Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureChooserQuerySourceTest	56	126	12	0.9857142698.6%	Show methods

Class StructureChooserQuerySourceTest

Class StructureChooserQuerySourceTest	Line # 56	Total Statements 126	Complexity 12	TOTAL Coverage 0.9857142698.6%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5959	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	7474	31.031	2.02	1.0 1.0100%
tearDown() : void   tearDown() : void	271271	5.05	1.01	1.0 1.0100%
buildPDBQueryTest() : void   buildPDBQueryTest() : void	281281	29.029	2.02	1.0 1.0100%
buildThreeDBQueryTest() : void   buildThreeDBQueryTest() : void	329329	13.013	1.01	1.0 1.0100%
cascadingThreeDBandPDBQuerys(SequenceI) : void   cascadingThreeDBandPDBQuerys(SequenceI) : void	405405	36.036	3.03	0.94736844 0.9473684494.7%
testUpSeqs() : Object[][]   testUpSeqs() : Object[][]	510510	2.02	1.01	1.0 1.0100%
sanitizeSeqNameTest() : void   sanitizeSeqNameTest() : void	519519	8.08	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2642857	jalview.gui.structurechooser.StructureChooserQuerySourceTest.testUpSeqsjalview.gui.structurechooser.StructureChooserQuerySourceTest.testUpSeqs	1PASS
	0.25714287	jalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerysjalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerys	1PASS
	0.22857143	jalview.gui.structurechooser.StructureChooserQuerySourceTest.buildPDBQueryTestjalview.gui.structurechooser.StructureChooserQuerySourceTest.buildPDBQueryTest	1PASS
	0.22857143	jalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerysjalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerys	1PASS
	0.22857143	jalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerysjalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerys	1PASS
	0.22857143	jalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerysjalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerys	1PASS
	0.22857143	jalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerysjalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerys	1PASS
	0.1	jalview.gui.structurechooser.StructureChooserQuerySourceTest.buildThreeDBQueryTestjalview.gui.structurechooser.StructureChooserQuerySourceTest.buildThreeDBQueryTest	1PASS
	0.06428572	jalview.gui.structurechooser.StructureChooserQuerySourceTest.sanitizeSeqNameTestjalview.gui.structurechooser.StructureChooserQuerySourceTest.sanitizeSeqNameTest	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
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.
11		*
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.
16		*
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.
20		*/
21		package jalview.gui.structurechooser;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertTrue;
25		import static org.testng.Assert.fail;
26
27		import java.util.ArrayList;
28		import java.util.List;
29		import java.util.Vector;
30
31		import org.junit.Assert;
32		import org.testng.AssertJUnit;
33		import org.testng.annotations.AfterMethod;
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.BeforeMethod;
36		import org.testng.annotations.DataProvider;
37		import org.testng.annotations.Test;
38
39		import jalview.datamodel.DBRefEntry;
40		import jalview.datamodel.DBRefSource;
41		import jalview.datamodel.PDBEntry;
42		import jalview.datamodel.Sequence;
43		import jalview.datamodel.SequenceI;
44		import jalview.fts.api.FTSData;
45		import jalview.fts.api.FTSDataColumnI;
46		import jalview.fts.core.FTSRestRequest;
47		import jalview.fts.core.FTSRestResponse;
48		import jalview.fts.service.pdb.PDBFTSRestClientTest;
49		import jalview.fts.service.threedbeacons.TDB_FTSData;
50		import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
51		import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
52		import jalview.gui.JvOptionPane;
53		import jalview.gui.StructureChooser;
54		import jalview.jbgui.FilterOption;
55
		98.6% Uncovered Elements: 2 (140) Complexity: 12 Complexity Density: 0.1
56		public class StructureChooserQuerySourceTest
57		{
58
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
59	1	@BeforeClass(alwaysRun = true)...
60		public void setUpJvOptionPane()
61		{
62	1	JvOptionPane.setInteractiveMode(false);
63	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64		}
65
66		Sequence seq, upSeq, upSeq_insulin, upSeq_r1ab;
67
68		private Sequence upSeq_fer1_maize;
69
70		private Sequence upSeq_epas1_human;
71
72		// same set up as for structurechooser test
73
		100% Uncovered Elements: 0 (33) Complexity: 2 Complexity Density: 0.06
74	9	@BeforeMethod(alwaysRun = true)...
75		public void setUp() throws Exception
76		{
77	9	seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
78		26);
79	9	seq.createDatasetSequence();
80	45	for (int x = 1; x < 5; x++)
81		{
82	36	DBRefEntry dbRef = new DBRefEntry();
83	36	dbRef.setAccessionId("XYZ_" + x);
84	36	seq.addDBRef(dbRef);
85		}
86
87	9	PDBEntry dbRef = new PDBEntry();
88	9	dbRef.setId("1tim");
89
90	9	Vector<PDBEntry> pdbIds = new Vector<>();
91	9	pdbIds.add(dbRef);
92
93	9	seq.setPDBId(pdbIds);
94
95		// Uniprot sequence for 3D-Beacons mocks
96	9	upSeq = new Sequence("P38398",
97		"MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
98		+ "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
99		+ "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
100		+ "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
101		+ "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
102		+ "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
103		+ "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
104		+ "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
105		+ "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
106		+ "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
107		+ "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
108		+ "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
109		+ "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
110		+ "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
111		+ "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
112		+ "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
113		+ "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
114		+ "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
115		+ "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
116		+ "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
117		+ "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
118		+ "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
119		+ "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
120		+ "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
121		+ "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
122		+ "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
123		+ "",
124		1, 1863);
125	9	upSeq.createDatasetSequence();
126	9	upSeq.setDescription("Breast cancer type 1 susceptibility protein");
127	9	upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
128
129	9	upSeq_insulin = new Sequence("INS_HUMAN",
130		"MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
131		+ "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
132	9	upSeq_insulin.createDatasetSequence();
133	9	upSeq_insulin.setDescription("Insulin");
134	9	upSeq_insulin
135		.addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
136
137	9	upSeq_r1ab = new Sequence("R1AB_SARS2",
138		"MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIK\n"
139		+ "RSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFD\n"
140		+ "LGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLS\n"
141		+ "EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRV\n"
142		+ "EKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL\n"
143		+ "PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIG\n"
144		+ "CNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVE\n"
145		+ "SCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQY\n"
146		+ "SLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEI\n"
147		+ "VKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC\n"
148		+ "VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLE\n"
149		+ "IKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVEL\n"
150		+ "GTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDC\n"
151		+ "EEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEV\n"
152		+ "QPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATN\n"
153		+ "NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAG\n"
154		+ "IFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQ\n"
155		+ "RKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVL\n"
156		+ "TAVVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEIL\n"
157		+ "GTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLND\n"
158		+ "LNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYK\n"
159		+ "DWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVV\n"
160		+ "DMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKW\n"
161		+ "KYPQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDV\n"
162		+ "RETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ\n"
163		+ "ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENS\n"
164		+ "YTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQL\n"
165		+ "TGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST\n"
166		+ "KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITE\n"
167		+ "EVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRC\n"
168		+ "LNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIW\n"
169		+ "FLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSL\n"
170		+ "ETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAP\n"
171		+ "ISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLH\n"
172		+ "NWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH\n"
173		+ "FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFD\n"
174		+ "AYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIE\n"
175		+ "VTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKN\n"
176		+ "NLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIG\n"
177		+ "YKAIDGGVTRDIASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD\n"
178		+ "FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDT\n"
179		+ "RYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGRWVLNNDYYRSLPGVFCGVDAV\n"
180		+ "NLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTP\n"
181		+ "VYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFN\n"
182		+ "GVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALND\n"
183		+ "FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM\n"
184		+ "LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGS\n"
185		+ "PSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQA\n"
186		+ "AGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMC\n"
187		+ "ASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQW\n"
188		+ "SLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDT\n"
189		+ "SLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNY\n"
190		+ "SGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVS\n"
191		+ "TQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLW\n"
192		+ "AQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATA\n"
193		+ "QEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTM\n"
194		+ "LFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA\n"
195		+ "DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTK\n"
196		+ "GGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAA\n"
197		+ "TVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES\n"
198		+ "FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQ\n"
199		+ "SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVV\n"
200		+ "KRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKE\n"
201		+ "ILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNW\n"
202		+ "YDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFK\n"
203		+ "YWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN\n"
204		+ "LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEG\n"
205		+ "SSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGF\n"
206		+ "PFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLL\n"
207		+ "KSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL\n"
208		+ "SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV\n"
209		+ "RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNV\n"
210		+ "FMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAI\n"
211		+ "DAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGA\n"
212		+ "CVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK\n"
213		+ "PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLS\n"
214		+ "YGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLN\n"
215		+ "VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFA\n"
216		+ "IGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALP\n"
217		+ "ETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM\n"
218		+ "FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK\n"
219		+ "AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRD\n"
220		+ "LYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTY\n"
221		+ "RRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTG\n"
222		+ "YVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM\n"
223		+ "KYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNA\n"
224		+ "HVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIK\n"
225		+ "CVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNL\n"
226		+ "PGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAV\n"
227		+ "CRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN\n"
228		+ "NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIG\n"
229		+ "VCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAV\n"
230		+ "KTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQ\n"
231		+ "LGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSK\n"
232		+ "VVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM\n"
233		+ "NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGD\n"
234		+ "CATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGH\n"
235		+ "FAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTA\n"
236		+ "VMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN");
237	9	upSeq_r1ab.setDescription("sars2 r1ab polyprotein");
238	9	upSeq_r1ab
239		.addDBRef(new DBRefEntry("UNIPROT", "0", "P0DTD1", null, true));
240	9	upSeq_r1ab.createDatasetSequence();
241	9	upSeq_fer1_maize = new Sequence("FER1_MAIZE",
242		"MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGE"
243		+ "VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV"
244		+ "VIETHKEEELTGA");
245	9	upSeq_fer1_maize.setDescription("Feredoxin 1 Maize");
246	9	upSeq_fer1_maize
247		.addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
248	9	upSeq_fer1_maize.createDatasetSequence();
249
250	9	upSeq_epas1_human = new Sequence("EPAS1_HUMAN",
251		"MTADKEKKRSSSERRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSS\n"
252		+ "VCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIR\n"
253		+ "ENLSLKNGSGFGKKSKDMSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVKVYNNCPPHNSLCGYKE\n"
254		+ "PLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSEN\n"
255		+ "MTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTE\n"
256		+ "SLFKPHLMAMNSIFDSSGKGAVSEKSNFLFTKLKEEPEELAQLAPTPGDAIISLDFGNQNFEESSAYGKAIL\n"
257		+ "PPSQPWATELRSHSTQSEAGSLPAFTVPQAAAPGSTTPSATSSSSSCSTPNSPEDYYTSLDNDLKIEVIEKL\n"
258		+ "FAMDTEAKDQCSTQTDFNELDLETLAPYIPMDGEDFQLSPICPEERLLAENPQSTPQHCFSAMTNIFQPLAP\n"
259		+ "VAPHSPFLLDKFQQQLESKKTEPEHRPMSSIFFDAGSKASLPPCCGQASTPLSSMGGRSNTQWPPDPPLHFG\n"
260		+ "PTKWAVGDQRTEFLGAAPLGPPVSPPHVSTFKTRSAKGFGARGPDVLSPAMVALSNKLKLKRQLEYEEQAFQ\n"
261		+ "DLSGGDPPGGSTSHLMWKRMKNLRGGSCPLMPDKPLSANVPNDKFTQNPMRGLGHPLRHLPLPQPPSAISPG\n"
262		+ "ENSKSRFPPQCYATQYQDYSLSSAHKVSGMASRLLGPSFESYLLPELTRYDCEVNVPVLGSSTLLQGGDLLR\n"
263		+ "ALDQAT");
264	9	upSeq_epas1_human
265		.setDescription("Endothelial PAS domain-containing protein 1");
266	9	upSeq_epas1_human
267		.addDBRef(new DBRefEntry("UNIPROT", "0", "Q99814", null, true));
268	9	upSeq_epas1_human.createDatasetSequence();
269		}
270
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
271	8	@AfterMethod(alwaysRun = true)...
272		public void tearDown() throws Exception
273		{
274	8	seq = null;
275	8	upSeq = null;
276	8	upSeq_r1ab = null;
277	8	upSeq_fer1_maize = null;
278	8	upSeq_epas1_human = null;
279		}
280
		100% Uncovered Elements: 0 (31) Complexity: 2 Complexity Density: 0.07 1PASS
281	1	@SuppressWarnings("deprecation")...
282		@Test(groups = { "Functional" })
283		public void buildPDBQueryTest()
284		{
285	1	System.out.println("seq >>>> " + seq);
286
287	1	StructureChooserQuerySource scquery = StructureChooserQuerySource
288		.getQuerySourceFor(new SequenceI[]
289		{ seq });
290	1	AssertJUnit
291		.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
292	1	String query = scquery.buildQuery(seq);
293	1	AssertJUnit.assertEquals("pdb_id:1tim", query);
294	1	seq.getAllPDBEntries().clear();
295	1	query = scquery.buildQuery(seq);
296	1	AssertJUnit.assertEquals(
297		"text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
298		query);
299	1	seq.setDBRefs(null);
300	1	query = scquery.buildQuery(seq);
301	1	System.out.println(query);
302	1	AssertJUnit.assertEquals("text:4kqy", query);
303
304	1	DBRefEntry uniprotDBRef = new DBRefEntry();
305	1	uniprotDBRef.setAccessionId("P12345");
306	1	uniprotDBRef.setSource(DBRefSource.UNIPROT);
307	1	seq.addDBRef(uniprotDBRef);
308
309	1	DBRefEntry pdbDBRef = new DBRefEntry();
310	1	pdbDBRef.setAccessionId("1XYZ");
311	1	pdbDBRef.setSource(DBRefSource.PDB);
312	1	seq.addDBRef(pdbDBRef);
313
314	5	for (int x = 1; x < 5; x++)
315		{
316	4	DBRefEntry dbRef = new DBRefEntry();
317	4	dbRef.setAccessionId("XYZ_" + x);
318	4	seq.addDBRef(dbRef);
319		}
320	1	System.out.println("");
321	1	System.out.println(seq.getDBRefs());
322	1	System.out.println(query);
323	1	query = scquery.buildQuery(seq);
324	1	AssertJUnit.assertEquals(
325		"uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
326		query);
327		}
328
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
329	1	@SuppressWarnings("deprecation")...
330		@Test(groups = { "Functional" })
331		public void buildThreeDBQueryTest()
332		{
333	1	System.out.println("seq >>>> " + upSeq);
334	1	TDBeaconsFTSRestClientTest.setMock();
335	1	PDBFTSRestClientTest.setMock();
336	1	StructureChooserQuerySource scquery = StructureChooserQuerySource
337		.getQuerySourceFor(new SequenceI[]
338		{ upSeq });
339		// gets the lightweight proxy rather than the
340		// ThreeDBStructureChooserQuerySource
341	1	AssertJUnit.assertTrue(
342		scquery instanceof ThreeDBStructureChooserQuerySource);
343	1	String query = scquery.buildQuery(upSeq);
344	1	AssertJUnit.assertEquals("P38398", query);
345
346		// query shouldn't change regardless of additional entries
347		// because 3DBeacons requires canonical entries.
348	1	upSeq.getAllPDBEntries().clear();
349	1	query = scquery.buildQuery(upSeq);
350	1	AssertJUnit.assertEquals("P38398", query);
351	1	upSeq.setDBRefs(null);
352	1	query = scquery.buildQuery(upSeq);
353		/*
354		* legacy projects/datasets will not have canonical flags set for uniprot dbrefs
355		* graceful behaviour would be to
356		* - pick one ? not possible
357		* - iterate through all until a 200 is obtained ?
358		* ---> ideal but could be costly
359		* ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
360		* ----> need a test to check that accessions can be promoted to canonical!
361		*/
362		// FIXME - need to be able to use ID to query here ?
363	1	AssertJUnit.assertEquals(null, query);
364
365		// TODO:
366		/**
367		* set of sequences: - no protein -> TDB not applicable, query PDBe only
368		* (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
369		* -> first consider trying to get uniprot refs (need a mark to say none are
370		* available) - protein and uniprot - no canonicals -> resolve to uniprot
371		* automatically to get canonicals - query uniprot against 3DBeacons -->
372		* decorate experimental structures with additional data from PDBe - query
373		* remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
374		* need to query twice Rank by - experimental > AlphaFold -> Model - start >
375		* end -> filters for -> experimental only -> experimental plus best models
376		* for other regions -> "best cover" -> need to be able to select correct
377		* reference (the longest one that covers all) for superposition
378		*/
379		//
380		// DBRefEntry uniprotDBRef = new DBRefEntry();
381		// uniprotDBRef.setAccessionId("P12345");
382		// uniprotDBRef.setSource(DBRefSource.UNIPROT);
383		// upSeq.addDBRef(uniprotDBRef);
384		//
385		// DBRefEntry pdbDBRef = new DBRefEntry();
386		// pdbDBRef.setAccessionId("1XYZ");
387		// pdbDBRef.setSource(DBRefSource.PDB);
388		// upSeq.addDBRef(pdbDBRef);
389		//
390		// for (int x = 1; x < 5; x++)
391		// {
392		// DBRefEntry dbRef = new DBRefEntry();
393		// dbRef.setAccessionId("XYZ_" + x);
394		// seq.addDBRef(dbRef);
395		// }
396		// System.out.println("");
397		// System.out.println(seq.getDBRefs());
398		// System.out.println(query);
399		// query = scquery.buildQuery(seq);
400		// assertEquals(
401		// "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
402		// query);
403		}
404
		94.7% Uncovered Elements: 2 (38) Complexity: 3 Complexity Density: 0.08 1PASS
405	5	@Test(groups = { "Functional" }, dataProvider = "testUpSeqs")...
406		public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
407		{
408	5	TDBeaconsFTSRestClientTest.setMock();
409	5	PDBFTSRestClientTest.setMock();
410	5	ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
411	5	PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
412
413	5	FTSRestResponse upResponse = null;
414	5	List<FTSRestResponse> pdbResponse = null;
415		// TODO test available options
416		// Best coverage
417		// Best Alphafold Model
418		// Best model (by confidence score)
419		// Will also need to develop a more sophisticated filtering system
420	5	List<FilterOption> opts = tdbquery
421		.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
422	5	FilterOption opt_singlebest = opts.get(0);
423	5	FilterOption opt_manybest = opts.get(1);
424	5	assertEquals(opt_singlebest.getValue(),
425		ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
426	5	assertEquals(opt_manybest.getValue(),
427		ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
428
429	5	try
430		{
431	5	upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
432		tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
433		opt_singlebest, false);
434	5	tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
435		opts, upResponse.getSearchSummary());
436		// test ranking without additional PDBe data
437	5	FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
438		testUpSeq, upResponse.getSearchSummary(),
439		tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
440		opt_singlebest.getValue(), false);
441	5	assertEquals(firstRanked.getNumberOfItemsFound(), 1);
442		// many best response
443	5	upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
444		tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
445		opt_manybest, false);
446	5	assertTrue(firstRanked.getSearchSummary().size() < upResponse
447		.getSearchSummary().size());
448		// NB Could have race condition here
449	5	List<String> pdb_Queries = tdbquery.buildPDBFTSQueryFor(upResponse);
450	5	assertTrue(pdb_Queries.size() > 0);
451	5	for (String pdb_Query : pdb_Queries)
452		{
453	10	assertTrue(pdb_Query.trim().length() > 0);
454		}
455
456	5	pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
457		upResponse);
458		// check all queries resulted in a response
459	5	assertEquals(pdbResponse.size(), pdb_Queries.size());
460	5	for (FTSRestResponse pdbr : pdbResponse)
461		{
462	10	assertTrue(pdbr.getNumberOfItemsFound() > 0);
463		}
464
465		// and finally that join works
466	5	FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
467		pdbResponse);
468	5	assertEquals(upResponse.getNumberOfItemsFound(),
469		joinedResp.getNumberOfItemsFound());
470
471		// Special data test case
472	5	if (testUpSeq.getDisplayId(true)
473		.equals(upSeq_epas1_human.getDisplayId(true)))
474		{
475
476	1	TDBResultAnalyser tDBResultAnalyz = new TDBResultAnalyser(testUpSeq,
477		joinedResp.getSearchSummary(), tdbquery.lastTdbRequest,
478		ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE,
479		tdbquery.remove_prefix(
480		ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE));
481	1	List<FTSData> ordered = tDBResultAnalyz.getFilteredResponse();
482	1	List<FTSData> selected = tDBResultAnalyz.selectStructures(ordered);
483	1	assertEquals(((TDB_FTSData) selected.get(0)).getProvider(),
484		"AlphaFold DB");
485		// to be sufficient, should also
486		// test that adjacent ordered structure in ordered is levyLab
487		// TDB_FTSData first = (TDB_FTSData) ordered.get(0),
488		// second = (TDB_FTSData) ordered.get(1),
489		// third = (TDB_FTSData) ordered.get(2);
490		// Assert.assertEquals("pLDDT", first.getConfidenceScoreType());
491		// Assert.assertTrue(first.getConfidenceScoreType()
492		// .equals(second.getConfidenceScoreType())); // pLDDT first and
493		// // second
494		}
495
496		} catch (
497
498		Exception x)
499		{
500	0	x.printStackTrace();
501	0	Assert.fail("Unexpected Exception");
502		}
503
504	5	StructureChooserQuerySource scquery = StructureChooserQuerySource
505		.getQuerySourceFor(new SequenceI[]
506		{ testUpSeq });
507
508		}
509
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5 1PASS
510	1	@DataProvider(name = "testUpSeqs")...
511		public Object[][] testUpSeqs() throws Exception
512		{
513	1	setUp();
514	1	return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
515		{ upSeq_fer1_maize },
516		{ upSeq_epas1_human } };
517		}
518
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
519	1	@Test(groups = { "Functional" })...
520		public void sanitizeSeqNameTest()
521		{
522	1	String name = "ab_cdEF|fwxyz012349";
523	1	AssertJUnit.assertEquals(name,
524		PDBStructureChooserQuerySource.sanitizeSeqName(name));
525
526		// remove a [nn] substring
527	1	name = "abcde12[345]fg";
528	1	AssertJUnit.assertEquals("abcde12fg",
529		PDBStructureChooserQuerySource.sanitizeSeqName(name));
530
531		// remove characters other than a-zA-Z0-9 | or _
532	1	name = "ab[cd],.\t£$*!- \\\"@:e";
533	1	AssertJUnit.assertEquals("abcde",
534		PDBStructureChooserQuerySource.sanitizeSeqName(name));
535
536	1	name = "abcde12[345a]fg";
537	1	AssertJUnit.assertEquals("abcde12345afg",
538		PDBStructureChooserQuerySource.sanitizeSeqName(name));
539		}
540		}