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 private Sequence upSeq_fer1_maize;
63 // same set up as for structurechooser test
65 @BeforeMethod(alwaysRun = true)
66 public void setUp() throws Exception
68 seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
70 seq.createDatasetSequence();
71 for (int x = 1; x < 5; x++)
73 DBRefEntry dbRef = new DBRefEntry();
74 dbRef.setAccessionId("XYZ_" + x);
78 PDBEntry dbRef = new PDBEntry();
81 Vector<PDBEntry> pdbIds = new Vector<>();
86 // Uniprot sequence for 3D-Beacons mocks
87 upSeq = new Sequence("P38398",
88 "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
89 + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
90 + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
91 + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
92 + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
93 + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
94 + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
95 + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
96 + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
97 + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
98 + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
99 + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
100 + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
101 + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
102 + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
103 + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
104 + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
105 + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
106 + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
107 + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
108 + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
109 + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
110 + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
111 + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
112 + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
113 + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
116 upSeq.createDatasetSequence();
117 upSeq.setDescription("Breast cancer type 1 susceptibility protein");
118 upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
120 upSeq_insulin = new Sequence("INS_HUMAN",
121 "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
122 + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
123 upSeq_insulin.createDatasetSequence();
124 upSeq_insulin.setDescription("Insulin");
126 .addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
128 upSeq_r1ab = new Sequence("R1AB_SARS2",
129 "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIK\n"
130 + "RSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFD\n"
131 + "LGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLS\n"
132 + "EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRV\n"
133 + "EKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL\n"
134 + "PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIG\n"
135 + "CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVE\n"
136 + "SCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY\n"
137 + "SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI\n"
138 + "VKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC\n"
139 + "VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLE\n"
140 + "IKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVEL\n"
141 + "GTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDC\n"
142 + "EEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEV\n"
143 + "QPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATN\n"
144 + "NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAG\n"
145 + "IFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQ\n"
146 + "RKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVL\n"
147 + "TAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEIL\n"
148 + "GTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLND\n"
149 + "LNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYK\n"
150 + "DWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVV\n"
151 + "DMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKW\n"
152 + "KYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDV\n"
153 + "RETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ\n"
154 + "ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENS\n"
155 + "YTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQL\n"
156 + "TGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST\n"
157 + "KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITE\n"
158 + "EVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRC\n"
159 + "LNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIW\n"
160 + "FLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSL\n"
161 + "ETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAP\n"
162 + "ISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLH\n"
163 + "NWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH\n"
164 + "FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFD\n"
165 + "AYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIE\n"
166 + "VTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKN\n"
167 + "NLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIG\n"
168 + "YKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD\n"
169 + "FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDT\n"
170 + "RYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAV\n"
171 + "NLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTP\n"
172 + "VYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFN\n"
173 + "GVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALND\n"
174 + "FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM\n"
175 + "LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGS\n"
176 + "PSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQA\n"
177 + "AGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMC\n"
178 + "ASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQW\n"
179 + "SLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDT\n"
180 + "SLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNY\n"
181 + "SGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVS\n"
182 + "TQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLW\n"
183 + "AQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATA\n"
184 + "QEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTM\n"
185 + "LFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA\n"
186 + "DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTK\n"
187 + "GGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAA\n"
188 + "TVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES\n"
189 + "FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ\n"
190 + "SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVV\n"
191 + "KRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKE\n"
192 + "ILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNW\n"
193 + "YDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFK\n"
194 + "YWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN\n"
195 + "LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEG\n"
196 + "SSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGF\n"
197 + "PFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLL\n"
198 + "KSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL\n"
199 + "SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV\n"
200 + "RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNV\n"
201 + "FMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAI\n"
202 + "DAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGA\n"
203 + "CVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK\n"
204 + "PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLS\n"
205 + "YGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLN\n"
206 + "VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFA\n"
207 + "IGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP\n"
208 + "ETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM\n"
209 + "FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK\n"
210 + "AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRD\n"
211 + "LYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTY\n"
212 + "RRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTG\n"
213 + "YVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM\n"
214 + "KYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNA\n"
215 + "HVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIK\n"
216 + "CVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNL\n"
217 + "PGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAV\n"
218 + "CRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN\n"
219 + "NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIG\n"
220 + "VCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAV\n"
221 + "KTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQ\n"
222 + "LGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSK\n"
223 + "VVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM\n"
224 + "NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGD\n"
225 + "CATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGH\n"
226 + "FAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTA\n"
227 + "VMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN");
228 upSeq_r1ab.setDescription("sars2 r1ab polyprotein");
230 .addDBRef(new DBRefEntry("UNIPROT", "0", "P0DTD1", null, true));
231 upSeq_r1ab.createDatasetSequence();
232 upSeq_fer1_maize = new Sequence("FER1_MAIZE",
233 "MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGE"
234 + "VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV"
236 upSeq_fer1_maize.setDescription("Feredoxin 1 Maize");
238 .addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
239 upSeq_fer1_maize.createDatasetSequence();
243 @AfterMethod(alwaysRun = true)
244 public void tearDown() throws Exception
249 upSeq_fer1_maize = null;
252 @SuppressWarnings("deprecation")
253 @Test(groups = { "Functional" })
254 public void buildPDBQueryTest()
256 System.out.println("seq >>>> " + seq);
258 StructureChooserQuerySource scquery = StructureChooserQuerySource
259 .getQuerySourceFor(new SequenceI[]
262 .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
263 String query = scquery.buildQuery(seq);
264 AssertJUnit.assertEquals("pdb_id:1tim", query);
265 seq.getAllPDBEntries().clear();
266 query = scquery.buildQuery(seq);
267 AssertJUnit.assertEquals(
268 "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
271 query = scquery.buildQuery(seq);
272 System.out.println(query);
273 AssertJUnit.assertEquals("text:4kqy", query);
275 DBRefEntry uniprotDBRef = new DBRefEntry();
276 uniprotDBRef.setAccessionId("P12345");
277 uniprotDBRef.setSource(DBRefSource.UNIPROT);
278 seq.addDBRef(uniprotDBRef);
280 DBRefEntry pdbDBRef = new DBRefEntry();
281 pdbDBRef.setAccessionId("1XYZ");
282 pdbDBRef.setSource(DBRefSource.PDB);
283 seq.addDBRef(pdbDBRef);
285 for (int x = 1; x < 5; x++)
287 DBRefEntry dbRef = new DBRefEntry();
288 dbRef.setAccessionId("XYZ_" + x);
291 System.out.println("");
292 System.out.println(seq.getDBRefs());
293 System.out.println(query);
294 query = scquery.buildQuery(seq);
295 AssertJUnit.assertEquals(
296 "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
300 @SuppressWarnings("deprecation")
301 @Test(groups = { "Functional" })
302 public void buildThreeDBQueryTest()
304 System.out.println("seq >>>> " + upSeq);
305 TDBeaconsFTSRestClientTest.setMock();
306 PDBFTSRestClientTest.setMock();
307 StructureChooserQuerySource scquery = StructureChooserQuerySource
308 .getQuerySourceFor(new SequenceI[]
310 // gets the lightweight proxy rather than the
311 // ThreeDBStructureChooserQuerySource
312 AssertJUnit.assertTrue(
313 scquery instanceof ThreeDBStructureChooserQuerySource);
314 String query = scquery.buildQuery(upSeq);
315 AssertJUnit.assertEquals("P38398", query);
317 // query shouldn't change regardless of additional entries
318 // because 3DBeacons requires canonical entries.
319 upSeq.getAllPDBEntries().clear();
320 query = scquery.buildQuery(upSeq);
321 AssertJUnit.assertEquals("P38398", query);
322 upSeq.setDBRefs(null);
323 query = scquery.buildQuery(upSeq);
325 * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
326 * graceful behaviour would be to
327 * - pick one ? not possible
328 * - iterate through all until a 200 is obtained ?
329 * ---> ideal but could be costly
330 * ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
331 * ----> need a test to check that accessions can be promoted to canonical!
333 // FIXME - need to be able to use ID to query here ?
334 AssertJUnit.assertEquals(null, query);
338 * set of sequences: - no protein -> TDB not applicable, query PDBe only
339 * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
340 * -> first consider trying to get uniprot refs (need a mark to say none are
341 * available) - protein and uniprot - no canonicals -> resolve to uniprot
342 * automatically to get canonicals - query uniprot against 3DBeacons -->
343 * decorate experimental structures with additional data from PDBe - query
344 * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
345 * need to query twice Rank by - experimental > AlphaFold -> Model - start >
346 * end -> filters for -> experimental only -> experimental plus best models
347 * for other regions -> "best cover" -> need to be able to select correct
348 * reference (the longest one that covers all) for superposition
351 // DBRefEntry uniprotDBRef = new DBRefEntry();
352 // uniprotDBRef.setAccessionId("P12345");
353 // uniprotDBRef.setSource(DBRefSource.UNIPROT);
354 // upSeq.addDBRef(uniprotDBRef);
356 // DBRefEntry pdbDBRef = new DBRefEntry();
357 // pdbDBRef.setAccessionId("1XYZ");
358 // pdbDBRef.setSource(DBRefSource.PDB);
359 // upSeq.addDBRef(pdbDBRef);
361 // for (int x = 1; x < 5; x++)
363 // DBRefEntry dbRef = new DBRefEntry();
364 // dbRef.setAccessionId("XYZ_" + x);
365 // seq.addDBRef(dbRef);
367 // System.out.println("");
368 // System.out.println(seq.getDBRefs());
369 // System.out.println(query);
370 // query = scquery.buildQuery(seq);
372 // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
376 @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
377 public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
379 TDBeaconsFTSRestClientTest.setMock();
380 PDBFTSRestClientTest.setMock();
381 ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
382 PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
384 FTSRestResponse upResponse = null;
385 List<FTSRestResponse> pdbResponse = null;
386 // TODO test available options
388 // Best Alphafold Model
389 // Best model (by confidence score)
390 // Will also need to develop a more sophisticated filtering system
391 List<FilterOption> opts = tdbquery
392 .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
393 FilterOption opt_singlebest = opts.get(0);
394 FilterOption opt_manybest = opts.get(1);
395 assertEquals(opt_singlebest.getValue(),
396 ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
397 assertEquals(opt_manybest.getValue(),
398 ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
402 upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
403 tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
404 opt_singlebest, false);
405 tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
406 opts, upResponse.getSearchSummary());
407 // test ranking without additional PDBe data
408 FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
409 testUpSeq, upResponse.getSearchSummary(),
410 tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
411 opt_singlebest.getValue(), false);
412 assertEquals(firstRanked.getNumberOfItemsFound(), 1);
413 // many best response
414 upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
415 tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
416 opt_manybest, false);
417 assertTrue(firstRanked.getSearchSummary().size() < upResponse
418 .getSearchSummary().size());
419 // NB Could have race condition here
420 List<String> pdb_Queries = tdbquery.buildPDBFTSQueryFor(upResponse);
421 assertTrue(pdb_Queries.size() > 0);
422 for (String pdb_Query : pdb_Queries)
424 assertTrue(pdb_Query.trim().length() > 0);
427 pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
429 // check all queries resulted in a response
430 assertEquals(pdbResponse.size(), pdb_Queries.size());
431 for (FTSRestResponse pdbr : pdbResponse)
433 assertTrue(pdbr.getNumberOfItemsFound() > 0);
436 // and finally that join works
437 FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
439 assertEquals(upResponse.getNumberOfItemsFound(),
440 joinedResp.getNumberOfItemsFound());
447 Assert.fail("Unexpected Exception");
450 StructureChooserQuerySource scquery = StructureChooserQuerySource
451 .getQuerySourceFor(new SequenceI[]
456 @DataProvider(name = "testUpSeqs")
457 public Object[][] testUpSeqs() throws Exception
460 return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
461 { upSeq_fer1_maize } };
464 @Test(groups = { "Functional" })
465 public void sanitizeSeqNameTest()
467 String name = "ab_cdEF|fwxyz012349";
468 AssertJUnit.assertEquals(name,
469 PDBStructureChooserQuerySource.sanitizeSeqName(name));
471 // remove a [nn] substring
472 name = "abcde12[345]fg";
473 AssertJUnit.assertEquals("abcde12fg",
474 PDBStructureChooserQuerySource.sanitizeSeqName(name));
476 // remove characters other than a-zA-Z0-9 | or _
477 name = "ab[cd],.\t£$*!- \\\"@:e";
478 AssertJUnit.assertEquals("abcde",
479 PDBStructureChooserQuerySource.sanitizeSeqName(name));
481 name = "abcde12[345a]fg";
482 AssertJUnit.assertEquals("abcde12345afg",
483 PDBStructureChooserQuerySource.sanitizeSeqName(name));