*/
package jalview.gui.structurechooser;
-
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq,upSeq,upSeq_insulin;
+ Sequence seq, upSeq, upSeq_insulin;
// same set up as for structurechooser test
-
-@BeforeMethod(alwaysRun = true)
+
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
-
+
// Uniprot sequence for 3D-Beacons mocks
- upSeq = new Sequence("P38398",
+ upSeq = new Sequence("P38398",
"MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
- + "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.createDatasetSequence();
upSeq.setDescription("Breast cancer type 1 susceptibility protein");
- 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",
"MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
- + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
+ + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
upSeq_insulin.createDatasetSequence();
upSeq_insulin.setDescription("Insulin");
- upSeq_insulin.addDBRef(new DBRefEntry("UNIPROT","0","P01308",null,true));
+ upSeq_insulin
+ .addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
}
-@AfterMethod(alwaysRun = true)
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
- upSeq=null;
+ upSeq = null;
}
@SuppressWarnings("deprecation")
public void buildPDBQueryTest()
{
System.out.println("seq >>>> " + seq);
-
- StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
- AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
+
+ StructureChooserQuerySource scquery = StructureChooserQuerySource
+ .getQuerySourceFor(new SequenceI[]
+ { seq });
+ AssertJUnit
+ .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
String query = scquery.buildQuery(seq);
AssertJUnit.assertEquals("pdb_id:1tim", query);
seq.getAllPDBEntries().clear();
System.out.println("seq >>>> " + upSeq);
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClientTest.setMock();
- 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);
String query = scquery.buildQuery(upSeq);
AssertJUnit.assertEquals("P38398", query);
-
+
// query shouldn't change regardless of additional entries
// because 3DBeacons requires canonical entries.
upSeq.getAllPDBEntries().clear();
* ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
* ----> need a test to check that accessions can be promoted to canonical!
*/
- //FIXME - need to be able to use ID to query here ?
+ // FIXME - need to be able to use ID to query here ?
AssertJUnit.assertEquals(null, query);
-
-
- // TODO:
+ // TODO:
/**
- * 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);
}
- @Test(groups= {"Functional"},dataProvider = "testUpSeqs")
+
+ @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
{
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClientTest.setMock();
ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
- PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
-
+ PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
-
FTSRestResponse upResponse = null;
FTSRestResponse pdbResponse = null;
// TODO test available options
// Best Alphafold Model
// Best model (by confidence score)
// Will also need to develop a more sophisticated filtering system
- List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
+ List<FilterOption> opts = tdbquery
+ .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
FilterOption opt_singlebest = opts.get(0);
FilterOption opt_manybest = opts.get(1);
- 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());
// test ranking without additional PDBe data
- 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);
// many best response
- 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
String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
- 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());
+
} catch (Exception x)
{
x.printStackTrace();
Assert.fail("Unexpected Exception");
}
- StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { testUpSeq});
+ StructureChooserQuerySource scquery = StructureChooserQuerySource
+ .getQuerySourceFor(new SequenceI[]
+ { testUpSeq });
}
-
+
@DataProvider(name = "testUpSeqs")
public Object[][] testUpSeqs() throws Exception
{
setUp();
- return new Object[][] { {upSeq},{upSeq_insulin}};
+ return new Object[][] { { upSeq }, { upSeq_insulin } };
}
-
+
@Test(groups = { "Functional" })
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals(name,
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals("abcde12fg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals("abcde",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals("abcde12345afg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}
git://source.jalview.org / jalview.git / blobdiff