import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.File;
import java.util.Collection;
+import java.util.List;
import java.util.Vector;
import org.junit.Assert;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.fts.service.pdb.PDBFTSRestClientTest;
import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.IdentifyFile;
import jalview.jbgui.FilterOption;
+import jalview.structure.StructureImportSettings.TFType;
import junit.extensions.PA;
@Test(singleThreaded = true)
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq,upSeq;
+ 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);
- upSeq.createDatasetSequence();
+ + "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.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
+ upSeq_nocanonical = new Sequence(upSeq);
+ upSeq.createDatasetSequence();
+ 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));
+
}
@AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
- upSeq=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());
}
+ @Test(groups = { "Functional" })
+ public void displayTDBQueryTest() throws InterruptedException
+ {
+ TDBeaconsFTSRestClientTest.setMock();
+ PDBFTSRestClientTest.setMock();
+
+ SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
+ 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));
}
+
+ @Test(groups = { "Functional" }, dataProvider = "openStructureFileParams")
+ public void openStructureFileForSequenceTest(String alfile, String seqid,
+ String sFilename, TFType tft, String paeFilename,
+ boolean showRefAnnotations, boolean doXferSettings,
+ ViewerType viewerType, int seqNum, int annNum, int viewerNum,
+ String propsFile)
+ {
+ Cache.loadProperties(
+ propsFile == null ? "test/jalview/io/testProps.jvprops"
+ : propsFile);
+
+ Jalview.main(
+ propsFile == null ? null : new String[]
+ { "--props", propsFile });
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.OK_OPTION);
+
+ FileLoader fileLoader = new FileLoader(true);
+ FileFormatI format = null;
+ File alFile = new File(alfile);
+ try
+ {
+ format = new IdentifyFile().identify(alFile, DataSourceType.FILE);
+ } catch (FileFormatException e1)
+ {
+ Assert.fail(
+ "Unknown file format for '" + alFile.getAbsolutePath() + "'");
+ }
+
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(alFile,
+ DataSourceType.FILE, format);
+ AlignmentPanel ap = af.alignPanel;
+ Assert.assertNotNull("No alignPanel", ap);
+
+ AlignmentI al = ap.getAlignment();
+ Assert.assertNotNull(al);
+
+ SequenceI seq = al.findName(seqid);
+ Assert.assertNotNull("Sequence '" + seqid + "' not found in alignment",
+ seq);
+
+ StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+ false, sFilename, tft, paeFilename, false, showRefAnnotations,
+ doXferSettings, viewerType);
+
+ List<SequenceI> seqs = al.getSequences();
+ Assert.assertNotNull(seqs);
+
+ Assert.assertEquals("Wrong number of sequences", seqNum, seqs.size());
+
+ AlignViewportI av = ap.getAlignViewport();
+ Assert.assertNotNull(av);
+
+ AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
+ int visibleAnn = 0;
+ for (AlignmentAnnotation aa : aas)
+ {
+ if (aa.visible)
+ visibleAnn++;
+ }
+ Assert.assertEquals("Wrong number of viewed annotations", annNum,
+ visibleAnn);
+
+ if (viewerNum > -1)
+ {
+ try
+ {
+ Thread.sleep(100);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ List<StructureViewerBase> openViewers = Desktop.instance
+ .getStructureViewers(ap, null);
+ Assert.assertNotNull(openViewers);
+ Assert.assertEquals("Wrong number of structure viewers opened",
+ viewerNum, openViewers.size());
+ }
+
+ if (af != null)
+ {
+ af.setVisible(false);
+ af.dispose();
+ }
+ }
+
+ @DataProvider(name = "openStructureFileParams")
+ public Object[][] openStructureFileParams()
+ {
+ /*
+ String alFile,
+ String seqid,
+ String structureFilename,
+ TFType tft,
+ String paeFilename,
+ boolean showRefAnnotations,
+ boolean doXferSettings, // false for Commands
+ ViewerType viewerType,
+ int seqNum,
+ int annNum,
+ int viewerNum,
+ String propsFile
+ */
+ return new Object[][] {
+ /*
+ */
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, null, 15, 7, 0, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, null, 15, 7, 0, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ false, false, null, 15, 4, 0, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, ViewerType.JMOL, 15, 7, 1, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, ViewerType.JMOL, 15, 7, 1, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ false, false, ViewerType.JMOL, 15, 4, 1, null }, };
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff