- + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
- + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
- + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
- + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
- + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
- + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
- + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
- + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
- + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
- + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
- + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
- + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
- + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
- + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
- + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
- + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
- + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
- + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
- + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
- + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
- + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
- + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
- + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
- + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
- + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
- + "", 1,
-1863);
+ + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+ + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+ + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+ + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+ + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+ + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+ + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+ + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+ + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+ + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+ + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+ + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+ + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+ + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+ + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+ + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+ + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+ + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+ + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+ + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+ + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+ + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+ + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+ + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+ + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+ + "",
+ 1, 1863);
- upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
-
- upSeq_insulin=new Sequence("INS_HUMAN",
+ upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
+
+ upSeq_insulin = new Sequence("INS_HUMAN",
- StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
- // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
- AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
+ StructureChooserQuerySource scquery = StructureChooserQuerySource
+ .getQuerySourceFor(new SequenceI[]
+ { upSeq });
+ // gets the lightweight proxy rather than the
+ // ThreeDBStructureChooserQuerySource
+ AssertJUnit.assertTrue(
+ scquery instanceof ThreeDBStructureChooserQuerySource);
- * set of sequences:
- * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
- * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
- * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
- * - query uniprot against 3DBeacons
- * --> decorate experimental structures with additional data from PDBe
- * - query remaining against PDBe
- * Ranking
- * - 3D Beacons
- * --> in memory ranking - no need to query twice
- * Rank by
- * - experimental > AlphaFold -> Model
- * - start > end
- * -> filters for
- * -> experimental only
- * -> experimental plus best models for other regions
- * -> "best cover"
- * -> need to be able to select correct reference (the longest one that covers all) for superposition
+ * set of sequences: - no protein -> TDB not applicable, query PDBe only
+ * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
+ * -> first consider trying to get uniprot refs (need a mark to say none are
+ * available) - protein and uniprot - no canonicals -> resolve to uniprot
+ * automatically to get canonicals - query uniprot against 3DBeacons -->
+ * decorate experimental structures with additional data from PDBe - query
+ * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
+ * need to query twice Rank by - experimental > AlphaFold -> Model - start >
+ * end -> filters for -> experimental only -> experimental plus best models
+ * for other regions -> "best cover" -> need to be able to select correct
+ * reference (the longest one that covers all) for superposition
-//
-// DBRefEntry uniprotDBRef = new DBRefEntry();
-// uniprotDBRef.setAccessionId("P12345");
-// uniprotDBRef.setSource(DBRefSource.UNIPROT);
-// upSeq.addDBRef(uniprotDBRef);
-//
-// DBRefEntry pdbDBRef = new DBRefEntry();
-// pdbDBRef.setAccessionId("1XYZ");
-// pdbDBRef.setSource(DBRefSource.PDB);
-// upSeq.addDBRef(pdbDBRef);
-//
-// for (int x = 1; x < 5; x++)
-// {
-// DBRefEntry dbRef = new DBRefEntry();
-// dbRef.setAccessionId("XYZ_" + x);
-// seq.addDBRef(dbRef);
-// }
-// System.out.println("");
-// System.out.println(seq.getDBRefs());
-// System.out.println(query);
-// query = scquery.buildQuery(seq);
-// assertEquals(
-// "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
-// query);
+ //
+ // DBRefEntry uniprotDBRef = new DBRefEntry();
+ // uniprotDBRef.setAccessionId("P12345");
+ // uniprotDBRef.setSource(DBRefSource.UNIPROT);
+ // upSeq.addDBRef(uniprotDBRef);
+ //
+ // DBRefEntry pdbDBRef = new DBRefEntry();
+ // pdbDBRef.setAccessionId("1XYZ");
+ // pdbDBRef.setSource(DBRefSource.PDB);
+ // upSeq.addDBRef(pdbDBRef);
+ //
+ // for (int x = 1; x < 5; x++)
+ // {
+ // DBRefEntry dbRef = new DBRefEntry();
+ // dbRef.setAccessionId("XYZ_" + x);
+ // seq.addDBRef(dbRef);
+ // }
+ // System.out.println("");
+ // System.out.println(seq.getDBRefs());
+ // System.out.println(query);
+ // query = scquery.buildQuery(seq);
+ // assertEquals(
+ // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
+ // query);
public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
{
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClientTest.setMock();
ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
{
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClientTest.setMock();
ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
- assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
- assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
-
- try {
- upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest, false);
- tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
+ assertEquals(opt_singlebest.getValue(),
+ ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
+ assertEquals(opt_manybest.getValue(),
+ ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
+
+ try
+ {
+ upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
+ tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
+ opt_singlebest, false);
+ tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
+ opts, upResponse.getSearchSummary());
- FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(testUpSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
- assertEquals(firstRanked.getNumberOfItemsFound(),1);
+ FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
+ testUpSeq, upResponse.getSearchSummary(),
+ tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
+ opt_singlebest.getValue(), false);
+ assertEquals(firstRanked.getNumberOfItemsFound(), 1);
- upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_manybest, false);
- assertTrue(firstRanked.getSearchSummary().size()<upResponse.getSearchSummary().size());
- // NB Could have race condition here
+ upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
+ tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
+ opt_manybest, false);
+ assertTrue(firstRanked.getSearchSummary().size() < upResponse
+ .getSearchSummary().size());
+ // NB Could have race condition here
- assertTrue(pdb_Query.trim().length()>0);
- pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
- assertTrue(pdbResponse.getNumberOfItemsFound()>0);
- FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
- assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
-
-
+ assertTrue(pdb_Query.trim().length() > 0);
+ pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
+ upResponse);
+ assertTrue(pdbResponse.getNumberOfItemsFound() > 0);
+ FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
+ pdbResponse);
+ assertEquals(upResponse.getNumberOfItemsFound(),
+ joinedResp.getNumberOfItemsFound());
+