BOOST_REQUIRE(composite);
104 if((*sd).IsSource()){
105vector<string> strains;
108strains.push_back((*orgmod)->GetSubname());
111BOOST_REQUIRE(strains.size() == 4);
112BOOST_CHECK_EQUAL(strains[0],
string(
"DSM 7876"));
113BOOST_CHECK_EQUAL(strains[1],
string(
"ATCC VR-111"));
114BOOST_CHECK_EQUAL(strains[2],
string(
"strain3"));
115BOOST_CHECK_EQUAL(strains[3],
string(
"C768L/7"));
130BOOST_REQUIRE(composite);
135 if((*sd).IsSource()){
136vector<string> strains;
139strains.push_back((*orgmod)->GetSubname());
142BOOST_REQUIRE(!strains.empty());
143BOOST_CHECK_EQUAL(strains[0],
string(
"DSM 7876"));
144BOOST_CHECK_EQUAL(strains.size(), 1);
158BOOST_REQUIRE(composite);
165 if((*sd).IsSource()){
166 stringtaxname = (*sd).GetSource().GetTaxname();
168 boolis_oldname =
false;
172 boolis_dbtaxon =
false;
179BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus (X-33(H5N9))"));
180BOOST_CHECK_EQUAL (is_oldname,
false);
181BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
182BOOST_CHECK_EQUAL (is_dbtaxon,
false);
185BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus (X-33(H7N8))"));
186BOOST_CHECK_EQUAL (is_oldname,
false);
187BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
188BOOST_CHECK_EQUAL (is_dbtaxon,
false);
191BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus (Y546)"));
192BOOST_CHECK_EQUAL (is_oldname,
true);
193BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
194BOOST_CHECK_EQUAL (is_dbtaxon,
true);
197BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus"));
198BOOST_CHECK_EQUAL (is_oldname,
true);
199BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
200BOOST_CHECK_EQUAL (is_dbtaxon,
true);
203BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus"));
204BOOST_CHECK_EQUAL (is_oldname,
true);
205BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
206BOOST_CHECK_EQUAL (is_dbtaxon,
true);
222BOOST_REQUIRE(composite);
229 if((*sd).IsSource()){
230 stringtaxname = (*sd).GetSource().GetTaxname();
232 boolis_oldname =
false;
236 boolis_dbtaxon =
false;
243BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus (DSM 7866(H2N8))"));
244BOOST_CHECK_EQUAL (is_oldname,
true);
245BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
246BOOST_CHECK_EQUAL (is_dbtaxon,
true);
249BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus (DSM 7866(H2N8))"));
250BOOST_CHECK_EQUAL (is_oldname,
false);
251BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
252BOOST_CHECK_EQUAL (is_dbtaxon,
false);
255BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus (DSM 7866)"));
256BOOST_CHECK_EQUAL (is_oldname,
false);
257BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
258BOOST_CHECK_EQUAL (is_dbtaxon,
false);
261BOOST_CHECK_EQUAL (taxname,
string(
"Influenza A virus (DSM 7866(H2N8))"));
262BOOST_CHECK_EQUAL (is_oldname,
false);
263BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
264BOOST_CHECK_EQUAL (is_dbtaxon,
false);
267BOOST_CHECK_EQUAL (taxname,
string(
"Influenza B virus (DSM 7866(H2N8))"));
268BOOST_CHECK_EQUAL (is_oldname,
true);
269BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
270BOOST_CHECK_EQUAL (is_dbtaxon,
true);
287BOOST_REQUIRE(composite);
292 if((*sd).IsSource()){
294 intcount_serotypes=0;
295 stringstrain, serotype;
298count_strains++; strain = (*orgmod)->GetSubname();
301count_serotypes++; serotype = (*orgmod)->GetSubname();
305BOOST_CHECK_EQUAL (count_strains, 1);
306BOOST_CHECK_EQUAL (count_serotypes, 1);
307BOOST_CHECK_EQUAL (strain,
string(
"DSM 7866"));
308BOOST_CHECK_EQUAL (serotype,
string(
"H2N8"));
322BOOST_REQUIRE(composite);
328 if((*sd).IsSource()){
330 intcount_serotypes=0;
331 stringstrain, serotype;
334count_strains++; strain = (*orgmod)->GetSubname();
337count_serotypes++; serotype = (*orgmod)->GetSubname();
341BOOST_CHECK_EQUAL (count_strains, 1);
344BOOST_CHECK_EQUAL (count_serotypes, 1);
345BOOST_CHECK_EQUAL (strain,
string(
"X-33"));
346BOOST_CHECK_EQUAL (serotype,
string(
"sero/H5N9"));
349BOOST_CHECK_EQUAL (count_serotypes, 0);
350BOOST_CHECK_EQUAL (strain,
string(
"X-33"));
353BOOST_CHECK_EQUAL (count_serotypes, 1);
354BOOST_CHECK_EQUAL (strain,
string(
"X-33"));
355BOOST_CHECK_EQUAL (serotype,
string(
"H2N8"));
371BOOST_REQUIRE(composite);
380 if((*sd).IsSource()){
381 stringtaxname = (*sd).GetSource().GetTaxname();
384 intcount_serotypes=0;
385 stringstrain, serotype;
388count_strains++; strain = (*orgmod)->GetSubname();
391count_serotypes++; serotype = (*orgmod)->GetSubname();
397BOOST_CHECK_EQUAL (count_strains, 1);
398BOOST_CHECK_EQUAL (count_serotypes, 1);
399BOOST_CHECK_EQUAL (strain,
string(
"DSM 7866"));
400BOOST_CHECK_EQUAL (serotype,
string(
"H2N8"));
403BOOST_CHECK_EQUAL (count_strains, 1);
404BOOST_CHECK_EQUAL (count_serotypes, 0);
405BOOST_CHECK_EQUAL (strain,
string(
"DSM_strain"));
408BOOST_CHECK_EQUAL (count_strains, 1);
409BOOST_CHECK_EQUAL (count_serotypes, 1);
410BOOST_CHECK_EQUAL (strain,
string(
"X-33"));
411BOOST_CHECK_EQUAL (serotype,
string(
"H2N8"));
428BOOST_REQUIRE(composite);
435 if((*sd).IsSource()){
436vector<string> bio_str;
437vector<string> ccol_str;
438vector<string> spec_str;
441bio_str.push_back((*orgmod)->GetSubname());
443ccol_str.push_back((*orgmod)->GetSubname());
445spec_str.push_back((*orgmod)->GetSubname());
450BOOST_CHECK_EQUAL(bio_str[0],
string(
"biom1:GH7899"));
451BOOST_CHECK_EQUAL(bio_str[1],
string(
"biom2/458966, Birmingham, England"));
452BOOST_CHECK_EQUAL(bio_str[2],
string(
"biom3:98jkk"));
453BOOST_CHECK_EQUAL(ccol_str[0],
string(
"ccol1:GH7899"));
454BOOST_CHECK_EQUAL(ccol_str[1],
string(
"ccol2/458966, Birmingham, England"));
455BOOST_CHECK_EQUAL(ccol_str[2],
string(
"ccol3:98jkk"));
456BOOST_CHECK_EQUAL(ccol_str[3],
string(
"new_ccol"));
457BOOST_CHECK_EQUAL(spec_str[0],
string(
"specv1:GH7899"));
458BOOST_CHECK_EQUAL(spec_str[1],
string(
"specv2/458966, Birmingham, England"));
459BOOST_CHECK_EQUAL(spec_str[2],
string(
"specv3:98jkk"));
462BOOST_CHECK_EQUAL(bio_str[0],
string(
"biom1:AD987"));
463BOOST_CHECK_EQUAL(bio_str[1],
string(
"biom2:AD987"));
464BOOST_CHECK_EQUAL(ccol_str[0],
string(
"cult:AD987"));
465BOOST_CHECK_EQUAL(spec_str[0],
string(
"spec:AD987"));
468BOOST_CHECK_EQUAL(bio_str[0],
string(
""));
469BOOST_CHECK_EQUAL(ccol_str[0],
string(
"ccol:4566"));
470BOOST_CHECK_EQUAL(spec_str[0],
string(
"spec:4566"));
472BOOST_CHECK_EQUAL(ccol_str.size(),
size);
473BOOST_CHECK_EQUAL(spec_str.size(),
size);
493BOOST_REQUIRE(composite);
499 if((*sd).IsSource()){
500 stringtaxname =(*sd).GetSource().GetTaxname();
502 boolis_dbtaxon =
false;
508BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus burgeri"));
509BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
510BOOST_CHECK_EQUAL (is_dbtaxon,
true);
513BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus burgeri"));
514BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
515BOOST_CHECK_EQUAL (is_dbtaxon,
false);
518BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus"));
519BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
520BOOST_CHECK_EQUAL (is_dbtaxon,
true);
523BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus aff."));
524BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
525BOOST_CHECK_EQUAL (is_dbtaxon,
true);
528BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus aff. burgeri"));
529BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
530BOOST_CHECK_EQUAL (is_dbtaxon,
true);
533BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus aff. burgeri"));
534BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
535BOOST_CHECK_EQUAL (is_dbtaxon,
false);
538BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus burgeri sp."));
539BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
540BOOST_CHECK_EQUAL (is_dbtaxon,
true);
543BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus burgeri sp. hagfish"));
544BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
545BOOST_CHECK_EQUAL (is_dbtaxon,
true);
548BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus burgeri sp. hagfish"));
549BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
550BOOST_CHECK_EQUAL (is_dbtaxon,
false);
553BOOST_CHECK_EQUAL (taxname,
string(
"Eptatretus burgeri sp. hagfish"));
554BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
555BOOST_CHECK_EQUAL (is_dbtaxon,
false);
558BOOST_CHECK_EQUAL (taxname,
string(
"uncultured Eptatretus burgeri"));
559BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
560BOOST_CHECK_EQUAL (is_dbtaxon,
true);
563BOOST_CHECK_EQUAL (taxname,
string(
"uncultured Eptatretus burgeri"));
564BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
565BOOST_CHECK_EQUAL (is_dbtaxon,
false);
568BOOST_CHECK_EQUAL (taxname,
string(
"uncultured Eptatretus"));
569BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
570BOOST_CHECK_EQUAL (is_dbtaxon,
true);
573BOOST_CHECK_EQUAL (taxname,
string(
"uncultured Eptatretus sp."));
574BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
575BOOST_CHECK_EQUAL (is_dbtaxon,
true);
578BOOST_CHECK_EQUAL (taxname,
string(
"Uncultured Eptatretus cf. burgeri"));
579BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
580BOOST_CHECK_EQUAL (is_dbtaxon,
true);
583BOOST_CHECK_EQUAL (taxname,
string(
"Uncultured Eptatretus cf. burgeri"));
584BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
585BOOST_CHECK_EQUAL (is_dbtaxon,
false);
588BOOST_CHECK_EQUAL (taxname,
string(
"Uncultured Eptatretus burgeri sp."));
589BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
590BOOST_CHECK_EQUAL (is_dbtaxon,
true);
593BOOST_CHECK_EQUAL (taxname,
string(
"Uncultured Eptatretus burgeri sp. fish"));
594BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
true);
595BOOST_CHECK_EQUAL (is_dbtaxon,
true);
598BOOST_CHECK_EQUAL (taxname,
string(
"uncultured Eptatretus burgeri sp. hagfish"));
599BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
600BOOST_CHECK_EQUAL (is_dbtaxon,
false);
603BOOST_CHECK_EQUAL (taxname,
string(
"uncultured Eptatretus burgeri sp. hagfish"));
604BOOST_CHECK_EQUAL ((*sd).GetSource().GetOrg().IsSetCommon(),
false);
605BOOST_CHECK_EQUAL (is_dbtaxon,
false);
608BOOST_CHECK_EQUAL(taxname,
string(
"Gibbula divaricata"));
609BOOST_CHECK_EQUAL((*sd).GetSource().GetOrg().IsSetCommon(),
false);
610BOOST_CHECK_EQUAL(is_dbtaxon,
false);
624 string rna(
"16S ribosomal RNA");
628 boolisftableset =
false, isrna =
false, isinterval =
false, isstrandplus =
false;
632BOOST_CHECK_EQUAL ((*bs).GetLength() != 204,
true);
633isftableset = (*bs).IsSetAnnot() && ((*bs).GetAnnot().front())->GetData().IsFtable();
634BOOST_CHECK_EQUAL (isftableset,
true);
636 CRef<CSeq_feat>check_feat = ((*bs).GetAnnot().front())->GetData().GetFtable().front();
638BOOST_CHECK_EQUAL (isrna,
true);
642BOOST_CHECK_EQUAL (check_feat->
IsSetPartial(),
true);
643BOOST_CHECK_EQUAL (check_feat->
GetPartial(),
true);
646BOOST_CHECK_EQUAL (isinterval,
true);
650BOOST_CHECK_EQUAL (check_loc->
GetInt().
GetTo(), (*bs).GetLength()-1);
653BOOST_CHECK_EQUAL (isstrandplus,
true);
656BOOST_CHECK_EQUAL (check_loc->
GetInt().
GetId().
Which(), (*bs).GetId().front()->Which());
670 boolisftableset =
false, isrna =
false, isinterval =
false, isstrandplus =
false;
674BOOST_CHECK_EQUAL ((*bs).GetLength() != 204,
true);
675isftableset = (*bs).IsSetAnnot() && ((*bs).GetAnnot().front())->GetData().IsFtable();
676BOOST_CHECK_EQUAL (isftableset,
true);
678 CRef<CSeq_feat>check_feat = ((*bs).GetAnnot().front())->GetData().GetFtable().front();
680BOOST_CHECK_EQUAL (isrna,
true);
681BOOST_CHECK_EQUAL (check_feat->
GetData().
GetImp().
GetKey(),
string(
"misc_feature"));
682BOOST_CHECK_EQUAL (check_feat->
GetComment(),
string(
"control region"));
683BOOST_CHECK_EQUAL (check_feat->
IsSetPartial(),
true);
684BOOST_CHECK_EQUAL (check_feat->
GetPartial(),
true);
687BOOST_CHECK_EQUAL (isinterval,
true);
691BOOST_CHECK_EQUAL (check_loc->
GetInt().
GetTo(), (*bs).GetLength()-1);
694BOOST_CHECK_EQUAL (isstrandplus,
true);
697BOOST_CHECK_EQUAL (check_loc->
GetInt().
GetId().
Which(), (*bs).GetId().front()->Which());
712 boolisftableset =
false, isrna =
false, isinterval =
false, isstrandplus =
false;
716BOOST_CHECK_EQUAL ((*bs).GetLength() != 204,
true);
717isftableset = (*bs).IsSetAnnot() && ((*bs).GetAnnot().front())->GetData().IsFtable();
718BOOST_CHECK_EQUAL (isftableset,
true);
720 CRef<CSeq_feat>check_feat = ((*bs).GetAnnot().front())->GetData().GetFtable().front();
722BOOST_CHECK_EQUAL (isrna,
true);
723BOOST_CHECK_EQUAL (check_feat->
GetData().
GetImp().
GetKey(),
string(
"repeat_region"));
724BOOST_CHECK_EQUAL (check_feat->
IsSetPartial(),
false);
727BOOST_CHECK_EQUAL (isinterval,
true);
731BOOST_CHECK_EQUAL (check_loc->
GetInt().
GetTo(), (*bs).GetLength()-1);
734BOOST_CHECK_EQUAL (isstrandplus,
true);
737BOOST_CHECK_EQUAL (check_loc->
GetInt().
GetId().
Which(), (*bs).GetId().front()->Which());
739BOOST_CHECK_EQUAL (check_feat->
GetQual().size(), 2);
740BOOST_CHECK_EQUAL (check_feat->
GetQual().at(0)->GetQual(),
string(
"rpt_type"));
741BOOST_CHECK_EQUAL (check_feat->
GetQual().at(0)->GetVal(),
string(
"tandem"));
742BOOST_CHECK_EQUAL (check_feat->
GetQual().at(1)->GetQual(),
string(
"satellite"));
743BOOST_CHECK_EQUAL (check_feat->
GetQual().at(1)->GetVal(),
string(
"microsatellite"));
755 stringtitle(
"random title");
757BOOST_CHECK_EQUAL (count_conflicts, 7);
758title =
"new definition line";
760BOOST_CHECK_EQUAL (count_conflicts, 5);
764BOOST_CHECK_EQUAL (update,
true);
770 if((*sd).IsTitle()){
771 if(seqs >=
'0'&& seqs <
'9')
772BOOST_CHECK_EQUAL ((*sd).GetTitle(),
string(
"new definition line"));
773 else if(seqs==
'9')
774BOOST_CHECK_EQUAL ((*sd).GetTitle(),
string(
"some other title"));
777BOOST_CHECK(!(*sd).IsUser());
792 shortnrTitle = 0, nrCrDate = 0, nrSource = 0, nrMolinfo = 0, other = 0;
797 else if((*sd).IsCreate_date())
799 else if((*sd).IsMolinfo())
801 else if((*sd).IsSource())
806BOOST_CHECK_EQUAL (nrTitle, 0);
807BOOST_CHECK_EQUAL (nrCrDate, 3);
808BOOST_CHECK_EQUAL (nrSource, 3);
809BOOST_CHECK_EQUAL (nrMolinfo, 6);
810BOOST_CHECK_EQUAL (other, 0);
827 if((*sd).IsTitle()){
828title = (*sd).GetTitle();
831BOOST_CHECK_EQUAL (title,
string(
"Mixed organisms SET_title_1"));
834BOOST_CHECK_EQUAL (title,
string(
"Influenza A virus title for seq_1"));
837BOOST_CHECK_EQUAL (title,
string(
"New orgname title for seq_2"));
840BOOST_CHECK_EQUAL (title,
string(
"Cryptomeria japonica SET_title_1"));
843BOOST_CHECK_EQUAL (title,
string(
"New orgname SET_title_1"));
846BOOST_CHECK_EQUAL (title,
string(
"Mixed organisms set title_2"));
849BOOST_CHECK_EQUAL (title,
string(
"New orgname set title_2"));
852BOOST_CHECK_EQUAL (title,
string(
"Influenza C virus title for seq_6"));
855BOOST_CHECK_EQUAL (title,
string(
"New orgname set title_2"));
858BOOST_CHECK_EQUAL (title,
string(
"New orgname title for seq_8"));
861BOOST_CHECK_EQUAL (title,
string(
"newtitle"));
870composite.
Reset(
new CCmdComposite(
"Testing prefixing strain to definition line"));
878 if(entry.
IsSeq() && (*sd).IsTitle()){
879title = (*sd).GetTitle();
882BOOST_CHECK_EQUAL (title,
string(
"SET_title_1"));
885BOOST_CHECK_EQUAL (title,
string(
"strain A/X-31 title for seq_1"));
888BOOST_CHECK_EQUAL (title,
string(
"strain Set strain title for seq_2"));
891BOOST_CHECK_EQUAL (title,
string(
"strain strain_989 SET_title_1"));
894BOOST_CHECK_EQUAL (title,
string(
"strain Set strain SET_title_1"));
897BOOST_CHECK_EQUAL (title,
string(
"set title_2"));
900BOOST_CHECK_EQUAL (title,
string(
"strain Set strain set title_2"));
903BOOST_CHECK_EQUAL (title,
string(
"strain strain_6 title for seq_6"));
906BOOST_CHECK_EQUAL (title,
string(
"strain Set strain set title_2"));
909BOOST_CHECK_EQUAL (title,
string(
"strain Set strain title for seq_8"));
912BOOST_CHECK_EQUAL (title,
string(
"newtitle"));
920composite.
Reset(
new CCmdComposite(
"Testing prefixing strain and haplotype to definition line"));
931 if((*sd).IsTitle()){
932title = (*sd).GetTitle();
935BOOST_CHECK_EQUAL (title,
string(
"SET_title_1"));
938BOOST_CHECK_EQUAL (title,
939 string(
"Influenza A virus haplotype haplo99 strain A/X-31 isolate iso_seq1 title for seq_1"));
942BOOST_CHECK_EQUAL (title,
943 string(
"New orgname haplotype set_haplot strain Set strain isolate iso45 title for seq_2"));
946BOOST_CHECK_EQUAL (title,
947 string(
"Cryptomeria japonica haplotype set_haplot strain strain_989 SET_title_1"));
950BOOST_CHECK_EQUAL (title,
951 string(
"New orgname haplotype set_haplot strain Set strain SET_title_1"));
954BOOST_CHECK_EQUAL (title,
string(
"set title_2"));
957BOOST_CHECK_EQUAL (title,
958 string(
"New orgname haplotype haplot.987 strain Set strain isolate iso456 set title_2"));
961BOOST_CHECK_EQUAL (title,
962 string(
"Influenza C virus haplotype haplot.987 strain strain_6 isolate iso456 title for seq_6"));
965BOOST_CHECK_EQUAL (title,
966 string(
"New orgname haplotype haplot.987 strain Set strain isolate iso456 set title_2"));
969BOOST_CHECK_EQUAL (title,
970 string(
"New orgname haplotype haplot.987 strain Set strain isolate iso456 title for seq_8"));
973BOOST_CHECK_EQUAL (title,
string(
"newtitle"));
985 title \"SET_title_1\" , \ 988 taxname \"New orgname\" , \ 993 subname \"Set strain\" } } } } , \ 996 subtype haplotype , \ 997 name \"set_haplot\" } } } } , \ 1001 local str \"seq_1\" },\ 1003 title \"title for seq_1\" , \ 1007 taxname \"Influenza A virus\" , \ 1012 subname \"A/X-31\" } , \ 1015 subname \"iso_seq1\" } , \ 1017 subtype serotype , \ 1018 subname \"H3N2\" } } } } , \ 1022 name \"clon45\" } , \ 1024 subtype haplotype , \ 1025 name \"haplo99\" } } }, \ 1027 biomol genomic } } , \ 1034 local str \"seq_2\" },\ 1036 title \"title for seq_2\" , \ 1043 subtype cultivar , \ 1044 subname \"Elegans\" } , \ 1047 subname \"iso45\" } , \ 1049 subtype serotype , \ 1050 subname \"H3N2\" } } } } , \ 1053 subtype haplotype , \ 1056 biomol genomic } } , \ 1062 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1065 local str \"seq_3\" },\ 1070 taxname \"Cryptomeria japonica\" , \ 1074 subtype cultivar , \ 1075 subname \"Elegans\" } , \ 1078 subname \"strain_989\" } , \ 1080 subtype serotype , \ 1081 subname \"H3N2\" } } } } } }, \ 1088 local str \"seq_4\" } , \ 1098 title \"set title_2\" , \ 1099 source { genome genomic , \ 1104 subtype cultivar , \ 1105 subname \"Elegans\" } , \ 1108 subname \"iso456\" } , \ 1111 subname \"\" } } } } , \ 1115 name \"agVLRB.198.short\" } , \ 1117 subtype haplotype , \ 1118 name \"haplot.987\" } } } , \ 1126 local str \"seq_5\" } , \ 1133 local str \"seq_6\" } , \ 1135 title \"title for seq_6\" , \ 1136 source { genome genomic , \ 1138 taxname \"Influenza C virus\" , \ 1142 subtype cultivar , \ 1143 subname \"Elegans\" } , \ 1146 subname \"strain_6\" } } } } , \ 1150 name \"clone9999\" } } } , \ 1152 biomol genomic } } , \ 1159 local str \"seq_7\" } , \ 1163 biomol genomic } } , \ 1170 local str \"seq_8\" } , \ 1172 title \"title for seq_8\" , \ 1173 source { genome genomic , \ 1178 subtype cultivar , \ 1179 subname \"Elegans\" } , \ 1181 subtype serotype , \ 1182 subname \"sero8\" } } } } }, \ 1184 biomol genomic } } , \ 1188 length 100 } } } } , \ 1191 local str \"seq_9\" },\ 1193 title \"newtitle\" , \ 1196 taxname \"Influenza B virus\" } } , \ 1198 biomol genomic } } , \ 1202 length 204 } } } } \ 1207 Seq-entry ::= set {\ 1210 title \"set title0\" , \ 1215 title \"set title1\" } , \ 1219 local str \"seq_1\" },\ 1221 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1223 biomol genomic } } , \ 1230 local str \"seq_2\" },\ 1232 title \"new definition line\" , \ 1233 title \"some other title\" , \ 1234 title \"some other interesting title\" , \ 1240 biomol genomic } } , \ 1246 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1249 local str \"seq_3\" },\ 1256 title \"set title2\" , \ 1265 local str \"seq_4\" } , \ 1267 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1268 source { genome genomic , \ 1270 taxname \"Eptatretus burgeri\" } } , \ 1272 biomol genomic } } , \ 1279 local str \"seq_5\" } , \ 1281 source { genome genomic , \ 1283 taxname \"Eptatretus burgeri\" } } , \ 1285 biomol genomic } } , \ 1292 local str \"seq_6\" } , \ 1296 biomol genomic } } , \ 1303 local str \"seq_7\" },\ 1307 length 3455 } } } } , \ 1310 local str \"seq_8\" },\ 1312 title \"new definition line\" , \ 1313 title \"some other title\" , \ 1314 source { genome genomic , \ 1316 taxname \"Eptatretus burgeri\" } } , \ 1318 biomol genomic } } , \ 1322 length 204 } } } } \ 1326 Seq-entry ::= set {\ 1329 title \"set title\" , \ 1337 local str \"seq_1\" },\ 1339 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1341 biomol genomic } } , \ 1348 local str \"seq_2\" },\ 1350 title \"new definition line\" , \ 1351 title \"some other title\" , \ 1352 title \"some other interesting title\" , \ 1358 biomol genomic } } , \ 1364 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1367 local str \"seq_3\" },\ 1376 local str \"seq_4\" } , \ 1378 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1379 source { genome genomic , \ 1381 taxname \"Eptatretus burgeri\" } } , \ 1384 type str \"AutodefOptions\" , \ 1387 label str \"FeatureListType\" , \ 1388 data str \"List All Features\" } } } } , \ 1395 local str \"seq_5\" } , \ 1397 source { genome genomic , \ 1399 taxname \"Eptatretus burgeri\" } } , \ 1401 biomol genomic } } , \ 1408 local str \"seq_6\" } , \ 1412 biomol genomic } } , \ 1419 local str \"seq_7\" },\ 1421 title \"new definition line\" , \ 1423 biomol genomic } } , \ 1427 length 3455 } } } } , \ 1430 local str \"seq_8\" },\ 1432 title \"new definition line\" , \ 1433 title \"some other title\" , \ 1434 source { genome genomic , \ 1436 taxname \"Eptatretus burgeri\" } } , \ 1438 biomol genomic } } , \ 1442 length 204 } } } } \ 1447 Seq-entry ::= set {\ 1457 local str \"seq_1\" },\ 1464 local str \"seq_2\" },\ 1470 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1473 local str \"seq_3\" },\ 1482 local str \"title1\" } , \ 1489 local str \"seq_15\" },\ 1493 length 3455 } } } } } } \ 1498 Seq-entry ::= set {\ 1508 local str \"seq_1\" },\ 1510 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1514 taxname \"Eptatretus burgeri\" , \ 1515 common \"hagfish\" , \ 1524 subname \"BoBM478\" } } } } }, \ 1526 biomol genomic } }, \ 1533 local str \"seq_2\" },\ 1535 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1539 taxname \"Eptatretus burgeri vertebrate\" , \ 1540 common \"hagfish\" , \ 1544 tag id 3652 } } } }, \ 1546 biomol genomic } }, \ 1552 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1555 local str \"seq_3\" },\ 1557 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1561 taxname \"Eptatretus\" , \ 1562 common \"hagfish\" , \ 1566 tag id 3652 } } } }, \ 1568 biomol genomic } }, \ 1574 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1577 local str \"seq_4\" },\ 1579 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 1583 taxname \"Eptatretus aff.\" , \ 1584 common \"hagfish\" , \ 1588 tag id 3652 } } } }, \ 1590 biomol genomic } }, \ 1596 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1599 local str \"seq_5\" },\ 1601 title \"New_title\" , \ 1605 taxname \"Eptatretus aff. burgeri\" , \ 1606 common \"hagfish\" , \ 1610 tag id 3652 } } } }, \ 1612 biomol genomic } }, \ 1617 topology circular , \ 1618 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1621 local str \"seq_6\" },\ 1623 title \"New_title\" , \ 1627 taxname \"Eptatretus aff. burgeri hagfish\" , \ 1628 common \"hagfish\" , \ 1632 tag id 3652 } } } }, \ 1634 biomol genomic } }, \ 1639 topology circular , \ 1640 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1643 local str \"seq_7\" },\ 1645 title \"Some_title\" , \ 1649 taxname \"Eptatretus burgeri sp.\" , \ 1650 common \"hagfish\" , \ 1654 tag id 3652 } } } }, \ 1656 biomol genomic } }, \ 1661 topology circular , \ 1662 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1665 local str \"seq_8\" },\ 1667 title \"Some_title\" , \ 1671 taxname \"Eptatretus burgeri sp. hagfish\" , \ 1672 common \"hagfish\" , \ 1676 tag id 3652 } } } }, \ 1678 biomol genomic } }, \ 1683 topology circular , \ 1684 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1687 local str \"seq_9\" },\ 1689 title \"Some new title\" , \ 1693 taxname \"Eptatretus burgeri sp. hagfish fish\" , \ 1694 common \"hagfish\" , \ 1698 tag id 3652 } } } }, \ 1700 biomol genomic } }, \ 1705 topology circular , \ 1706 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1709 local str \"seq_10\" },\ 1711 title \"New_title\" , \ 1715 taxname \"Eptatretus burgeri sp. hagfish aff. some\" , \ 1716 common \"hagfish\" , \ 1724 subtype serotype , \ 1725 subname \"H2N8\" } , \ 1727 subtype old-name , \ 1728 subname \"a_flu\" } } } } }, \ 1730 biomol genomic } }, \ 1735 topology circular , \ 1736 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1739 local str \"seq_11\" },\ 1741 title \"Some new title\" , \ 1745 taxname \"uncultured Eptatretus burgeri\" , \ 1746 common \"hagfish\" , \ 1750 tag id 3652 } } } }, \ 1752 biomol genomic } }, \ 1757 topology circular , \ 1758 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1761 local str \"seq_12\" },\ 1763 title \"Some new title\" , \ 1767 taxname \"uncultured Eptatretus burgeri hagfish\" , \ 1768 common \"hagfish\" , \ 1772 tag id 3652 } } } }, \ 1774 biomol genomic } }, \ 1779 topology circular , \ 1780 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1783 local str \"seq_13\" },\ 1785 title \"Some new title\" , \ 1789 taxname \"uncultured Eptatretus\" , \ 1790 common \"hagfish\" , \ 1794 tag id 3652 } } } }, \ 1796 biomol genomic } }, \ 1801 topology circular , \ 1802 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1805 local str \"seq_14\" },\ 1807 title \"Some new title\" , \ 1811 taxname \"uncultured Eptatretus sp.\" , \ 1812 common \"hagfish\" , \ 1816 tag id 3652 } } } }, \ 1818 biomol genomic } }, \ 1823 topology circular , \ 1824 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1827 local str \"seq_15\" },\ 1829 title \"New_title\" , \ 1833 taxname \"Uncultured Eptatretus cf. burgeri\" , \ 1834 common \"hagfish\" , \ 1842 subtype serotype , \ 1843 subname \"H2N8\" } , \ 1845 subtype old-name , \ 1846 subname \"a_flu\" } } } } }, \ 1848 biomol genomic } }, \ 1853 topology circular , \ 1854 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1857 local str \"seq_16\" },\ 1859 title \"Some_title\" , \ 1863 taxname \"Uncultured Eptatretus cf. burgeri hagfish\" , \ 1864 common \"hagfish\" , \ 1868 tag id 3652 } } } }, \ 1870 biomol genomic } }, \ 1875 topology circular , \ 1876 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1879 local str \"seq_17\" },\ 1881 title \"Some_title\" , \ 1885 taxname \"Uncultured Eptatretus burgeri sp.\" , \ 1886 common \"hagfish\" , \ 1890 tag id 3652 } } } }, \ 1892 biomol genomic } }, \ 1897 topology circular , \ 1898 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1901 local str \"seq_18\" },\ 1903 title \"Some_title\" , \ 1907 taxname \"Uncultured Eptatretus burgeri sp. fish\" , \ 1908 common \"hagfish\" , \ 1912 tag id 3652 } } } }, \ 1914 biomol genomic } }, \ 1919 topology circular , \ 1920 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1923 local str \"seq_19\" },\ 1925 title \"New_title\" , \ 1929 taxname \"uncultured Eptatretus burgeri sp. hagfish fish\" , \ 1930 common \"hagfish\" , \ 1938 subtype serotype , \ 1939 subname \"H2N8\" } , \ 1941 subtype old-name , \ 1942 subname \"a_flu\" } } } } }, \ 1944 biomol genomic } }, \ 1949 topology circular , \ 1950 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1953 local str \"seq_20\" },\ 1955 title \"New_title\" , \ 1959 taxname \"uncultured Eptatretus burgeri sp. hagfish aff. some\" , \ 1960 common \"hagfish\" , \ 1968 subtype serotype , \ 1969 subname \"H2N8\" } , \ 1971 subtype old-name , \ 1972 subname \"a_flu\" } } } } }, \ 1974 biomol genomic } }, \ 1979 topology circular , \ 1980 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 1983 local str \"seq_21\" },\ 1987 taxname \"Gibbula divaricata: Trochidae: Vetigastropoda: Mollusca\" } }, \ 1989 biomol genomic } }, \ 1995 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } } } \ 1999 Seq-entry ::= set {\ 2009 local str \"seq_1\" },\ 2011 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2015 taxname \"Mus Musculus\" , \ 2016 common \"house mouse\" , \ 2021 subname \"DSM 7866\" } , \ 2023 subtype serotype , \ 2024 subname \"H2N8\" } , \ 2026 subtype bio-material , \ 2027 subname \"biom1:GH7899; biom2/458966, Birmingham, England ; biom3:98jkk \" } , \ 2029 subtype culture-collection , \ 2030 subname \"ccol1:GH7899; ccol2/458966, Birmingham, England ; ccol3:98jkk \" } ,\ 2032 subtype specimen-voucher , \ 2033 subname \"specv1:GH7899; specv2/458966, Birmingham, England ;specv3:98jkk\" } , \ 2035 subtype culture-collection , \ 2036 subname \"new_ccol\" } } } } }, \ 2038 biomol genomic } }, \ 2045 local str \"seq_3\" },\ 2047 title \"New_title\" , \ 2051 taxname \"Escherichia coli\" , \ 2056 subtype bio-material , \ 2057 subname \"biom1:AD987; \" } , \ 2060 subname \"DSM_strain\" } , \ 2062 subtype old-name , \ 2063 subname \"a_flu\" } , \ 2065 subtype specimen-voucher , \ 2066 subname \" spec:AD987 ;\" } , \ 2068 subtype bio-material , \ 2069 subname \"biom2:AD987; \" } , \ 2071 subtype culture-collection , \ 2072 subname \"cult:AD987; \" } } } } }, \ 2074 biomol genomic } }, \ 2079 topology circular , \ 2080 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2083 local str \"seq_5\" },\ 2085 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2089 taxname \"Gorilla gorilla\" , \ 2094 subtype serotype , \ 2095 subname \"H2N8\" } , \ 2097 subtype old-name , \ 2098 subname \"a_flu\" } , \ 2100 subtype bio-material , \ 2103 subtype culture-collection , \ 2104 subname \" ; ccol:4566 \" } , \ 2106 subtype specimen-voucher , \ 2107 subname \" ; spec:4566 ; \" } } } } }, \ 2109 biomol genomic } }, \ 2114 topology circular , \ 2115 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } \ 2122 Seq-entry ::= set {\ 2132 local str \"seq_1\" },\ 2134 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2138 taxname \"Influenza A virus (X-33(sero/H5N9))\" , \ 2144 subname \"DSM 7866\" } , \ 2146 subtype serotype , \ 2147 subname \"H2N8\" } , \ 2150 subname \"BoBM478\" } } } } }, \ 2152 biomol genomic } }, \ 2159 local str \"seq_3\" },\ 2161 title \"New_title\" , \ 2165 taxname \"Influenza A virus (X-33()) \" , \ 2171 subname \"DSM_strain\" } , \ 2173 subtype old-name , \ 2174 subname \"a_flu\" } } } } }, \ 2176 biomol genomic } }, \ 2181 topology circular , \ 2182 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2185 local str \"seq_5\" },\ 2187 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2191 taxname \"Influenza A virus (X-33)\" , \ 2196 subtype serotype , \ 2197 subname \"H2N8\" } , \ 2199 subtype old-name , \ 2200 subname \"a_flu\" } , \ 2203 subname \"my_isolate\" } } } } }, \ 2205 biomol genomic } }, \ 2210 topology circular , \ 2211 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } \ 2216 Seq-entry ::= set {\ 2226 local str \"seq_1\" },\ 2228 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2232 taxname \"Influenza A virus (DSM 7866(H2N8))\" , \ 2238 subname \"BoBM478\" } } } } }, \ 2240 biomol genomic } }, \ 2247 local str \"seq_2\" },\ 2249 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2253 taxname \"Influenza A virus (DSM 7866(H2N8))\" , \ 2258 tag id 5966 } } } }, \ 2260 biomol genomic } }, \ 2266 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2269 local str \"seq_3\" },\ 2271 title \"New_title\" , \ 2275 taxname \"Influenza A virus (DSM 7866(H2N8)) \" , \ 2281 subname \"DSM 7866\" } , \ 2283 subtype serotype , \ 2284 subname \"H2N8\" } , \ 2286 subtype old-name , \ 2287 subname \"a_flu\" } } } } }, \ 2289 biomol genomic } }, \ 2294 topology circular , \ 2295 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2298 local str \"seq_4\" },\ 2300 title \"New_title\" , \ 2304 taxname \"Influenza A virus (DSM 7866) \" , \ 2309 subtype serotype , \ 2310 subname \"H2N8\" } , \ 2312 subtype old-name , \ 2313 subname \"a_flu\" } } } } }, \ 2315 biomol genomic } }, \ 2320 topology circular , \ 2321 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } } } \ 2332 Seq-entry ::= set {\ 2342 local str \"seq_1\" },\ 2344 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2348 taxname \"Influenza A virus\" , \ 2361 subtype old-name , \ 2362 subname \"a_flu\" } , \ 2365 subname \"BoBM478\" } } } } }, \ 2367 biomol genomic } }, \ 2374 local str \"seq_2\" },\ 2376 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2384 biomol genomic } }, \ 2390 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } } } \ 2394 Seq-entry ::= set {\ 2404 local str \"seq_1\" },\ 2406 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2410 taxname \"Influenza A virus (DSM 7866(H2N8))\" , \ 2424 subname \"DSM 7866\" } , \ 2426 subtype serotype , \ 2427 subname \"H2N8\" } , \ 2429 subtype old-name , \ 2430 subname \"a_flu\" } , \ 2433 subname \"BoBM478\" } } } } }, \ 2435 biomol genomic } }, \ 2442 local str \"seq_2\" },\ 2444 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2448 taxname \"Influenza A virus(DSM 7866 ( H2N8 ) ) \" , \ 2458 subname \"my_isolate\" }, \ 2460 subtype old-name , \ 2461 subname \"a_flu\" } } } } }, \ 2463 biomol genomic } }, \ 2469 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2472 local str \"seq_3\" },\ 2474 title \"New_title\" , \ 2478 taxname \"Influenza A virus( DSM 7866 ) \" , \ 2491 subname \"DSM 7866\" } , \ 2493 subtype old-name , \ 2494 subname \"a_flu\" } } } } }, \ 2496 biomol genomic } }, \ 2501 topology circular , \ 2502 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2505 local str \"seq_4\" } , \ 2507 title \"different sequence 4\" , \ 2511 taxname \"Influenza A virus ( DSM 7866 ( H2N8 ) ) \" , \ 2523 subtype old-name , \ 2524 subname \"a_flu\" } , \ 2527 subname \"my_isolate\" } } } } }, \ 2529 biomol genomic } }, \ 2534 topology circular , \ 2535 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2538 local str \"seq_5\" },\ 2540 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2544 taxname \"Influenza B virus (DSM 7866(H2N8))\" , \ 2556 subtype serotype , \ 2557 subname \"H2N8\" } , \ 2559 subtype old-name , \ 2560 subname \"a_flu\" } , \ 2563 subname \"my_isolate\" } } } } }, \ 2565 biomol genomic } }, \ 2570 topology circular , \ 2571 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } \ 2578 Seq-entry ::= set {\ 2588 local str \"seq_1\" },\ 2590 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2594 taxname \"Influenza A virus\" , \ 2608 subname \"X-33\" } , \ 2610 subtype serotype , \ 2611 subname \"H5N9\" } , \ 2613 subtype old-name , \ 2614 subname \"a_flu\" } , \ 2617 subname \"BoBM478\" } } } } }, \ 2619 biomol genomic } }, \ 2626 local str \"seq_2\" },\ 2628 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2632 taxname \"influenZa A Virus (X-33)\" , \ 2642 subname \"X-33\" } , \ 2644 subtype serotype , \ 2645 subname \"H7N8\" } , \ 2648 subname \"my_isolate\" }, \ 2650 subtype old-name , \ 2651 subname \"a_flu\" } } } } }, \ 2653 biomol genomic } }, \ 2659 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2662 local str \"seq_3\" },\ 2664 title \"New_title\" , \ 2668 taxname \"Influenza A virus (Y546)\" , \ 2681 subname \"X-33\" } , \ 2683 subtype serotype , \ 2684 subname \"H5N9\" } , \ 2686 subtype old-name , \ 2687 subname \"a_flu\" } } } } }, \ 2689 biomol genomic } }, \ 2694 topology circular , \ 2695 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2698 local str \"seq_4\" } , \ 2700 title \"different sequence 4\" , \ 2704 taxname \"Influenza A virus\" , \ 2717 subname \"X-33\" } , \ 2719 subtype old-name , \ 2720 subname \"a_flu\" } , \ 2723 subname \"my_isolate\" } } } } }, \ 2725 biomol genomic } }, \ 2730 topology circular , \ 2731 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2734 local str \"seq_5\" },\ 2736 title \"toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2740 taxname \"Influenza A virus\" , \ 2752 subtype serotype , \ 2753 subname \"H3N5\" } , \ 2755 subtype old-name , \ 2756 subname \"a_flu\" } , \ 2759 subname \"my_isolate\" } } } } }, \ 2761 biomol genomic } }, \ 2766 topology circular , \ 2767 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } \ 2776 Seq-entry ::= set { \ 2786 local str \"seq_1\" },\ 2788 title \"TitleA: toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2792 taxname \"Influenza A virus\" , \ 2797 subname \"DSM 7876, ATCC VR-111, strain3, C768L/7\" } , \ 2799 subtype serotype , \ 2800 subname \"this is my serotype\" } , \ 2803 subname \"BoBM478\" } } } } }, \ 2805 biomol genomic } }, \ 2812 local str \"seq_2\" },\ 2814 title \"TitleB: toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2818 taxname \"Influenza A virus\" , \ 2823 subname \" DSM 7876 , ATCC VR-111 , strain3 , C768L/7 \" } , \ 2825 subtype serotype , \ 2826 subname \"this is my serotype\" } } } } }, \ 2828 biomol genomic } }, \ 2834 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } } } \ 2838 Seq-entry ::= set { \ 2848 local str \"seq_1\" },\ 2850 title \"TitleA: toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2854 taxname \"Mus Musculus\" , \ 2859 subname \"DSM 7876, \" } , \ 2861 subtype serotype , \ 2862 subname \"this is my serotype\" } , \ 2865 subname \"BoBM478\" } } } } }, \ 2867 biomol genomic } }, \ 2874 local str \"seq_2\" },\ 2876 title \"TitleB: toll-like receptor 5 (TLR5) gene, complete cds\" , \ 2880 taxname \"Giraffa\" , \ 2885 subname \" DSM 7876 , \" } , \ 2888 subname \"78GB98\" } } } } }, \ 2890 biomol genomic } }, \ 2896 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } } } \ 2910vector<string> field_names;
2911field_names.push_back(
"SeqID");
2912field_names.push_back(
"taxname");
2913field_names.push_back(
"product");
2914field_names.push_back(
"acronym");
2918field_names.push_back(
"something odd");
2919field_names.push_back(
"another mismatch");
2920field_names.push_back(
"unrecognizable");
2921field_names.push_back(
"also bad");
2922field_names.push_back(
"not matching");
2923field_names.push_back(
"a mistake");
2924field_names.push_back(
"a typo");
2925field_names.push_back(
"wrong");
2926field_names.push_back(
"not found");
2937 local str \"seq_1\" } ,\ 2941 taxname \"foo\" } , \ 2944 subtype chromosome , \ 2947 biomol genomic } } , \ 2952 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2955 local str \"seq_2\" } ,\ 2959 taxname \"bar\" } , \ 2962 subtype chromosome , \ 2965 biomol genomic } } , \ 2970 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } } , \ 2973 local str \"seq_3\" } ,\ 2977 taxname \"foobar\" } , \ 2980 subtype chromosome , \ 2983 biomol genomic } } , \ 2988 seq-data iupacna \"AAAATTTTGGGGCCCCAAAA\" } }\ 2995 for(
size_t i= 0;
i< num_cols;
i++) {
2998 returntext_options;
3003 const string&
match,
const string& field,
3004 constvector<string>& match_vals,
3005 constvector<string>& field_vals)
3010id_col->
SetData().SetString().insert(id_col->
SetData().SetString().begin(),
3011match_vals.begin(), match_vals.end());
3012 table->SetColumns().push_back(id_col);
3015data_col->
SetHeader().SetTitle(field);
3016data_col->
SetData().SetString().insert(data_col->
SetData().SetString().begin(),
3017field_vals.begin(), field_vals.end());
3018 table->SetColumns().push_back(data_col);
3030vector<string> retrieve_fields;
3032retrieve_fields.push_back(
match);
3034retrieve_fields.push_back(field);
3038 if(return_table->
GetColumns().size() == 2) {
3039r_match_col = return_table->
GetColumns()[0];
3040r_data_col = return_table->
GetColumns()[1];
3042r_match_col = return_table->
GetColumns()[1];
3043r_data_col = return_table->
GetColumns()[2];
3046 boolfound =
false;
3048 for(
unsigned intresult_row = 0; result_row < r_data_col->
GetData().GetString().
size(); result_row++) {
3049 stringthis_id =
"";
3059BOOST_CHECK_EQUAL (was_applied, is_now);
3063BOOST_CHECK_EQUAL (
"All data found",
"Can't find row for "+ search);
3071 const string&
match,
constvector<string>& field_list,
3072 constvector<string>& match_vals,
3073 constvector<vector<string> > & field_vals)
3078id_col->
SetData().SetString().insert(id_col->
SetData().SetString().begin(),
3079match_vals.begin(), match_vals.end());
3080 table->SetColumns().push_back(id_col);
3082 for(
size_tcol = 0; col < field_list.size(); col++) {
3083 stringfield = field_list[col];
3085data_col->
SetHeader().SetTitle(field);
3086data_col->
SetData().SetString().insert(data_col->
SetData().SetString().end(),
3087field_vals[col].begin(), field_vals[col].end());
3088 table->SetColumns().push_back(data_col);
3101vector<string> retrieve_fields;
3104retrieve_fields.push_back(
match);
3107retrieve_fields.insert(retrieve_fields.end(), field_list.begin(), field_list.end());
3112 boolfound =
false;
3114 for(
unsigned intresult_row = 0; result_row < r_match_col->
GetData().GetSize(); result_row++) {
3115 stringthis_id =
"";
3123 for(
unsigned intcol = 1; col <
table->GetColumns().
size(); col++) {
3124 stringwas_applied =
table->GetColumns()[col]->GetData().GetString()[
row];
3125 stringis_now = return_table->
GetColumns()[col + col_start]->GetData().GetString()[result_row];
3126BOOST_CHECK_EQUAL (was_applied, is_now);
3131BOOST_CHECK_EQUAL (
"All data found",
"Can't find row for "+ search);
@ eExtreme_Biological
5' and 3'
User-defined methods of the data storage class.
void RemoveTitlesSeqEntry(CSeq_entry_Handle seh, const CSeq_entry &entry, CCmdComposite *composite)
bool UpdateAllDefinitionLine(CSeq_entry_Handle entry, CCmdComposite *composite, const string &title, edit::EExistingText existing_text)
int CountDefLineConflicts(CSeq_entry_Handle entry, const string &title)
vector< CAutoDefAvailableModifier > TAvailableModifierVector
virtual void Unexecute()
Undo (opposite to Execute())
virtual void Execute()
Do the editing action.
static bool LooksLikeHeader(const vector< string > &field_names)
static string AutoMatch(string field_name)
bool IsPartialStop(ESeqLocExtremes ext) const
bool IsPartialStart(ESeqLocExtremes ext) const
CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse, const string &title)
@ eCommandInfluenza_fixup
@ eCommandTrimOrganismNames
@ eCommandSplitQualsAtCommas
@ eCommandSplitStructuredCollections
@ eCommandInfluenza_parse
CRef< CCmdComposite > CreateControlRegion(objects::CSeq_entry_Handle entry)
CRef< CCmdComposite > AddNamedrRna(objects::CSeq_entry_Handle entry, string rna_name, bool ispartial5, bool ispartial3)
CRef< CCmdComposite > CreateMicrosatellite(objects::CSeq_entry_Handle entry)
const char * kSequenceIdColLabel
#define MSerial_AsnText
I/O stream manipulators â.
@ eContent
Untagged human-readable accession or the like.
static CRef< CObjectManager > GetInstance(void)
Return the existing object manager or create one.
CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)
Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...
CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const
Complete and get const reference to the seq-entry.
void Reset(void)
Reset reference object.
NCBI_NS_STD::string::size_type SIZE_TYPE
static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)
Test for equality of a substring with another string.
@ eNocase
Case insensitive compare.
TData & SetData(void)
Assign a value to Data data member.
@ eSubtype_specimen_voucher
@ eSubtype_culture_collection
TType GetType(void) const
Get the Type member data.
const TName & GetName(void) const
Get the variant data.
const TExt & GetExt(void) const
Get the Ext member data.
const TColumns & GetColumns(void) const
Get the Columns member data.
void SetHeader(THeader &value)
Assign a value to Header data member.
bool IsId(void) const
Check if variant Id is selected.
void SetData(TData &value)
Assign a value to Data data member.
const TString & GetString(void) const
Get the variant data.
const TData & GetData(void) const
Get the Data member data.
const TId & GetId(void) const
Get the variant data.
const TKey & GetKey(void) const
Get the Key member data.
bool IsSetData(void) const
the specific data Check if a value has been assigned to Data data member.
void SetLocation(TLocation &value)
Assign a value to Location data member.
bool IsImp(void) const
Check if variant Imp is selected.
const TQual & GetQual(void) const
Get the Qual member data.
bool IsSetPartial(void) const
incomplete in some way? Check if a value has been assigned to Partial data member.
const TLocation & GetLocation(void) const
Get the Location member data.
const TData & GetData(void) const
Get the Data member data.
const TComment & GetComment(void) const
Get the Comment member data.
TPartial GetPartial(void) const
Get the Partial member data.
const TRna & GetRna(void) const
Get the variant data.
bool IsRna(void) const
Check if variant Rna is selected.
const TImp & GetImp(void) const
Get the variant data.
bool IsSetLocation(void) const
feature made from Check if a value has been assigned to Location data member.
const TId & GetId(void) const
Get the Id member data.
TFrom GetFrom(void) const
Get the From member data.
E_Choice Which(void) const
Which variant is currently selected.
bool IsSetStrand(void) const
Check if a value has been assigned to Strand data member.
TStrand GetStrand(void) const
Get the Strand member data.
TTo GetTo(void) const
Get the To member data.
bool IsInt(void) const
Check if variant Int is selected.
const TInt & GetInt(void) const
Get the variant data.
bool IsSeq(void) const
Check if variant Seq is selected.
<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table
CRef< objects::CSeq_table > GetMiscTableFromSeqEntry(const vector< string > &fields, objects::CSeq_entry_Handle entry)
CRef< objects::CUser_field > MakeTableMetaInfoField(objects::edit::EExistingText rule, bool erase_blanks)
const struct ncbi::grid::netcache::search::fields::SIZE size
Defines the CNcbiApplication and CAppException classes for creating NCBI applications.
static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)
bool AddModVectorToDefline(objects::CSeq_entry_Handle entry, CCmdComposite *composite, const objects::CAutoDefSourceDescription::TAvailableModifierVector &mod_vector, bool show_label, bool show_org)
bool AddOrgToDefline(objects::CSeq_entry_Handle seh, CCmdComposite *composite)
bool AddModToDefline(objects::CSeq_entry_Handle entry, CCmdComposite *composite, const objects::CAutoDefAvailableModifier &mod, bool show_label)
#define FOR_EACH_DBXREF_ON_ORGREF(Itr, Var)
FOR_EACH_DBXREF_ON_ORGREF EDIT_EACH_DBXREF_ON_ORGREF.
#define FOR_EACH_ORGMOD_ON_BIOSOURCE(Itr, Var)
FOR_EACH_ORGMOD_ON_BIOSOURCE EDIT_EACH_ORGMOD_ON_BIOSOURCE.
#define VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY(Itr, Var)
VISIT_ALL_SEQDESCS_WITHIN_SEQENTRY.
#define VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY(Itr, Var)
VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY.
CRef< CCmdComposite > TestCStrainSerotypeInfluenza_Parse(CStrainSerotypeInfluenza &parser, CSeq_entry_Handle tse, const string &title, bool overwrite)
#define row(bind, expected)
@ eExistingText_replace_old
Utility stuff for more convenient using of Boost.Test library.
void x_TestPair(CSeq_entry_Handle seh, const string &match, const string &field, const vector< string > &match_vals, const vector< string > &field_vals)
const char * sc_TestEntry_mtplstrains_empty
const char * sc_TestEntry_fixorganismnames
const char * sc_TestEntry_apply_table
const char * sc_TestEntry_removedeflines
const char * sc_TestEntry_parsingwithconflicts
const char * sc_TestEntry_trimorgnames
BOOST_AUTO_TEST_CASE(Test_MultipleStrains)
const char * sc_TestEntry_splitstructcollections
CRef< CUser_object > x_MakeDefaultTextOptions(size_t num_cols)
const char * sc_TestEntry_prefixtodeflines
const char * sc_TestEntry_multiplestrains
const char * sc_TestEntry_noparsing
const char * sc_TestEntry_addfeat
void x_TestList(CSeq_entry_Handle seh, const string &match, const vector< string > &field_list, const vector< string > &match_vals, const vector< vector< string > > &field_vals)
void ReadEntry(const string &name, CSeq_entry_Handle &seh)
const char * sc_TestEntry_adddefline
const char * sc_TestEntry_addstrainserotype
const char * sc_TestEntry_parsingnoconflicts
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