2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.gui.structurechooser;
23 import static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertTrue;
26 import java.util.List;
27 import java.util.Vector;
29 import org.junit.Assert;
30 import org.testng.AssertJUnit;
31 import org.testng.annotations.AfterMethod;
32 import org.testng.annotations.BeforeClass;
33 import org.testng.annotations.BeforeMethod;
34 import org.testng.annotations.DataProvider;
35 import org.testng.annotations.Test;
37 import jalview.datamodel.DBRefEntry;
38 import jalview.datamodel.DBRefSource;
39 import jalview.datamodel.PDBEntry;
40 import jalview.datamodel.Sequence;
41 import jalview.datamodel.SequenceI;
42 import jalview.fts.core.FTSRestResponse;
43 import jalview.fts.service.pdb.PDBFTSRestClientTest;
44 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
45 import jalview.gui.JvOptionPane;
46 import jalview.gui.StructureChooser;
47 import jalview.jbgui.FilterOption;
49 public class StructureChooserQuerySourceTest
52 @BeforeClass(alwaysRun = true)
53 public void setUpJvOptionPane()
55 JvOptionPane.setInteractiveMode(false);
56 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
59 Sequence seq, upSeq, upSeq_insulin, upSeq_r1ab;
61 // same set up as for structurechooser test
63 @BeforeMethod(alwaysRun = true)
64 public void setUp() throws Exception
66 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
68 seq.createDatasetSequence();
69 for (int x = 1; x < 5; x++)
71 DBRefEntry dbRef = new DBRefEntry();
72 dbRef.setAccessionId("XYZ_" + x);
76 PDBEntry dbRef = new PDBEntry();
79 Vector<PDBEntry> pdbIds = new Vector<>();
84 // Uniprot sequence for 3D-Beacons mocks
85 upSeq = new Sequence("P38398",
86 "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
87 + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
88 + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
89 + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
90 + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
91 + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
92 + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
93 + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
94 + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
95 + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
96 + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
97 + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
98 + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
99 + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
100 + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
101 + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
102 + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
103 + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
104 + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
105 + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
106 + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
107 + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
108 + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
109 + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
110 + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
111 + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
114 upSeq.createDatasetSequence();
115 upSeq.setDescription("Breast cancer type 1 susceptibility protein");
116 upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
118 upSeq_insulin = new Sequence("INS_HUMAN",
119 "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
120 + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
121 upSeq_insulin.createDatasetSequence();
122 upSeq_insulin.setDescription("Insulin");
124 .addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
126 upSeq_r1ab = new Sequence("R1AB_SARS2",
127 "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIK\n"
128 + "RSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFD\n"
129 + "LGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLS\n"
130 + "EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRV\n"
131 + "EKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL\n"
132 + "PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIG\n"
133 + "CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVE\n"
134 + "SCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY\n"
135 + "SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI\n"
136 + "VKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC\n"
137 + "VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLE\n"
138 + "IKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVEL\n"
139 + "GTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDC\n"
140 + "EEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEV\n"
141 + "QPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATN\n"
142 + "NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAG\n"
143 + "IFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQ\n"
144 + "RKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVL\n"
145 + "TAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEIL\n"
146 + "GTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLND\n"
147 + "LNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYK\n"
148 + "DWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVV\n"
149 + "DMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKW\n"
150 + "KYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDV\n"
151 + "RETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ\n"
152 + "ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENS\n"
153 + "YTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQL\n"
154 + "TGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST\n"
155 + "KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITE\n"
156 + "EVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRC\n"
157 + "LNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIW\n"
158 + "FLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSL\n"
159 + "ETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAP\n"
160 + "ISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLH\n"
161 + "NWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH\n"
162 + "FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFD\n"
163 + "AYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIE\n"
164 + "VTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKN\n"
165 + "NLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIG\n"
166 + "YKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD\n"
167 + "FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDT\n"
168 + "RYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAV\n"
169 + "NLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTP\n"
170 + "VYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFN\n"
171 + "GVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALND\n"
172 + "FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM\n"
173 + "LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGS\n"
174 + "PSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQA\n"
175 + "AGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMC\n"
176 + "ASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQW\n"
177 + "SLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDT\n"
178 + "SLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNY\n"
179 + "SGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVS\n"
180 + "TQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLW\n"
181 + "AQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATA\n"
182 + "QEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTM\n"
183 + "LFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA\n"
184 + "DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTK\n"
185 + "GGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAA\n"
186 + "TVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES\n"
187 + "FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ\n"
188 + "SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVV\n"
189 + "KRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKE\n"
190 + "ILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNW\n"
191 + "YDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFK\n"
192 + "YWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN\n"
193 + "LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEG\n"
194 + "SSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGF\n"
195 + "PFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLL\n"
196 + "KSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL\n"
197 + "SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV\n"
198 + "RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNV\n"
199 + "FMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAI\n"
200 + "DAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGA\n"
201 + "CVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK\n"
202 + "PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLS\n"
203 + "YGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLN\n"
204 + "VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFA\n"
205 + "IGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP\n"
206 + "ETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM\n"
207 + "FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK\n"
208 + "AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRD\n"
209 + "LYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTY\n"
210 + "RRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTG\n"
211 + "YVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM\n"
212 + "KYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNA\n"
213 + "HVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIK\n"
214 + "CVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNL\n"
215 + "PGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAV\n"
216 + "CRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN\n"
217 + "NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIG\n"
218 + "VCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAV\n"
219 + "KTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQ\n"
220 + "LGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSK\n"
221 + "VVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM\n"
222 + "NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGD\n"
223 + "CATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGH\n"
224 + "FAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTA\n"
225 + "VMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN");
226 upSeq_r1ab.setDescription("sars2 r1ab polyprotein");
228 .addDBRef(new DBRefEntry("UNIPROT", "0", "P0DTD1", null, true));
229 upSeq_r1ab.createDatasetSequence();
233 @AfterMethod(alwaysRun = true)
234 public void tearDown() throws Exception
241 @SuppressWarnings("deprecation")
242 @Test(groups = { "Functional" })
243 public void buildPDBQueryTest()
245 System.out.println("seq >>>> " + seq);
247 StructureChooserQuerySource scquery = StructureChooserQuerySource
248 .getQuerySourceFor(new SequenceI[]
251 .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
252 String query = scquery.buildQuery(seq);
253 AssertJUnit.assertEquals("pdb_id:1tim", query);
254 seq.getAllPDBEntries().clear();
255 query = scquery.buildQuery(seq);
256 AssertJUnit.assertEquals(
257 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
260 query = scquery.buildQuery(seq);
261 System.out.println(query);
262 AssertJUnit.assertEquals("text:4kqy", query);
264 DBRefEntry uniprotDBRef = new DBRefEntry();
265 uniprotDBRef.setAccessionId("P12345");
266 uniprotDBRef.setSource(DBRefSource.UNIPROT);
267 seq.addDBRef(uniprotDBRef);
269 DBRefEntry pdbDBRef = new DBRefEntry();
270 pdbDBRef.setAccessionId("1XYZ");
271 pdbDBRef.setSource(DBRefSource.PDB);
272 seq.addDBRef(pdbDBRef);
274 for (int x = 1; x < 5; x++)
276 DBRefEntry dbRef = new DBRefEntry();
277 dbRef.setAccessionId("XYZ_" + x);
280 System.out.println("");
281 System.out.println(seq.getDBRefs());
282 System.out.println(query);
283 query = scquery.buildQuery(seq);
284 AssertJUnit.assertEquals(
285 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
289 @SuppressWarnings("deprecation")
290 @Test(groups = { "Functional" })
291 public void buildThreeDBQueryTest()
293 System.out.println("seq >>>> " + upSeq);
294 TDBeaconsFTSRestClientTest.setMock();
295 PDBFTSRestClientTest.setMock();
296 StructureChooserQuerySource scquery = StructureChooserQuerySource
297 .getQuerySourceFor(new SequenceI[]
299 // gets the lightweight proxy rather than the
300 // ThreeDBStructureChooserQuerySource
301 AssertJUnit.assertTrue(
302 scquery instanceof ThreeDBStructureChooserQuerySource);
303 String query = scquery.buildQuery(upSeq);
304 AssertJUnit.assertEquals("P38398", query);
306 // query shouldn't change regardless of additional entries
307 // because 3DBeacons requires canonical entries.
308 upSeq.getAllPDBEntries().clear();
309 query = scquery.buildQuery(upSeq);
310 AssertJUnit.assertEquals("P38398", query);
311 upSeq.setDBRefs(null);
312 query = scquery.buildQuery(upSeq);
314 * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
315 * graceful behaviour would be to
316 * - pick one ? not possible
317 * - iterate through all until a 200 is obtained ?
318 * ---> ideal but could be costly
319 * ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
320 * ----> need a test to check that accessions can be promoted to canonical!
322 // FIXME - need to be able to use ID to query here ?
323 AssertJUnit.assertEquals(null, query);
327 * set of sequences: - no protein -> TDB not applicable, query PDBe only
328 * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
329 * -> first consider trying to get uniprot refs (need a mark to say none are
330 * available) - protein and uniprot - no canonicals -> resolve to uniprot
331 * automatically to get canonicals - query uniprot against 3DBeacons -->
332 * decorate experimental structures with additional data from PDBe - query
333 * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
334 * need to query twice Rank by - experimental > AlphaFold -> Model - start >
335 * end -> filters for -> experimental only -> experimental plus best models
336 * for other regions -> "best cover" -> need to be able to select correct
337 * reference (the longest one that covers all) for superposition
340 // DBRefEntry uniprotDBRef = new DBRefEntry();
341 // uniprotDBRef.setAccessionId("P12345");
342 // uniprotDBRef.setSource(DBRefSource.UNIPROT);
343 // upSeq.addDBRef(uniprotDBRef);
345 // DBRefEntry pdbDBRef = new DBRefEntry();
346 // pdbDBRef.setAccessionId("1XYZ");
347 // pdbDBRef.setSource(DBRefSource.PDB);
348 // upSeq.addDBRef(pdbDBRef);
350 // for (int x = 1; x < 5; x++)
352 // DBRefEntry dbRef = new DBRefEntry();
353 // dbRef.setAccessionId("XYZ_" + x);
354 // seq.addDBRef(dbRef);
356 // System.out.println("");
357 // System.out.println(seq.getDBRefs());
358 // System.out.println(query);
359 // query = scquery.buildQuery(seq);
361 // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
365 @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
366 public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
368 TDBeaconsFTSRestClientTest.setMock();
369 PDBFTSRestClientTest.setMock();
370 ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
371 PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
373 FTSRestResponse upResponse = null;
374 List<FTSRestResponse> pdbResponse = null;
375 // TODO test available options
377 // Best Alphafold Model
378 // Best model (by confidence score)
379 // Will also need to develop a more sophisticated filtering system
380 List<FilterOption> opts = tdbquery
381 .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
382 FilterOption opt_singlebest = opts.get(0);
383 FilterOption opt_manybest = opts.get(1);
384 assertEquals(opt_singlebest.getValue(),
385 ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
386 assertEquals(opt_manybest.getValue(),
387 ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
391 upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
392 tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
393 opt_singlebest, false);
394 tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
395 opts, upResponse.getSearchSummary());
396 // test ranking without additional PDBe data
397 FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
398 testUpSeq, upResponse.getSearchSummary(),
399 tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
400 opt_singlebest.getValue(), false);
401 assertEquals(firstRanked.getNumberOfItemsFound(), 1);
402 // many best response
403 upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
404 tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
405 opt_manybest, false);
406 assertTrue(firstRanked.getSearchSummary().size() < upResponse
407 .getSearchSummary().size());
408 // NB Could have race condition here
409 List<String> pdb_Queries = tdbquery.buildPDBFTSQueryFor(upResponse);
410 for (String pdb_Query : pdb_Queries)
412 assertTrue(pdb_Query.trim().length() > 0);
415 pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
417 // check all queries resulted in a response
418 assertEquals(pdbResponse.size(), pdb_Queries.size());
419 for (FTSRestResponse pdbr : pdbResponse)
421 assertTrue(pdbr.getNumberOfItemsFound() > 0);
424 // and finally that join works
425 FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
427 assertEquals(upResponse.getNumberOfItemsFound(),
428 joinedResp.getNumberOfItemsFound());
435 Assert.fail("Unexpected Exception");
438 StructureChooserQuerySource scquery = StructureChooserQuerySource
439 .getQuerySourceFor(new SequenceI[]
444 @DataProvider(name = "testUpSeqs")
445 public Object[][] testUpSeqs() throws Exception
448 return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab } };
451 @Test(groups = { "Functional" })
452 public void sanitizeSeqNameTest()
454 String name = "ab_cdEF|fwxyz012349";
455 AssertJUnit.assertEquals(name,
456 PDBStructureChooserQuerySource.sanitizeSeqName(name));
458 // remove a [nn] substring
459 name = "abcde12[345]fg";
460 AssertJUnit.assertEquals("abcde12fg",
461 PDBStructureChooserQuerySource.sanitizeSeqName(name));
463 // remove characters other than a-zA-Z0-9 | or _
464 name = "ab[cd],.\t£$*!- \\\"@:e";
465 AssertJUnit.assertEquals("abcde",
466 PDBStructureChooserQuerySource.sanitizeSeqName(name));
468 name = "abcde12[345a]fg";
469 AssertJUnit.assertEquals("abcde12345afg",
470 PDBStructureChooserQuerySource.sanitizeSeqName(name));