X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=44a6a0258fc378e6ae26f313ad4da00f5d7a8663;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=4c94f66306c98b3c710a3c9a0f48a8519203ff35;hpb=49f0437d385ee4c6dbe701180a4ba704da76b5f8;p=jalview.git diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index 4c94f66..44a6a02 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -20,72 +20,184 @@ */ 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 expectedMapping = new HashMap(); + + @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) @@ -94,44 +206,56 @@ public class SiftsClientTest 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); @@ -139,7 +263,7 @@ public class SiftsClientTest Assert.assertTrue(siftsClient.getAllMappingAccession().size() > 1); } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) public void getGreedyMappingTest() { Assert.assertNotNull(siftsClient); @@ -148,18 +272,28 @@ public class SiftsClientTest // 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 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> it = expectedMapping.entrySet() + .iterator(); + while (it.hasNext()) + { + Map.Entry pair = it.next(); + Assert.assertTrue(actualMapping.containsKey(pair.getKey())); + Assert.assertEquals(actualMapping.get(pair.getKey()), + pair.getValue()); + } + } catch (Exception e) { e.printStackTrace(); @@ -167,42 +301,222 @@ public class SiftsClientTest } } - @Test(groups = { "Functional" }) + @Test(groups = { "Network" }) private void getAtomIndexTest() { - // siftsClient.getAtomIndex(1, null); - // Assert.assertTrue(true); + ArrayList atoms = new ArrayList(); + 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> it = expectedMapping.entrySet() + .iterator(); + while (it.hasNext()) + { + Map.Entry 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); } }