X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;fp=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=ebe7f2570940b786655b587e8a013188abef6a87;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=44a6a0258fc378e6ae26f313ad4da00f5d7a8663;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java index 44a6a02..ebe7f25 100644 --- a/test/jalview/ws/sifts/SiftsClientTest.java +++ b/test/jalview/ws/sifts/SiftsClientTest.java @@ -23,16 +23,6 @@ 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.File; import java.io.IOException; @@ -48,6 +38,16 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeTest; import org.testng.annotations.Test; +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 mc_view.Atom; import mc_view.PDBfile; @@ -62,18 +62,19 @@ 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; @@ -188,15 +189,14 @@ public class SiftsClientTest Cache.loadProperties("test/jalview/io/testProps.jvprops"); // 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); } @@ -277,8 +277,8 @@ 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); // Can't do Assert.assertEquals(actualMapping, expectedMapping); @@ -310,14 +310,13 @@ public class SiftsClientTest atom.atomIndex = 7; atoms.add(atom); int actualAtomIndex = siftsClient.getAtomIndex(1, atoms); - Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED); + 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() { @@ -330,14 +329,18 @@ 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 { @@ -356,14 +359,18 @@ public class SiftsClientTest 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"); @@ -387,10 +394,11 @@ public class SiftsClientTest 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" @@ -414,8 +422,8 @@ public class SiftsClientTest while (it.hasNext()) { Map.Entry pair = it.next(); - Assert.assertTrue( - strucMapping.getMapping().containsKey(pair.getKey())); + Assert.assertTrue(strucMapping.getMapping() + .containsKey(pair.getKey())); Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()), pair.getValue()); } @@ -462,13 +470,13 @@ public class SiftsClientTest } @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"); @@ -482,8 +490,8 @@ public class SiftsClientTest } @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 @@ -505,18 +513,4 @@ public class SiftsClientTest 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); - } }