*/
package jalview.ws.sifts;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.structure.StructureMapping;
+import jalview.xml.binding.sifts.Entry.Entity;
-import java.io.ByteArrayOutputStream;
import java.io.File;
-import java.io.PrintStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
import org.testng.Assert;
import org.testng.FileAssert;
import org.testng.annotations.AfterTest;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBfile;
public class SiftsClientTest
{
- private final ByteArrayOutputStream outContent = new ByteArrayOutputStream();
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+ .getProperty("user.home") + File.separatorChar
+ + ".sifts_downloads" + File.separatorChar;
private String testPDBId = "1a70";
private SiftsClient siftsClient = null;
- SequenceI testSeq = new Sequence(
- "P00221",
+ SequenceI testSeq = new Sequence("P00221",
"MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA"
+ "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD"
- + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147);
+ + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.",
+ 1, 147);
int u = SiftsClient.UNASSIGNED;
- int[][] expectedMapping = { { u, u }, { u, u }, { u, u }, { u, u },
- { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
- { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
- { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
- { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
- { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
- { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { u, u },
- { u, u }, { u, u }, { u, u }, { u, u }, { u, u }, { 1, u }, { 2, u },
- { 3, u }, { 4, u }, { 5, u }, { 6, u }, { 7, u }, { 8, u }, { 9, u },
- { 10, u }, { 11, u }, { 12, u }, { 13, u }, { 14, u }, { 15, u },
- { 16, u }, { 17, u }, { 18, u }, { 19, u }, { 20, u }, { 21, u },
- { 22, u }, { 23, u }, { 24, u }, { 25, u }, { 26, u }, { 27, u },
- { 28, u }, { 29, u }, { 30, u }, { 31, u }, { 32, u }, { 33, u },
- { 34, u }, { 35, u }, { 36, u }, { 37, u }, { 38, u }, { 39, u },
- { 40, u }, { 41, u }, { 42, u }, { 43, u }, { 44, u }, { 45, u },
- { 46, u }, { 47, u }, { 48, u }, { 49, u }, { 50, u }, { 51, u },
- { 52, u }, { 53, u }, { 54, u }, { 55, u }, { 56, u }, { 57, u },
- { 58, u }, { 59, u }, { 60, u }, { 61, u }, { 62, u }, { 63, u },
- { 64, u }, { 65, u }, { 66, u }, { 67, u }, { 68, u }, { 69, u },
- { 70, u }, { 71, u }, { 72, u }, { 73, u }, { 74, u }, { 75, u },
- { 76, u }, { 77, u }, { 78, u }, { 79, u }, { 80, u }, { 81, u },
- { 82, u }, { 83, u }, { 84, u }, { 85, u }, { 86, u }, { 87, u },
- { 88, u }, { 89, u }, { 90, u }, { 91, u }, { 92, u }, { 93, u },
- { 94, u }, { 95, u }, { 96, u }, { 97, u } };
+ HashMap<Integer, int[]> expectedMapping = new HashMap<Integer, int[]>();
+
+ @BeforeTest(alwaysRun = true)
+ public void populateExpectedMapping() throws SiftsException
+ {
+ expectedMapping.put(51, new int[] { 1, 2, 1 });
+ expectedMapping.put(52, new int[] { 2, 7, 2 });
+ expectedMapping.put(53, new int[] { 3, 12, 3 });
+ expectedMapping.put(54, new int[] { 4, 24, 4 });
+ expectedMapping.put(55, new int[] { 5, 33, 5 });
+ expectedMapping.put(56, new int[] { 6, 40, 6 });
+ expectedMapping.put(57, new int[] { 7, 47, 7 });
+ expectedMapping.put(58, new int[] { 8, 55, 8 });
+ expectedMapping.put(59, new int[] { 9, 62, 9 });
+ expectedMapping.put(60, new int[] { 10, 69, 10 });
+ expectedMapping.put(61, new int[] { 11, 76, 11 });
+ expectedMapping.put(62, new int[] { 12, 83, 12 });
+ expectedMapping.put(63, new int[] { 13, 87, 13 });
+ expectedMapping.put(64, new int[] { 14, 95, 14 });
+ expectedMapping.put(65, new int[] { 15, 102, 15 });
+ expectedMapping.put(66, new int[] { 16, 111, 16 });
+ expectedMapping.put(67, new int[] { 17, 122, 17 });
+ expectedMapping.put(68, new int[] { 18, 131, 18 });
+ expectedMapping.put(69, new int[] { 19, 137, 19 });
+ expectedMapping.put(70, new int[] { 20, 144, 20 });
+ expectedMapping.put(71, new int[] { 21, 152, 21 });
+ expectedMapping.put(72, new int[] { 22, 160, 22 });
+ expectedMapping.put(73, new int[] { 23, 167, 23 });
+ expectedMapping.put(74, new int[] { 24, 179, 24 });
+ expectedMapping.put(75, new int[] { 25, 187, 25 });
+ expectedMapping.put(76, new int[] { 26, 195, 26 });
+ expectedMapping.put(77, new int[] { 27, 203, 27 });
+ expectedMapping.put(78, new int[] { 28, 208, 28 });
+ expectedMapping.put(79, new int[] { 29, 213, 29 });
+ expectedMapping.put(80, new int[] { 30, 222, 30 });
+ expectedMapping.put(81, new int[] { 31, 231, 31 });
+ expectedMapping.put(82, new int[] { 32, 240, 32 });
+ expectedMapping.put(83, new int[] { 33, 244, 33 });
+ expectedMapping.put(84, new int[] { 34, 252, 34 });
+ expectedMapping.put(85, new int[] { 35, 260, 35 });
+ expectedMapping.put(86, new int[] { 36, 268, 36 });
+ expectedMapping.put(87, new int[] { 37, 275, 37 });
+ expectedMapping.put(88, new int[] { 38, 287, 38 });
+ expectedMapping.put(89, new int[] { 39, 293, 39 });
+ expectedMapping.put(90, new int[] { 40, 299, 40 });
+ expectedMapping.put(91, new int[] { 41, 310, 41 });
+ expectedMapping.put(92, new int[] { 42, 315, 42 });
+ expectedMapping.put(93, new int[] { 43, 319, 43 });
+ expectedMapping.put(94, new int[] { 44, 325, 44 });
+ expectedMapping.put(95, new int[] { 45, 331, 45 });
+ expectedMapping.put(96, new int[] { 46, 337, 46 });
+ expectedMapping.put(97, new int[] { 47, 343, 47 });
+ expectedMapping.put(98, new int[] { 48, 349, 48 });
+ expectedMapping.put(99, new int[] { 49, 354, 49 });
+ expectedMapping.put(100, new int[] { 50, 358, 50 });
+ expectedMapping.put(101, new int[] { 51, 367, 51 });
+ expectedMapping.put(102, new int[] { 52, 375, 52 });
+ expectedMapping.put(103, new int[] { 53, 384, 53 });
+ expectedMapping.put(104, new int[] { 54, 391, 54 });
+ expectedMapping.put(105, new int[] { 55, 395, 55 });
+ expectedMapping.put(106, new int[] { 56, 401, 56 });
+ expectedMapping.put(107, new int[] { 57, 409, 57 });
+ expectedMapping.put(108, new int[] { 58, 417, 58 });
+ expectedMapping.put(109, new int[] { 59, 426, 59 });
+ expectedMapping.put(110, new int[] { 60, 434, 60 });
+ expectedMapping.put(111, new int[] { 61, 442, 61 });
+ expectedMapping.put(112, new int[] { 62, 451, 62 });
+ expectedMapping.put(113, new int[] { 63, 457, 63 });
+ expectedMapping.put(114, new int[] { 64, 468, 64 });
+ expectedMapping.put(115, new int[] { 65, 476, 65 });
+ expectedMapping.put(116, new int[] { 66, 484, 66 });
+ expectedMapping.put(117, new int[] { 67, 492, 67 });
+ expectedMapping.put(118, new int[] { 68, 500, 68 });
+ expectedMapping.put(119, new int[] { 69, 509, 69 });
+ expectedMapping.put(120, new int[] { 70, 517, 70 });
+ expectedMapping.put(121, new int[] { 71, 525, 71 });
+ expectedMapping.put(122, new int[] { 72, 534, 72 });
+ expectedMapping.put(123, new int[] { 73, 538, 73 });
+ expectedMapping.put(124, new int[] { 74, 552, 74 });
+ expectedMapping.put(125, new int[] { 75, 559, 75 });
+ expectedMapping.put(126, new int[] { 76, 567, 76 });
+ expectedMapping.put(127, new int[] { 77, 574, 77 });
+ expectedMapping.put(128, new int[] { 78, 580, 78 });
+ expectedMapping.put(129, new int[] { 79, 585, 79 });
+ expectedMapping.put(130, new int[] { 80, 590, 80 });
+ expectedMapping.put(131, new int[] { 81, 602, 81 });
+ expectedMapping.put(132, new int[] { 82, 609, 82 });
+ expectedMapping.put(133, new int[] { 83, 616, 83 });
+ expectedMapping.put(134, new int[] { 84, 622, 84 });
+ expectedMapping.put(135, new int[] { 85, 630, 85 });
+ expectedMapping.put(136, new int[] { 86, 637, 86 });
+ expectedMapping.put(137, new int[] { 87, 644, 87 });
+ expectedMapping.put(138, new int[] { 88, 652, 88 });
+ expectedMapping.put(139, new int[] { 89, 661, 89 });
+ expectedMapping.put(140, new int[] { 90, 668, 90 });
+ expectedMapping.put(141, new int[] { 91, 678, 91 });
+ expectedMapping.put(142, new int[] { 92, 687, 92 });
+ expectedMapping.put(143, new int[] { 93, 696, 93 });
+ expectedMapping.put(144, new int[] { 94, 705, 94 });
+ expectedMapping.put(145, new int[] { 95, 714, 95 });
+ expectedMapping.put(146, new int[] { 96, 722, 96 });
+ expectedMapping.put(147, new int[] { 97, 729, 97 });
+ }
@BeforeTest(alwaysRun = true)
- public void setUpSiftsClient() throws SiftsException
+ public void setUpSiftsClient() throws SiftsException, IOException
{
+ // read test props before manipulating config
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
// SIFTs entries are updated weekly - so use saved SIFTs file to enforce
// test reproducibility
- File testSiftsFile = new File("test/jalview/io/" + testPDBId
- + ".xml.gz");
- PDBfile pdbFile = new PDBfile(false, false, false);
- siftsClient = new SiftsClient(pdbFile, testSiftsFile);
+ new SiftsSettings();
+ SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+ SiftsSettings.setMapWithSifts(true);
+ SiftsSettings.setCacheThresholdInDays("2");
+ SiftsSettings.setFailSafePIDThreshold("70");
+ PDBfile pdbFile;
+ pdbFile = new PDBfile(false, false, false,
+ "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
+ siftsClient = new SiftsClient(pdbFile);
}
@AfterTest(alwaysRun = true)
siftsClient = null;
}
- @BeforeTest(alwaysRun = true)
- public void setUpStreams()
+ @Test(groups = { "Network" })
+ public void getSIFTsFileTest() throws SiftsException, IOException
{
- System.setOut(new PrintStream(outContent));
- }
+ File siftsFile;
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ long t1 = siftsFile.lastModified();
- @AfterTest(alwaysRun = true)
- public void cleanUpStreams()
- {
- System.setOut(null);
- }
+ // re-read file should be returned from cache
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ long t2 = siftsFile.lastModified();
+ assertEquals(t1, t2);
- @Test(groups = { "Functional" })
- public void getSIFTsFileTest()
- {
- Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
- SiftsClient.getSiftsFile(testPDBId);
- Assert.assertFalse(outContent.toString().contains(
- ">>> SIFTS File already downloaded for " + testPDBId));
+ /*
+ * force fetch by having 0 expiry of cache
+ * also wait one second, because file timestamp does not
+ * give millisecond resolution :-(
+ */
+ synchronized (this)
+ {
+ try
+ {
+ wait(1000);
+ } catch (InterruptedException e)
+ {
+ }
+ }
+ SiftsSettings.setCacheThresholdInDays("0");
+ siftsFile = SiftsClient.getSiftsFile(testPDBId);
+ FileAssert.assertFile(siftsFile);
+ long t3 = siftsFile.lastModified();
+ assertTrue(t3 > t2, "file timestamp unchanged at " + t3);
- // test for SIFTs file caching
- SiftsClient.getSiftsFile(testPDBId);
- Assert.assertTrue(outContent.toString().contains(
- ">>> SIFTS File already downloaded for " + testPDBId));
+ SiftsSettings.setCacheThresholdInDays("2");
}
- @Test(groups = { "Functional" })
- public void downloadSiftsFileTest()
+ @Test(groups = { "Network" })
+ public void downloadSiftsFileTest() throws SiftsException, IOException
{
// Assert that file isn't yet downloaded - if already downloaded, assert it
// is deleted
Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
- File siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+ File siftsFile;
+ siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
FileAssert.assertFile(siftsFile);
SiftsClient.downloadSiftsFile(testPDBId);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getAllMappingAccessionTest()
{
Assert.assertNotNull(siftsClient);
Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void getGreedyMappingTest()
{
Assert.assertNotNull(siftsClient);
// TODO delete when auto-fetching of DBRefEntry is implemented
DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
- dbRef.setStartRes(1);
- dbRef.setEndRes(147);
testSeq.addDBRef(dbRef);
// testSeq.setSourceDBRef(dbRef);
try
{
- int[][] actualMapping = siftsClient.getGreedyMapping("A", testSeq,
- null);
- Assert.assertEquals(actualMapping, expectedMapping);
+ HashMap<Integer, int[]> actualMapping = siftsClient
+ .getGreedyMapping("A", testSeq, null);
Assert.assertEquals(testSeq.getStart(), 1);
Assert.assertEquals(testSeq.getEnd(), 147);
+ // Can't do Assert.assertEquals(actualMapping, expectedMapping);
+ // because this fails in our version of TestNG
+ Assert.assertEquals(actualMapping.size(), expectedMapping.size());
+ Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
+ .iterator();
+ while (it.hasNext())
+ {
+ Map.Entry<Integer, int[]> pair = it.next();
+ Assert.assertTrue(actualMapping.containsKey(pair.getKey()));
+ Assert.assertEquals(actualMapping.get(pair.getKey()),
+ pair.getValue());
+ }
+
} catch (Exception e)
{
e.printStackTrace();
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
private void getAtomIndexTest()
{
- // siftsClient.getAtomIndex(1, null);
- // Assert.assertTrue(true);
+ ArrayList<Atom> atoms = new ArrayList<Atom>();
+ Atom atom = new Atom(u, u, u);
+ atom.resNumber = 43;
+ atom.atomIndex = 7;
+ atoms.add(atom);
+ int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
+ Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED);
+ actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
+ Assert.assertEquals(actualAtomIndex, 7);
}
@Test(
- groups = { "Functional" },
+ groups =
+ { "Network" },
expectedExceptions = IllegalArgumentException.class)
private void getAtomIndexNullTest()
{
siftsClient.getAtomIndex(1, null);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
private void padWithGapsTest()
{
}
- @Test(groups = { "Functional" })
- private void populateAtomPositionsTest()
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
+ private void populateAtomPositionsNullTest1()
+ throws IllegalArgumentException, SiftsException
+ {
+ siftsClient.populateAtomPositions(null, null);
+ }
+
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
+ private void populateAtomPositionsNullTest2()
+ throws IllegalArgumentException, SiftsException
{
+ siftsClient.populateAtomPositions("A", null);
+ }
+ @Test(groups = { "Network" })
+ public void getValidSourceDBRefTest() throws SiftsException
+ {
+ DBRefEntryI actualValidSrcDBRef = siftsClient
+ .getValidSourceDBRef(testSeq);
+ DBRefEntryI expectedDBRef = new DBRefEntry();
+ expectedDBRef.setSource(DBRefSource.UNIPROT);
+ expectedDBRef.setAccessionId("P00221");
+ expectedDBRef.setVersion("");
+ Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
}
- @Test(groups = { "Functional" })
- public void getValidSourceDBRefTest()
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
+ public void getValidSourceDBRefExceptionTest() throws SiftsException
{
+ SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+ siftsClient.getValidSourceDBRef(invalidTestSeq);
+ }
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
+ public void getValidSourceDBRefExceptionXTest() throws SiftsException
+ {
+ SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+ DBRefEntry invalidDBRef = new DBRefEntry();
+ invalidDBRef.setAccessionId("BLAR");
+ invalidTestSeq.addDBRef(invalidDBRef);
+ siftsClient.getValidSourceDBRef(invalidTestSeq);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" })
public void isValidDBRefEntryTest()
{
+ DBRefEntryI validDBRef = new DBRefEntry();
+ validDBRef.setSource(DBRefSource.UNIPROT);
+ validDBRef.setAccessionId("P00221");
+ validDBRef.setVersion("");
+ Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
+ }
+
+ @Test(groups = { "Network" })
+ public void getSiftsStructureMappingTest() throws SiftsException
+ {
+ Assert.assertTrue(SiftsSettings.isMapWithSifts());
+ StructureMapping strucMapping = siftsClient
+ .getSiftsStructureMapping(testSeq, testPDBId, "A");
+ String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
+ + "Method: SIFTS\n\n" + "P00221 : 51 - 147 Maps to \n"
+ + "1A70|A : 1 - 97\n\n"
+ + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
+ + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
+ + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
+ + "P00221 DDQIDEGWVLTCAAYPVSDVTIETHKEEELTA\n"
+ + " |||||||||||||||||||||||||| |||||\n"
+ + "1A70|A DDQIDEGWVLTCAAYPVSDVTIETHKKEELTA\n\n" +
+
+ "Length of alignment = 97\n" + "Percentage ID = 98.97\n";
+
+ Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
+ expectedMappingOutput);
+
+ // Can't do Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
+ // because this fails in our version of TestNG
+ Assert.assertEquals(strucMapping.getMapping().size(),
+ expectedMapping.size());
+ Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
+ .iterator();
+ while (it.hasNext())
+ {
+ Map.Entry<Integer, int[]> pair = it.next();
+ Assert.assertTrue(
+ strucMapping.getMapping().containsKey(pair.getKey()));
+ Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
+ pair.getValue());
+ }
+ }
+
+ @Test(groups = { "Network" })
+ public void getEntityCountTest()
+ {
+ int actualEntityCount = siftsClient.getEntityCount();
+ System.out.println("actual entity count : " + actualEntityCount);
+ Assert.assertEquals(actualEntityCount, 1);
+ }
+
+ @Test(groups = { "Network" })
+ public void getDbAccessionIdTest()
+ {
+ String actualDbAccId = siftsClient.getDbAccessionId();
+ System.out.println("Actual Db Accession Id: " + actualDbAccId);
+ Assert.assertEquals(actualDbAccId, "1a70");
+ }
+
+ @Test(groups = { "Network" })
+ public void getDbCoordSysTest()
+ {
+ String actualDbCoordSys = siftsClient.getDbCoordSys();
+ System.out.println("Actual DbCoordSys: " + actualDbCoordSys);
+ Assert.assertEquals(actualDbCoordSys, "PDBe");
+ }
+
+ @Test(groups = { "Network" })
+ public void getDbSourceTest()
+ {
+ String actualDbSource = siftsClient.getDbSource();
+ System.out.println("Actual DbSource: " + actualDbSource);
+ Assert.assertEquals(actualDbSource, "PDBe");
+ }
+
+ @Test(groups = { "Network" })
+ public void getDbVersionTest()
+ {
+ String actualDbVersion = siftsClient.getDbVersion();
+ System.out.println("Actual DbVersion: " + actualDbVersion);
+ Assert.assertEquals(actualDbVersion, "2.0");
+ }
+
+ @Test(groups = { "Network" })
+ public void getEntityByMostOptimalMatchedIdTest1()
+ throws IOException, SiftsException
+ {
+ SiftsClient siftsClientX = null;
+ PDBfile pdbFile;
+ pdbFile = new PDBfile(false, false, false,
+ "test/jalview/io/2nq2" + ".pdb", DataSourceType.FILE);
+ siftsClientX = new SiftsClient(pdbFile);
+ Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
+ Assert.assertEquals(entityA.getEntityId(), "A");
+ Entity entityB = siftsClientX.getEntityByMostOptimalMatchedId("B");
+ Assert.assertEquals(entityB.getEntityId(), "C");
+ Entity entityC = siftsClientX.getEntityByMostOptimalMatchedId("C");
+ Assert.assertEquals(entityC.getEntityId(), "B");
+ Entity entityD = siftsClientX.getEntityByMostOptimalMatchedId("D");
+ Assert.assertEquals(entityD.getEntityId(), "D");
+
+ }
+
+ @Test(groups = { "Network" })
+ public void getEntityByMostOptimalMatchedIdTest2()
+ throws IOException, SiftsException
+ {
+ // This test is for a SIFTS file in which entity A should map to chain P for
+ // the given PDB Id. All the other chains shouldn't be mapped as there are
+ // no SIFTS entity records for them.
+ SiftsClient siftsClientX = null;
+ PDBfile pdbFile;
+ pdbFile = new PDBfile(false, false, false, "test/jalview/io/3ucu.cif",
+ DataSourceType.FILE);
+ siftsClientX = new SiftsClient(pdbFile);
+ Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
+ Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
+ Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
+ Assert.assertEquals(entityA.getEntityId(), "A");
+ Assert.assertNotEquals(entityR, "A");
+ Assert.assertNotEquals(entityP, "A");
+ Assert.assertNotEquals(entityR, "R");
+ Assert.assertNotEquals(entityP, "P");
+ Assert.assertNull(entityR);
+ Assert.assertNull(entityP);
+
+ }
+
+ @Test(groups = { "Network" })
+ public void getLeadingIntegerFromString()
+ {
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234abcd", -1),
+ 1234);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234", -1),
+ 1234);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd1234", -1),
+ -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("None", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("Null", -1), -1);
}
}
git://source.jalview.org / jalview.git / blobdiff