bool &bad_format, bool &in_future)
Definition: SubSource.cpp:420
CTitle_Base::C_E
C_E –.
Definition: Title_.hpp:96
CTitle
Definition: Title.hpp:51
CUser_object::CRefGeneTrackingAccession
Definition: User_object.hpp:283
CUser_object
Definition: User_object.hpp:51
CUser_object::GetRefGeneTrackingCollaborator
const string & GetRefGeneTrackingCollaborator() const
Definition: User_object.cpp:1055
CUser_object::SetObjectType
void SetObjectType(EObjectType obj_type)
Definition: User_object.cpp:647
CUser_object::ResetRefGeneTrackingAssembly
void ResetRefGeneTrackingAssembly()
Definition: User_object.cpp:1306
CUser_object::ResetRefGeneTrackingStatus
void ResetRefGeneTrackingStatus()
Definition: User_object.cpp:1022
CUser_object::RemoveUnverifiedFeature
void RemoveUnverifiedFeature()
Definition: User_object.cpp:821
CUser_object::AddUnverifiedOrganism
void AddUnverifiedOrganism()
Definition: User_object.cpp:797
CUser_object::SetRefGeneTrackingCollaboratorURL
void SetRefGeneTrackingCollaboratorURL(const string &collaborator_url)
Definition: User_object.cpp:1068
CUser_object::GetRefGeneTrackingCollaboratorURL
const string & GetRefGeneTrackingCollaboratorURL() const
Definition: User_object.cpp:1074
CUser_object::AddUnverifiedContaminant
void AddUnverifiedContaminant()
Definition: User_object.cpp:851
CUser_object::eRefGeneTrackingStatus_INFERRED
@ eRefGeneTrackingStatus_INFERRED
Definition: User_object.hpp:224
CUser_object::eRefGeneTrackingStatus_NotSet
@ eRefGeneTrackingStatus_NotSet
Definition: User_object.hpp:221
CUser_object::eRefGeneTrackingStatus_PIPELINE
@ eRefGeneTrackingStatus_PIPELINE
Definition: User_object.hpp:227
CUser_object::ResetRefGeneTrackingCollaboratorURL
void ResetRefGeneTrackingCollaboratorURL()
Definition: User_object.cpp:1080
CUser_object::IsRefGeneTracking
bool IsRefGeneTracking() const
Definition: User_object.hpp:185
CUser_object::SetRefGeneTrackingAssembly
void SetRefGeneTrackingAssembly(const TRefGeneTrackingAccessions &acc_list)
Definition: User_object.cpp:1270
CUser_object::ResetRefGeneTrackingGenerated
void ResetRefGeneTrackingGenerated()
Definition: User_object.cpp:1111
CUser_object::RemoveUnverifiedMisassembled
void RemoveUnverifiedMisassembled()
Definition: User_object.cpp:839
CUser_object::ResetRefGeneTrackingGenomicSource
void ResetRefGeneTrackingGenomicSource()
Definition: User_object.cpp:1042
CUser_object::IsSetRefGeneTrackingIdenticalTo
bool IsSetRefGeneTrackingIdenticalTo() const
Definition: User_object.hpp:340
CUser_object::IsSetRefGeneTrackingGenomicSource
bool IsSetRefGeneTrackingGenomicSource() const
Definition: User_object.hpp:242
CUser_object::SetRefGeneTrackingStatus
void SetRefGeneTrackingStatus(ERefGeneTrackingStatus status)
Definition: User_object.cpp:988
CUser_object::RemoveUnverifiedContaminant
void RemoveUnverifiedContaminant()
Definition: User_object.cpp:857
CUser_object::SetRefGeneTrackingCollaborator
void SetRefGeneTrackingCollaborator(const string &collaborator)
Definition: User_object.cpp:1049
CUser_object::SetRefGeneTrackingIdenticalTo
void SetRefGeneTrackingIdenticalTo(const CRefGeneTrackingAccession &accession)
Definition: User_object.cpp:1238
CUser_object::SetRefGeneTrackingGenomicSource
void SetRefGeneTrackingGenomicSource(const string &genomic_source)
Definition: User_object.cpp:1030
CUser_object::eObjectType_RefGeneTracking
@ eObjectType_RefGeneTracking
Definition: User_object.hpp:171
CUser_object::eObjectType_Unverified
@ eObjectType_Unverified
Definition: User_object.hpp:166
CUser_object::eObjectType_FileTrack
@ eObjectType_FileTrack
Definition: User_object.hpp:170
CUser_object::IsUnverifiedMisassembled
bool IsUnverifiedMisassembled() const
Definition: User_object.cpp:827
CUser_object::IsSetRefGeneTrackingCollaboratorURL
bool IsSetRefGeneTrackingCollaboratorURL() const
Definition: User_object.hpp:259
CUser_object::SetRefGeneTrackingGenerated
void SetRefGeneTrackingGenerated(bool val=true)
Definition: User_object.cpp:1088
CUser_object::SetFileTrackUploadId
void SetFileTrackUploadId(const string &upload_id)
Definition: User_object.cpp:940
CUser_object::TRefGeneTrackingAccessions
vector< CConstRef< CRefGeneTrackingAccession > > TRefGeneTrackingAccessions
Definition: User_object.hpp:334
CUser_object::GetRefGeneTrackingGenomicSource
const string & GetRefGeneTrackingGenomicSource() const
Definition: User_object.cpp:1036
CUser_object::IsSetRefGeneTrackingStatus
bool IsSetRefGeneTrackingStatus() const
Definition: User_object.hpp:233
CUser_object::IsUnverifiedOrganism
bool IsUnverifiedOrganism() const
Definition: User_object.cpp:791
CUser_object::GetRefGeneTrackingGenerated
bool GetRefGeneTrackingGenerated() const
Definition: User_object.cpp:1096
CUser_object::ResetRefGeneTrackingCollaborator
void ResetRefGeneTrackingCollaborator()
Definition: User_object.cpp:1061
CUser_object::GetRefGeneTrackingStatus
ERefGeneTrackingStatus GetRefGeneTrackingStatus() const
Definition: User_object.cpp:999
CUser_object::IsUnverifiedContaminant
bool IsUnverifiedContaminant() const
Definition: User_object.cpp:845
CUser_object::GetRefGeneTrackingAssembly
TRefGeneTrackingAccessions GetRefGeneTrackingAssembly() const
Definition: User_object.cpp:1285
CUser_object::IsUnverifiedFeature
bool IsUnverifiedFeature() const
Definition: User_object.cpp:809
CUser_object::IsUnverified
bool IsUnverified() const
Definition: User_object.hpp:180
CUser_object::RemoveUnverifiedOrganism
void RemoveUnverifiedOrganism()
Definition: User_object.cpp:803
CUser_object::AddUnverifiedMisassembled
void AddUnverifiedMisassembled()
Definition: User_object.cpp:833
CUser_object::GetRefGeneTrackingIdenticalTo
CConstRef< CRefGeneTrackingAccession > GetRefGeneTrackingIdenticalTo() const
Definition: User_object.cpp:1250
CUser_object::IsSetRefGeneTrackingCollaborator
bool IsSetRefGeneTrackingCollaborator() const
Definition: User_object.hpp:252
CUser_object::ResetRefGeneTrackingIdenticalTo
void ResetRefGeneTrackingIdenticalTo()
Definition: User_object.cpp:1263
CUser_object::GetObjectType
EObjectType GetObjectType() const
Definition: User_object.cpp:625
CUser_object::AddUnverifiedFeature
void AddUnverifiedFeature()
Definition: User_object.cpp:815
set
Definition: set.hpp:45
ITERATE_0_IDX
#define ITERATE_0_IDX(idx, up_to)
idx loops from 0 (inclusive) to up_to (exclusive)
Definition: ncbimisc.hpp:865
TAX_ID_CONST
#define TAX_ID_CONST(id)
Definition: ncbimisc.hpp:1112
ArraySize
constexpr size_t ArraySize(const Element(&)[Size])
Definition: ncbimisc.hpp:1532
ITERATE
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
Definition: ncbimisc.hpp:815
ERASE_ITERATE
#define ERASE_ITERATE(Type, Var, Cont)
Non-constant version with ability to erase current element, if container permits.
Definition: ncbimisc.hpp:843
TIntId
Int8 TIntId
Definition: ncbimisc.hpp:999
VECTOR_ERASE
#define VECTOR_ERASE(Var, Cont)
Use this macro inside body of ERASE_ITERATE cycle to erase from vector-like container.
Definition: ncbimisc.hpp:852
GI_CONST
#define GI_CONST(gi)
Definition: ncbimisc.hpp:1087
ENTREZ_ID_FROM
#define ENTREZ_ID_FROM(T, value)
Definition: ncbimisc.hpp:1098
NULL
#define NULL
Definition: ncbistd.hpp:225
CAliasBase::Set
TPrim & Set(void)
Definition: serialbase.hpp:351
CSerialObject::Assign
virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)
Set object to copy of another one.
Definition: serialobject.cpp:84
CSeq_id::IsValidLocalID
static bool IsValidLocalID(const CTempString &s)
Perform rudimentary validation on potential local IDs, whose contents should be pure ASCII and limite...
Definition: Seq_id.cpp:2575
CRef::Reset
void Reset(void)
Reset reference object.
Definition: ncbiobj.hpp:773
kEmptyStr
#define kEmptyStr
Definition: ncbistr.hpp:123
NStr::Split
static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)
Split a string using specified delimiters.
Definition: ncbistr.cpp:3457
NStr::IsBlank
static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)
Check if a string is blank (has no text).
Definition: ncbistr.cpp:106
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
CCit_proc_Base::SetBook
void SetBook(TBook &value)
Assign a value to Book data member.
Definition: Cit_proc_.cpp:61
CCit_gen_Base::SetIssue
void SetIssue(const TIssue &value)
Assign a value to Issue data member.
Definition: Cit_gen_.hpp:780
CCit_art_Base::SetTitle
void SetTitle(TTitle &value)
Assign a value to Title data member.
Definition: Cit_art_.cpp:210
CCit_art_Base::GetFrom
const TFrom & GetFrom(void) const
Get the From member data.
Definition: Cit_art_.hpp:567
CCit_gen_Base::SetJournal
void SetJournal(TJournal &value)
Assign a value to Journal data member.
Definition: Cit_gen_.cpp:81
CCit_jour_Base::SetImp
void SetImp(TImp &value)
Assign a value to Imp data member.
Definition: Cit_jour_.cpp:75
CCit_book_Base::SetTitle
void SetTitle(TTitle &value)
Assign a value to Title data member.
Definition: Cit_book_.cpp:62
CAuthor_Base::SetName
void SetName(TName &value)
Assign a value to Name data member.
Definition: Author_.cpp:81
CCit_art_Base::SetFrom
void SetFrom(TFrom &value)
Assign a value to From data member.
Definition: Cit_art_.cpp:248
CAuth_list_Base::SetAffil
void SetAffil(TAffil &value)
Assign a value to Affil data member.
Definition: Auth_list_.cpp:160
CCit_art_Base::IsSetFrom
bool IsSetFrom(void) const
Check if a value has been assigned to From data member.
Definition: Cit_art_.hpp:555
CCit_art_Base::SetAuthors
void SetAuthors(TAuthors &value)
Assign a value to Authors data member.
Definition: Cit_art_.cpp:227
CCit_gen_Base::SetSerial_number
void SetSerial_number(TSerial_number value)
Assign a value to Serial_number data member.
Definition: Cit_gen_.hpp:902
CCit_gen_Base::SetPages
void SetPages(const TPages &value)
Assign a value to Pages data member.
Definition: Cit_gen_.hpp:827
CCit_gen_Base::SetDate
void SetDate(TDate &value)
Assign a value to Date data member.
Definition: Cit_gen_.cpp:116
CCit_sub_Base::SetAuthors
void SetAuthors(TAuthors &value)
Assign a value to Authors data member.
Definition: Cit_sub_.cpp:74
CImprint_Base::SetPub
void SetPub(TPub &value)
Assign a value to Pub data member.
Definition: Imprint_.cpp:107
CCit_jour_Base::SetTitle
void SetTitle(TTitle &value)
Assign a value to Title data member.
Definition: Cit_jour_.cpp:61
CCit_book_Base::SetImp
void SetImp(TImp &value)
Assign a value to Imp data member.
Definition: Cit_book_.cpp:107
CCit_let_Base::SetCit
void SetCit(TCit &value)
Assign a value to Cit data member.
Definition: Cit_let_.cpp:70
CCit_gen_Base::SetCit
void SetCit(const TCit &value)
Assign a value to Cit data member.
Definition: Cit_gen_.hpp:597
CImprint_Base::SetVolume
void SetVolume(const TVolume &value)
Assign a value to Volume data member.
Definition: Imprint_.hpp:767
CAuth_list_Base::SetNames
void SetNames(TNames &value)
Assign a value to Names data member.
Definition: Auth_list_.cpp:149
CCit_book_Base::SetAuthors
void SetAuthors(TAuthors &value)
Assign a value to Authors data member.
Definition: Cit_book_.cpp:93
CImprint_Base::SetDate
void SetDate(TDate &value)
Assign a value to Date data member.
Definition: Imprint_.cpp:73
CCit_gen_Base::SetVolume
void SetVolume(const TVolume &value)
Assign a value to Volume data member.
Definition: Cit_gen_.hpp:733
CCit_gen_Base::SetTitle
void SetTitle(const TTitle &value)
Assign a value to Title data member.
Definition: Cit_gen_.hpp:942
CCit_gen_Base::SetMuid
void SetMuid(TMuid value)
Assign a value to Muid data member.
Definition: Cit_gen_.hpp:672
CCit_art_Base::C_From::IsBook
bool IsBook(void) const
Check if variant Book is selected.
Definition: Cit_art_.hpp:501
CCit_art_Base::C_From::IsJournal
bool IsJournal(void) const
Check if variant Journal is selected.
Definition: Cit_art_.hpp:495
CImprint_Base::SetPrepub
void SetPrepub(TPrepub value)
Assign a value to Prepub data member.
Definition: Imprint_.hpp:1108
CCit_sub_Base::SetImp
void SetImp(TImp &value)
Assign a value to Imp data member.
Definition: Cit_sub_.cpp:84
CCit_gen_Base::SetAuthors
void SetAuthors(TAuthors &value)
Assign a value to Authors data member.
Definition: Cit_gen_.cpp:64
CTitle_Base::Set
Tdata & Set(void)
Assign a value to data member.
Definition: Title_.hpp:787
CImprint_Base::ePrepub_in_press
@ ePrepub_in_press
accepted, not published
Definition: Imprint_.hpp:96
CImprint_Base::ePrepub_submitted
@ ePrepub_submitted
submitted, not accepted
Definition: Imprint_.hpp:95
CBioSource_Base::GetSubtype
const TSubtype & GetSubtype(void) const
Get the Subtype member data.
Definition: BioSource_.hpp:539
CBioSource_Base::GetGenome
TGenome GetGenome(void) const
Get the Genome member data.
Definition: BioSource_.hpp:422
CBioSource_Base::ResetGenome
void ResetGenome(void)
Reset Genome data member.
Definition: BioSource_.hpp:409
CSubSource_Base::SetSubtype
void SetSubtype(TSubtype value)
Assign a value to Subtype data member.
Definition: SubSource_.hpp:319
CBioSource_Base::IsSetSubtype
bool IsSetSubtype(void) const
Check if a value has been assigned to Subtype data member.
Definition: BioSource_.hpp:527
CBioSource_Base::GetOrg
const TOrg & GetOrg(void) const
Get the Org member data.
Definition: BioSource_.hpp:509
CBioSource_Base::SetGenome
void SetGenome(TGenome value)
Assign a value to Genome data member.
Definition: BioSource_.hpp:428
CBioSource_Base::SetOrg
void SetOrg(TOrg &value)
Assign a value to Org data member.
Definition: BioSource_.cpp:108
CSubSource_Base::SetName
void SetName(const TName &value)
Assign a value to Name data member.
Definition: SubSource_.hpp:359
CSubSource_Base::GetName
const TName & GetName(void) const
Get the Name member data.
Definition: SubSource_.hpp:350
CBioSource_Base::EGenome
EGenome
biological context
Definition: BioSource_.hpp:97
CSubSource_Base::IsSetName
bool IsSetName(void) const
Check if a value has been assigned to Name data member.
Definition: SubSource_.hpp:338
CBioSource_Base::SetSubtype
TSubtype & SetSubtype(void)
Assign a value to Subtype data member.
Definition: BioSource_.hpp:545
CBioSource_Base::ResetSubtype
void ResetSubtype(void)
Reset Subtype data member.
Definition: BioSource_.cpp:113
CSubSource_Base::eSubtype_altitude
@ eSubtype_altitude
Definition: SubSource_.hpp:127
CSubSource_Base::eSubtype_insertion_seq_name
@ eSubtype_insertion_seq_name
Definition: SubSource_.hpp:105
CSubSource_Base::eSubtype_mating_type
@ eSubtype_mating_type
Definition: SubSource_.hpp:122
CSubSource_Base::eSubtype_plastid_name
@ eSubtype_plastid_name
Definition: SubSource_.hpp:106
CSubSource_Base::eSubtype_other
@ eSubtype_other
Definition: SubSource_.hpp:128
CSubSource_Base::eSubtype_sex
@ eSubtype_sex
Definition: SubSource_.hpp:91
CSubSource_Base::eSubtype_metagenomic
@ eSubtype_metagenomic
Definition: SubSource_.hpp:121
CSubSource_Base::eSubtype_segment
@ eSubtype_segment
Definition: SubSource_.hpp:108
CSubSource_Base::eSubtype_chromosome
@ eSubtype_chromosome
Definition: SubSource_.hpp:85
CSubSource_Base::eSubtype_plasmid_name
@ eSubtype_plasmid_name
Definition: SubSource_.hpp:103
CSubSource_Base::eSubtype_environmental_sample
@ eSubtype_environmental_sample
Definition: SubSource_.hpp:111
CSubSource_Base::eSubtype_endogenous_virus_name
@ eSubtype_endogenous_virus_name
Definition: SubSource_.hpp:109
CSubSource_Base::eSubtype_linkage_group
@ eSubtype_linkage_group
Definition: SubSource_.hpp:123
CBioSource_Base::eOrigin_mut
@ eOrigin_mut
artificially mutagenized
Definition: BioSource_.hpp:132
CBioSource_Base::eOrigin_artificial
@ eOrigin_artificial
artificially engineered
Definition: BioSource_.hpp:133
CBioSource_Base::eGenome_apicoplast
@ eGenome_apicoplast
Definition: BioSource_.hpp:114
CBioSource_Base::eGenome_kinetoplast
@ eGenome_kinetoplast
Definition: BioSource_.hpp:102
CBioSource_Base::eGenome_hydrogenosome
@ eGenome_hydrogenosome
Definition: BioSource_.hpp:118
CBioSource_Base::eGenome_transposon
@ eGenome_transposon
Definition: BioSource_.hpp:108
CBioSource_Base::eGenome_chromatophore
@ eGenome_chromatophore
Definition: BioSource_.hpp:120
CBioSource_Base::eGenome_mitochondrion
@ eGenome_mitochondrion
Definition: BioSource_.hpp:103
CBioSource_Base::eGenome_proviral
@ eGenome_proviral
Definition: BioSource_.hpp:111
CBioSource_Base::eGenome_endogenous_virus
@ eGenome_endogenous_virus
Definition: BioSource_.hpp:117
CBioSource_Base::eGenome_chloroplast
@ eGenome_chloroplast
Definition: BioSource_.hpp:100
CBioSource_Base::eGenome_proplastid
@ eGenome_proplastid
Definition: BioSource_.hpp:116
CBioSource_Base::eGenome_plasmid_in_mitochondrion
@ eGenome_plasmid_in_mitochondrion
Definition: BioSource_.hpp:121
CBioSource_Base::eGenome_unknown
@ eGenome_unknown
Definition: BioSource_.hpp:98
CBioSource_Base::eGenome_plasmid
@ eGenome_plasmid
Definition: BioSource_.hpp:107
CBioSource_Base::eGenome_extrachrom
@ eGenome_extrachrom
Definition: BioSource_.hpp:106
CBioSource_Base::eGenome_nucleomorph
@ eGenome_nucleomorph
Definition: BioSource_.hpp:113
CBioSource_Base::eGenome_chromosome
@ eGenome_chromosome
Definition: BioSource_.hpp:119
CBioSource_Base::eGenome_plasmid_in_plastid
@ eGenome_plasmid_in_plastid
Definition: BioSource_.hpp:122
CBioSource_Base::eGenome_plastid
@ eGenome_plastid
Definition: BioSource_.hpp:104
CBioSource_Base::eGenome_cyanelle
@ eGenome_cyanelle
Definition: BioSource_.hpp:110
CBioSource_Base::eGenome_insertion_seq
@ eGenome_insertion_seq
Definition: BioSource_.hpp:109
CBioSource_Base::eGenome_chromoplast
@ eGenome_chromoplast
Definition: BioSource_.hpp:101
CBioSource_Base::eGenome_leucoplast
@ eGenome_leucoplast
Definition: BioSource_.hpp:115
CBioSource_Base::eGenome_macronuclear
@ eGenome_macronuclear
Definition: BioSource_.hpp:105
CDate_std_Base::SetYear
void SetYear(TYear value)
Assign a value to Year data member.
Definition: Date_std_.hpp:435
CDate_Base::SetStd
TStd & SetStd(void)
Select the variant.
Definition: Date_.cpp:115
CObject_id_Base::GetStr
const TStr & GetStr(void) const
Get the variant data.
Definition: Object_id_.hpp:297
CUser_object_Base::GetData
const TData & GetData(void) const
Get the Data member data.
Definition: User_object_.hpp:335
CUser_object_Base::GetType
const TType & GetType(void) const
Get the Type member data.
Definition: User_object_.hpp:305
COrgName_Base::GetMod
const TMod & GetMod(void) const
Get the Mod member data.
Definition: OrgName_.hpp:839
COrgName_Base::GetDiv
const TDiv & GetDiv(void) const
Get the Div member data.
Definition: OrgName_.hpp:1005
COrgMod_Base::GetSubname
const TSubname & GetSubname(void) const
Get the Subname member data.
Definition: OrgMod_.hpp:347
COrgName_Base::SetDiv
void SetDiv(const TDiv &value)
Assign a value to Div data member.
Definition: OrgName_.hpp:1014
COrgMod_Base::SetSubtype
void SetSubtype(TSubtype value)
Assign a value to Subtype data member.
Definition: OrgMod_.hpp:316
COrgName_Base::IsSetMod
bool IsSetMod(void) const
Check if a value has been assigned to Mod data member.
Definition: OrgName_.hpp:827
COrg_ref_Base::IsSetTaxname
bool IsSetTaxname(void) const
preferred formal name Check if a value has been assigned to Taxname data member.
Definition: Org_ref_.hpp:360
COrgName_Base::SetMod
TMod & SetMod(void)
Assign a value to Mod data member.
Definition: OrgName_.hpp:845
COrgMod_Base::SetSubname
void SetSubname(const TSubname &value)
Assign a value to Subname data member.
Definition: OrgMod_.hpp:356
COrg_ref_Base::GetOrgname
const TOrgname & GetOrgname(void) const
Get the Orgname member data.
Definition: Org_ref_.hpp:541
COrgMod_Base::eSubtype_anamorph
@ eSubtype_anamorph
Definition: OrgMod_.hpp:112
COrgMod_Base::eSubtype_sub_species
@ eSubtype_sub_species
Definition: OrgMod_.hpp:105
COrgMod_Base::eSubtype_nat_host
@ eSubtype_nat_host
natural host of this specimen
Definition: OrgMod_.hpp:104
COrgMod_Base::eSubtype_cultivar
@ eSubtype_cultivar
Definition: OrgMod_.hpp:93
COrgMod_Base::eSubtype_metagenome_source
@ eSubtype_metagenome_source
Definition: OrgMod_.hpp:120
COrgMod_Base::eSubtype_acronym
@ eSubtype_acronym
Definition: OrgMod_.hpp:102
COrgMod_Base::eSubtype_specimen_voucher
@ eSubtype_specimen_voucher
Definition: OrgMod_.hpp:106
COrgMod_Base::eSubtype_serovar
@ eSubtype_serovar
Definition: OrgMod_.hpp:92
COrgMod_Base::eSubtype_breed
@ eSubtype_breed
Definition: OrgMod_.hpp:114
CPub_Base::SetProc
TProc & SetProc(void)
Select the variant.
Definition: Pub_.cpp:305
CPub_Base::SetPmid
TPmid & SetPmid(void)
Select the variant.
Definition: Pub_.hpp:690
CPub_Base::SetBook
TBook & SetBook(void)
Select the variant.
Definition: Pub_.cpp:283
CPub_equiv_Base::Set
Tdata & Set(void)
Assign a value to data member.
Definition: Pub_equiv_.hpp:171
CPub_Base::GetArticle
const TArticle & GetArticle(void) const
Get the variant data.
Definition: Pub_.cpp:233
CPub_Base::Which
E_Choice Which(void) const
Which variant is currently selected.
Definition: Pub_.hpp:555
CPub_Base::SetMan
TMan & SetMan(void)
Select the variant.
Definition: Pub_.cpp:371
CPub_Base::SetSub
TSub & SetSub(void)
Select the variant.
Definition: Pub_.cpp:195
CPub_Base::SetGen
TGen & SetGen(void)
Select the variant.
Definition: Pub_.cpp:173
CPub_Base::SetJournal
TJournal & SetJournal(void)
Select the variant.
Definition: Pub_.cpp:261
CPub_Base::SetArticle
TArticle & SetArticle(void)
Select the variant.
Definition: Pub_.cpp:239
CPub_Base::IsGen
bool IsGen(void) const
Check if variant Gen is selected.
Definition: Pub_.hpp:584
CPub_Base::e_Article
@ e_Article
Definition: Pub_.hpp:106
CPub_Base::e_Book
@ e_Book
Definition: Pub_.hpp:108
CPub_Base::e_Gen
@ e_Gen
general or generic unparsed
Definition: Pub_.hpp:102
CPub_Base::e_Journal
@ e_Journal
Definition: Pub_.hpp:107
CPub_Base::e_Proc
@ e_Proc
proceedings of a meeting
Definition: Pub_.hpp:109
CPub_Base::e_Man
@ e_Man
manuscript, thesis, or letter
Definition: Pub_.hpp:112
CPub_Base::e_Sub
@ e_Sub
submission
Definition: Pub_.hpp:103
CRNA_ref_Base::eType_rRNA
@ eType_rRNA
Definition: RNA_ref_.hpp:100
CRNA_ref_Base::eType_ncRNA
@ eType_ncRNA
non-coding RNA; subsumes snRNA, scRNA, snoRNA
Definition: RNA_ref_.hpp:104
CRNA_ref_Base::eType_mRNA
@ eType_mRNA
Definition: RNA_ref_.hpp:98
CRNA_ref_Base::eType_miscRNA
@ eType_miscRNA
Definition: RNA_ref_.hpp:106
CRNA_ref_Base::eType_tRNA
@ eType_tRNA
Definition: RNA_ref_.hpp:99
orig
where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig
Definition: introspection_html.hpp:116
ncbi::grid::netcache::search::fields::size
const struct ncbi::grid::netcache::search::fields::SIZE size
rapidjson::source
const CharType(& source)[N]
Definition: pointer.h:1149
t
EIPRangeType t
Definition: ncbi_localip.c:101
ncbi_pch.hpp
ncbiapp.hpp
Defines the CNcbiApplication and CAppException classes for creating NCBI applications.
ncbimisc.hpp
Miscellaneous common-use basic types and functionality.
max
T max(T x_, T y_)
Definition: njn_function.hpp:105
min
T min(T x_, T y_)
Definition: njn_function.hpp:107
random_gen.hpp
USING_SCOPE
USING_SCOPE(objects)
s_ChangeAuthorLastName
void s_ChangeAuthorLastName(CAuth_list &auth_list)
Definition: seqfeatdata_unit_test.cpp:409
s_TestAuthorChanges
void s_TestAuthorChanges(CPub &pub)
Definition: seqfeatdata_unit_test.cpp:708
s_ChangeNameTitle
void s_ChangeNameTitle(CTitle &title)
Definition: seqfeatdata_unit_test.cpp:527
ESUBTYPE_SHOULD_FAIL
#define ESUBTYPE_SHOULD_FAIL(name)
CHECK_COMMON_FIELD
#define CHECK_COMMON_FIELD(o1, o2, c, Field, val1, val2)
Definition: seqfeatdata_unit_test.cpp:960
s_SetImprint
CRef< CImprint > s_SetImprint(CPub &pub)
Definition: seqfeatdata_unit_test.cpp:483
s_MakeJournalArticlePub
CRef< CPub > s_MakeJournalArticlePub()
Definition: seqfeatdata_unit_test.cpp:671
s_ChangeImprintNoMatch
void s_ChangeImprintNoMatch(CImprint &imp, int change_no)
Definition: seqfeatdata_unit_test.cpp:585
s_MakeBook
CRef< CCit_book > s_MakeBook()
Definition: seqfeatdata_unit_test.cpp:683
SetSubSource
static void SetSubSource(objects::CBioSource &src, objects::CSubSource::TSubtype subtype, string val)
Definition: seqfeatdata_unit_test.cpp:80
BOOST_AUTO_TEST_CASE
BOOST_AUTO_TEST_CASE(s_TestSubtypeMaps)
Definition: seqfeatdata_unit_test.cpp:118
s_MakeBookChapterPub
CRef< CPub > s_MakeBookChapterPub()
Definition: seqfeatdata_unit_test.cpp:696
s_SetAuthList
CRef< CAuth_list > s_SetAuthList(CPub &pub)
Definition: seqfeatdata_unit_test.cpp:420
s_ChangeImprintMatch
void s_ChangeImprintMatch(CImprint &imp, int change_no)
Definition: seqfeatdata_unit_test.cpp:600
s_MakeJournal
CRef< CCit_jour > s_MakeJournal()
Definition: seqfeatdata_unit_test.cpp:658
s_TestImprintChanges
void s_TestImprintChanges(CPub &pub)
Definition: seqfeatdata_unit_test.cpp:723
CheckBioProjectLocationVals
void CheckBioProjectLocationVals(CBioSource::EGenome genome, const string &bioprojectlocation)
Definition: seqfeatdata_unit_test.cpp:1899
s_ChangeJTATitle
void s_ChangeJTATitle(CTitle &title)
Definition: seqfeatdata_unit_test.cpp:544
s_AddJTATitle
void s_AddJTATitle(CTitle &title)
Definition: seqfeatdata_unit_test.cpp:536
s_AddNameTitle
void s_AddNameTitle(CTitle &title)
Definition: seqfeatdata_unit_test.cpp:519
s_MakeImprint
CRef< CImprint > s_MakeImprint()
Definition: seqfeatdata_unit_test.cpp:474
s_ChangeTitle
void s_ChangeTitle(CPub &pub)
Definition: seqfeatdata_unit_test.cpp:552
s_ChangeDate
void s_ChangeDate(CDate &date)
Definition: seqfeatdata_unit_test.cpp:579
CheckPlasmid
void CheckPlasmid(CBioSource &src)
Definition: seqfeatdata_unit_test.cpp:1890
s_TestTitleChange
void s_TestTitleChange(CPub &pub)
Definition: seqfeatdata_unit_test.cpp:756
s_MakeAuthList
CRef< CAuth_list > s_MakeAuthList()
Definition: seqfeatdata_unit_test.cpp:373
USING_NCBI_SCOPE
USING_NCBI_SCOPE
Definition: seqfeatdata_unit_test.cpp:77
CheckViruses
void CheckViruses(CBioSource &src)
Definition: seqfeatdata_unit_test.cpp:1878
s_ChangeAuthorFirstName
void s_ChangeAuthorFirstName(CAuth_list &auth_list)
Definition: seqfeatdata_unit_test.cpp:398
CHECK_COMMON_STRING_LIST
#define CHECK_COMMON_STRING_LIST(o1, o2, c, Field, val1, val2)
Definition: seqfeatdata_unit_test.cpp:1028
om
CRef< objects::CObjectManager > om
Definition: srsearch_app.cpp:359
SCollDateInfo::expected_result
const char * expected_result
Definition: seqfeatdata_unit_test.cpp:1413
eFiles::val
@ val
test2
#define test2(s, m, d, r)
Definition: t0007.c:124
test_assert.h
test_boost.hpp
Utility stuff for more convenient using of Boost.Test library.
NCBITEST_CHECK
#define NCBITEST_CHECK(P)
Definition: test_boost.hpp:616
util_exception.hpp
util_misc.hpp
ambig
static bool ambig(char c)
Definition: win_mask_gen_counts.cpp:75
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Modified on Wed Sep 27 02:42:18 2023 by modify_doxy.py rev. 669887