JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq,upSeq,upSeq_nocanonical;
+ Sequence seq, upSeq, upSeq_nocanonical;
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
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.setDescription("Breast cancer type 1 susceptibility protein");
upSeq_nocanonical = new Sequence(upSeq);
upSeq.createDatasetSequence();
- upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
-
+ upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
+
upSeq_nocanonical.createDatasetSequence();
// not a canonical reference
- upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
+ upSeq_nocanonical.addDBRef(
+ new DBRefEntry("UNIPROT", "0", "P38398", null, false));
}
public void tearDown() throws Exception
{
seq = null;
- upSeq=null;
- upSeq_nocanonical=null;
+ upSeq = null;
+ upSeq_nocanonical = null;
}
@Test(groups = { "Functional" })
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
ThreadwaitFor(200, sc);
-
+
// if structures are not discovered then don't
// populate filter options
sc.populateFilterComboBox(false, false);
int optionsSize = sc.getCmbFilterOption().getItemCount();
System.out.println("Items (no data, no cache): ");
StringBuilder items = new StringBuilder();
- for (int p=0;p<optionsSize;p++)
+ for (int p = 0; p < optionsSize; p++)
{
- items.append
- ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
+ items.append("- ")
+ .append(sc.getCmbFilterOption().getItemAt(p).getName())
+ .append("\n");
}
// report items when this fails - seems to be a race condition
- Assert.assertEquals(items.toString(),optionsSize,2);
+ Assert.assertEquals(items.toString(), optionsSize, 2);
sc.populateFilterComboBox(true, false);
optionsSize = sc.getCmbFilterOption().getItemCount();
FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
.getSelectedItem();
assertEquals("Cached Structures", filterOpt.getName());
- FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+ FTSRestClient
+ .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
}
PDBFTSRestClientTest.setMock();
SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
- StructureChooser sc = new StructureChooser(selectedSeqs, upSeq_nocanonical, null);
+ StructureChooser sc = new StructureChooser(selectedSeqs,
+ upSeq_nocanonical, null);
// mock so should be quick. Exceptions from mocked PDBFTS are expected too
ThreadwaitFor(500, sc);
-
+
assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
}
@Test(groups = { "Network" })
public void fetchStructuresInfoTest()
{
- FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+ FTSRestClient
+ .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
- // not mocked, wait for 2s
+ // not mocked, wait for 2s
ThreadwaitFor(2000, sc);
-
+
sc.fetchStructuresMetaData();
Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
"discoveredStructuresSet");
SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
ThreadwaitFor(500, sc);
-
+
sc.fetchStructuresMetaData();
Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
"discoveredStructuresSet");
private void ThreadwaitFor(int i, StructureChooser sc)
{
- long timeout = i+System.currentTimeMillis();
+ long timeout = i + System.currentTimeMillis();
while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
{
- try {
+ try
+ {
Thread.sleep(50);
} catch (InterruptedException x)
{
-
+
}
}
-
- }
+ }
@Test(groups = { "Functional" })
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals(name,
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12fg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12345afg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}