X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=44a6a0258fc378e6ae26f313ad4da00f5d7a8663;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=d805e4739dd96e3e461765bf79fb913fa9b5e9f6;hpb=f1ad88cc8d9b26244086e5c24b73fb80b0ff0a38;p=jalview.git diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index d805e47..44a6a02 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -38,6 +38,8 @@ import java.io.File; 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; @@ -46,8 +48,8 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeTest; import org.testng.annotations.Test; -import MCview.Atom; -import MCview.PDBfile; +import mc_view.Atom; +import mc_view.PDBfile; public class SiftsClientTest { @@ -60,19 +62,18 @@ public class SiftsClientTest } public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System - .getProperty("user.home") - + File.separatorChar + .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; @@ -81,103 +82,103 @@ public class SiftsClientTest @BeforeTest(alwaysRun = true) public void populateExpectedMapping() throws SiftsException { - expectedMapping.put(51, new int[] { 1, 2 }); - expectedMapping.put(52, new int[] { 2, 7 }); - expectedMapping.put(53, new int[] { 3, 12 }); - expectedMapping.put(54, new int[] { 4, 24 }); - expectedMapping.put(55, new int[] { 5, 33 }); - expectedMapping.put(56, new int[] { 6, 40 }); - expectedMapping.put(57, new int[] { 7, 47 }); - expectedMapping.put(58, new int[] { 8, 55 }); - expectedMapping.put(59, new int[] { 9, 62 }); - expectedMapping.put(60, new int[] { 10, 69 }); - expectedMapping.put(61, new int[] { 11, 76 }); - expectedMapping.put(62, new int[] { 12, 83 }); - expectedMapping.put(63, new int[] { 13, 87 }); - expectedMapping.put(64, new int[] { 14, 95 }); - expectedMapping.put(65, new int[] { 15, 102 }); - expectedMapping.put(66, new int[] { 16, 111 }); - expectedMapping.put(67, new int[] { 17, 122 }); - expectedMapping.put(68, new int[] { 18, 131 }); - expectedMapping.put(69, new int[] { 19, 137 }); - expectedMapping.put(70, new int[] { 20, 144 }); - expectedMapping.put(71, new int[] { 21, 152 }); - expectedMapping.put(72, new int[] { 22, 160 }); - expectedMapping.put(73, new int[] { 23, 167 }); - expectedMapping.put(74, new int[] { 24, 179 }); - expectedMapping.put(75, new int[] { 25, 187 }); - expectedMapping.put(76, new int[] { 26, 195 }); - expectedMapping.put(77, new int[] { 27, 203 }); - expectedMapping.put(78, new int[] { 28, 208 }); - expectedMapping.put(79, new int[] { 29, 213 }); - expectedMapping.put(80, new int[] { 30, 222 }); - expectedMapping.put(81, new int[] { 31, 231 }); - expectedMapping.put(82, new int[] { 32, 240 }); - expectedMapping.put(83, new int[] { 33, 244 }); - expectedMapping.put(84, new int[] { 34, 252 }); - expectedMapping.put(85, new int[] { 35, 260 }); - expectedMapping.put(86, new int[] { 36, 268 }); - expectedMapping.put(87, new int[] { 37, 275 }); - expectedMapping.put(88, new int[] { 38, 287 }); - expectedMapping.put(89, new int[] { 39, 293 }); - expectedMapping.put(90, new int[] { 40, 299 }); - expectedMapping.put(91, new int[] { 41, 310 }); - expectedMapping.put(92, new int[] { 42, 315 }); - expectedMapping.put(93, new int[] { 43, 319 }); - expectedMapping.put(94, new int[] { 44, 325 }); - expectedMapping.put(95, new int[] { 45, 331 }); - expectedMapping.put(96, new int[] { 46, 337 }); - expectedMapping.put(97, new int[] { 47, 343 }); - expectedMapping.put(98, new int[] { 48, 349 }); - expectedMapping.put(99, new int[] { 49, 354 }); - expectedMapping.put(100, new int[] { 50, 358 }); - expectedMapping.put(101, new int[] { 51, 367 }); - expectedMapping.put(102, new int[] { 52, 375 }); - expectedMapping.put(103, new int[] { 53, 384 }); - expectedMapping.put(104, new int[] { 54, 391 }); - expectedMapping.put(105, new int[] { 55, 395 }); - expectedMapping.put(106, new int[] { 56, 401 }); - expectedMapping.put(107, new int[] { 57, 409 }); - expectedMapping.put(108, new int[] { 58, 417 }); - expectedMapping.put(109, new int[] { 59, 426 }); - expectedMapping.put(110, new int[] { 60, 434 }); - expectedMapping.put(111, new int[] { 61, 442 }); - expectedMapping.put(112, new int[] { 62, 451 }); - expectedMapping.put(113, new int[] { 63, 457 }); - expectedMapping.put(114, new int[] { 64, 468 }); - expectedMapping.put(115, new int[] { 65, 476 }); - expectedMapping.put(116, new int[] { 66, 484 }); - expectedMapping.put(117, new int[] { 67, 492 }); - expectedMapping.put(118, new int[] { 68, 500 }); - expectedMapping.put(119, new int[] { 69, 509 }); - expectedMapping.put(120, new int[] { 70, 517 }); - expectedMapping.put(121, new int[] { 71, 525 }); - expectedMapping.put(122, new int[] { 72, 534 }); - expectedMapping.put(123, new int[] { 73, 538 }); - expectedMapping.put(124, new int[] { 74, 552 }); - expectedMapping.put(125, new int[] { 75, 559 }); - expectedMapping.put(126, new int[] { 76, 567 }); - expectedMapping.put(127, new int[] { 77, 574 }); - expectedMapping.put(128, new int[] { 78, 580 }); - expectedMapping.put(129, new int[] { 79, 585 }); - expectedMapping.put(130, new int[] { 80, 590 }); - expectedMapping.put(131, new int[] { 81, 602 }); - expectedMapping.put(132, new int[] { 82, 609 }); - expectedMapping.put(133, new int[] { 83, 616 }); - expectedMapping.put(134, new int[] { 84, 622 }); - expectedMapping.put(135, new int[] { 85, 630 }); - expectedMapping.put(136, new int[] { 86, 637 }); - expectedMapping.put(137, new int[] { 87, 644 }); - expectedMapping.put(138, new int[] { 88, 652 }); - expectedMapping.put(139, new int[] { 89, 661 }); - expectedMapping.put(140, new int[] { 90, 668 }); - expectedMapping.put(141, new int[] { 91, 678 }); - expectedMapping.put(142, new int[] { 92, 687 }); - expectedMapping.put(143, new int[] { 93, 696 }); - expectedMapping.put(144, new int[] { 94, 705 }); - expectedMapping.put(145, new int[] { 95, 714 }); - expectedMapping.put(146, new int[] { 96, 722 }); - expectedMapping.put(147, new int[] { 97, 729 }); + 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) @@ -188,14 +189,14 @@ public class SiftsClientTest // SIFTs entries are updated weekly - so use saved SIFTs file to enforce // test reproducibility new SiftsSettings(); - SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault( - "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); + 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); + pdbFile = new PDBfile(false, false, false, + "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE); siftsClient = new SiftsClient(pdbFile); } @@ -276,11 +277,23 @@ public class SiftsClientTest try { - HashMap actualMapping = siftsClient.getGreedyMapping( - "A", testSeq, null); + HashMap actualMapping = siftsClient + .getGreedyMapping("A", testSeq, null); Assert.assertEquals(testSeq.getStart(), 1); Assert.assertEquals(testSeq.getEnd(), 147); - Assert.assertEquals(actualMapping, expectedMapping); + // 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(); @@ -297,13 +310,14 @@ public class SiftsClientTest atom.atomIndex = 7; atoms.add(atom); int actualAtomIndex = siftsClient.getAtomIndex(1, atoms); - Assert.assertEquals(actualAtomIndex, -1); + Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED); actualAtomIndex = siftsClient.getAtomIndex(43, atoms); Assert.assertEquals(actualAtomIndex, 7); } @Test( - groups = { "Network" }, + groups = + { "Network" }, expectedExceptions = IllegalArgumentException.class) private void getAtomIndexNullTest() { @@ -316,18 +330,14 @@ public class SiftsClientTest } - @Test( -groups = { "Network" }, - expectedExceptions = SiftsException.class) + @Test(groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest1() throws IllegalArgumentException, SiftsException { siftsClient.populateAtomPositions(null, null); } - @Test( -groups = { "Network" }, - expectedExceptions = SiftsException.class) + @Test(groups = { "Network" }, expectedExceptions = SiftsException.class) private void populateAtomPositionsNullTest2() throws IllegalArgumentException, SiftsException { @@ -346,18 +356,14 @@ groups = { "Network" }, Assert.assertEquals(actualValidSrcDBRef, expectedDBRef); } - @Test( -groups = { "Network" }, - expectedExceptions = SiftsException.class) + @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) + @Test(groups = { "Network" }, expectedExceptions = SiftsException.class) public void getValidSourceDBRefExceptionXTest() throws SiftsException { SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH"); @@ -381,11 +387,10 @@ groups = { "Network" }, public void getSiftsStructureMappingTest() throws SiftsException { Assert.assertTrue(SiftsSettings.isMapWithSifts()); - StructureMapping strucMapping = siftsClient.getSiftsStructureMapping( - testSeq, testPDBId, "A"); + StructureMapping strucMapping = siftsClient + .getSiftsStructureMapping(testSeq, testPDBId, "A"); String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n" - + "Method: SIFTS\n\n" - + "P00221 : 51 - 147 Maps to \n" + + "Method: SIFTS\n\n" + "P00221 : 51 - 147 Maps to \n" + "1A70|A : 1 - 97\n\n" + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n" + " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n" @@ -399,7 +404,21 @@ groups = { "Network" }, Assert.assertEquals(strucMapping.getMappingDetailsOutput(), expectedMappingOutput); - Assert.assertEquals(strucMapping.getMapping(), expectedMapping); + + // 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" }) @@ -443,13 +462,13 @@ groups = { "Network" }, } @Test(groups = { "Network" }) - public void getEntityByMostOptimalMatchedIdTest1() throws IOException, - SiftsException + public void getEntityByMostOptimalMatchedIdTest1() + throws IOException, SiftsException { SiftsClient siftsClientX = null; PDBfile pdbFile; - pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2" - + ".pdb", DataSourceType.FILE); + 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"); @@ -463,8 +482,8 @@ groups = { "Network" }, } @Test(groups = { "Network" }) - public void getEntityByMostOptimalMatchedIdTest2() throws IOException, - SiftsException + 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 @@ -486,4 +505,18 @@ groups = { "Network" }, 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); + } }