X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fphyre2%2FPhyre2ClientTest.java;h=394ea6997f929694746b45a0d3acd3558f28e4bb;hb=19b5db52eb1285a22f8225f4baa914c2d7b15edd;hp=811ddd067a041d3caf698a3ef2025850b144aec8;hpb=e95ce7b42f95c193fc6ef5b6efb803d13dbac8b9;p=jalview.git diff --git a/test/jalview/ws/phyre2/Phyre2ClientTest.java b/test/jalview/ws/phyre2/Phyre2ClientTest.java index 811ddd0..394ea69 100644 --- a/test/jalview/ws/phyre2/Phyre2ClientTest.java +++ b/test/jalview/ws/phyre2/Phyre2ClientTest.java @@ -23,7 +23,8 @@ public class Phyre2ClientTest @Test(groups = { "Functional" }) public void getPhyre2FastaMappingTest() { - String phyre2ModelFile = "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.pdb"; + String phyre2ModelFile = "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb"; + String fastaMappingFile = "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta"; SequenceI testSeq = new Sequence( "FER_CAPAN", @@ -32,55 +33,7 @@ public class Phyre2ClientTest + "EEGWVLTCVAYPQSDVTIETHKEAELVG", 1, 144); HashMap expectedMapping = new HashMap(); - - expectedMapping.put(1, new int[] { -1, -1 }); - expectedMapping.put(2, new int[] { -1, -1 }); - expectedMapping.put(3, new int[] { -1, -1 }); - expectedMapping.put(4, new int[] { -1, -1 }); - expectedMapping.put(5, new int[] { -1, -1 }); - expectedMapping.put(6, new int[] { -1, -1 }); - expectedMapping.put(7, new int[] { -1, -1 }); - expectedMapping.put(8, new int[] { -1, -1 }); - expectedMapping.put(9, new int[] { -1, -1 }); - expectedMapping.put(10, new int[] { -1, -1 }); - expectedMapping.put(11, new int[] { -1, -1 }); - expectedMapping.put(12, new int[] { -1, -1 }); - expectedMapping.put(13, new int[] { -1, -1 }); - expectedMapping.put(14, new int[] { -1, -1 }); - expectedMapping.put(15, new int[] { -1, -1 }); - expectedMapping.put(16, new int[] { -1, -1 }); - expectedMapping.put(17, new int[] { -1, -1 }); - expectedMapping.put(18, new int[] { -1, -1 }); - expectedMapping.put(19, new int[] { -1, -1 }); - expectedMapping.put(20, new int[] { -1, -1 }); - expectedMapping.put(21, new int[] { -1, -1 }); - expectedMapping.put(22, new int[] { -1, -1 }); - expectedMapping.put(23, new int[] { -1, -1 }); - expectedMapping.put(24, new int[] { -1, -1 }); - expectedMapping.put(25, new int[] { -1, -1 }); - expectedMapping.put(26, new int[] { -1, -1 }); - expectedMapping.put(27, new int[] { -1, -1 }); - expectedMapping.put(28, new int[] { -1, -1 }); - expectedMapping.put(29, new int[] { -1, -1 }); - expectedMapping.put(30, new int[] { -1, -1 }); - expectedMapping.put(31, new int[] { -1, -1 }); - expectedMapping.put(32, new int[] { -1, -1 }); - expectedMapping.put(33, new int[] { -1, -1 }); - expectedMapping.put(34, new int[] { -1, -1 }); - expectedMapping.put(35, new int[] { -1, -1 }); - expectedMapping.put(36, new int[] { -1, -1 }); - expectedMapping.put(37, new int[] { -1, -1 }); - expectedMapping.put(38, new int[] { -1, -1 }); - expectedMapping.put(39, new int[] { -1, -1 }); - expectedMapping.put(40, new int[] { -1, -1 }); - expectedMapping.put(41, new int[] { -1, -1 }); - expectedMapping.put(42, new int[] { -1, -1 }); - expectedMapping.put(43, new int[] { -1, -1 }); - expectedMapping.put(44, new int[] { -1, -1 }); - expectedMapping.put(45, new int[] { -1, -1 }); - expectedMapping.put(46, new int[] { -1, -1 }); - expectedMapping.put(47, new int[] { -1, -1 }); - // forty eight gaps in PDB sequence + // PDB sequence starts with residue 48 expectedMapping.put(48, new int[] { 48, 1 }); expectedMapping.put(49, new int[] { 49, 6 }); expectedMapping.put(50, new int[] { 50, 12 }); @@ -93,11 +46,8 @@ public class Phyre2ClientTest expectedMapping.put(57, new int[] { 57, 72 }); expectedMapping.put(58, new int[] { 58, 79 }); expectedMapping.put(59, new int[] { 59, 87 }); - expectedMapping.put(60, new int[] { -1, -1 }); - expectedMapping.put(61, new int[] { -1, -1 }); - // two gaps in PDB sequence - expectedMapping.put(62, new int[] { 60, -1 }); - expectedMapping.put(63, new int[] { 61, -1 }); + // residues 60, 61 absent in PDB file + // residues 62, 63 also skipped in map (is this right?) expectedMapping.put(64, new int[] { 62, 91 }); expectedMapping.put(65, new int[] { 63, 100 }); expectedMapping.put(66, new int[] { 64, 111 }); @@ -150,11 +100,10 @@ public class Phyre2ClientTest expectedMapping.put(113, new int[] { 111, 445 }); expectedMapping.put(114, new int[] { 112, 453 }); expectedMapping.put(115, new int[] { 113, 461 }); - // one gap in PDB sequence - expectedMapping.put(116, new int[] { -1, -1 }); + // residue 116 absent in PDB file expectedMapping.put(117, new int[] { 114, 469 }); expectedMapping.put(118, new int[] { 115, 477 }); - expectedMapping.put(119, new int[] { 116, -1 }); + // residue 119 gets removed as mapped to 116 - is this right? expectedMapping.put(120, new int[] { 117, 486 }); expectedMapping.put(121, new int[] { 118, 495 }); expectedMapping.put(122, new int[] { 119, 504 }); @@ -179,13 +128,14 @@ public class Phyre2ClientTest expectedMapping.put(141, new int[] { 138, 652 }); expectedMapping.put(142, new int[] { 139, 661 }); expectedMapping.put(143, new int[] { 140, 670 }); - expectedMapping.put(144, new int[] { -1, -1 }); + // residue 144 absent in PDB file StructureFile structureFile; try { structureFile = new JmolParser(phyre2ModelFile, DataSourceType.FILE); phyre2Client = new Phyre2Client(structureFile); + phyre2Client.setFastaMappingFile(fastaMappingFile); } catch (IOException e1) { e1.printStackTrace(); @@ -212,6 +162,7 @@ public class Phyre2ClientTest public void getPhyre2FastaMappingTest2() { String phyre2ModelFile = "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.pdb"; + String fastaMappingFile = "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.fasta"; SequenceI testSeq = new Sequence( "FER_CAPAN", @@ -219,40 +170,7 @@ public class Phyre2ClientTest 13, 139); HashMap expectedMapping = new HashMap(); - - expectedMapping.put(13, new int[] { -1, -1 }); - expectedMapping.put(14, new int[] { -1, -1 }); - expectedMapping.put(15, new int[] { -1, -1 }); - expectedMapping.put(16, new int[] { -1, -1 }); - expectedMapping.put(17, new int[] { -1, -1 }); - expectedMapping.put(18, new int[] { -1, -1 }); - expectedMapping.put(19, new int[] { -1, -1 }); - expectedMapping.put(20, new int[] { -1, -1 }); - expectedMapping.put(21, new int[] { -1, -1 }); - expectedMapping.put(22, new int[] { -1, -1 }); - expectedMapping.put(23, new int[] { -1, -1 }); - expectedMapping.put(24, new int[] { -1, -1 }); - expectedMapping.put(25, new int[] { -1, -1 }); - expectedMapping.put(26, new int[] { -1, -1 }); - expectedMapping.put(27, new int[] { -1, -1 }); - expectedMapping.put(28, new int[] { -1, -1 }); - expectedMapping.put(29, new int[] { -1, -1 }); - expectedMapping.put(30, new int[] { -1, -1 }); - expectedMapping.put(31, new int[] { -1, -1 }); - expectedMapping.put(32, new int[] { -1, -1 }); - expectedMapping.put(33, new int[] { -1, -1 }); - expectedMapping.put(34, new int[] { -1, -1 }); - expectedMapping.put(35, new int[] { -1, -1 }); - expectedMapping.put(36, new int[] { -1, -1 }); - expectedMapping.put(37, new int[] { -1, -1 }); - expectedMapping.put(38, new int[] { -1, -1 }); - expectedMapping.put(39, new int[] { -1, -1 }); - expectedMapping.put(40, new int[] { -1, -1 }); - expectedMapping.put(41, new int[] { -1, -1 }); - expectedMapping.put(42, new int[] { -1, -1 }); - expectedMapping.put(43, new int[] { -1, -1 }); - expectedMapping.put(44, new int[] { -1, -1 }); - // thirty two gaps in PDB sequence + // PDB sequence starts with residue 33 expectedMapping.put(45, new int[] { 33, 1 }); expectedMapping.put(46, new int[] { 34, 6 }); expectedMapping.put(47, new int[] { 35, 13 }); @@ -354,6 +272,7 @@ public class Phyre2ClientTest { structureFile = new JmolParser(phyre2ModelFile, DataSourceType.FILE); phyre2Client = new Phyre2Client(structureFile); + phyre2Client.setFastaMappingFile(fastaMappingFile); } catch (IOException e1) { e1.printStackTrace(); @@ -368,6 +287,7 @@ public class Phyre2ClientTest Assert.assertEquals(testSeq.getStart(), 13); Assert.assertEquals(testSeq.getEnd(), 139); + Assert.assertEquals(actualMapping, expectedMapping); testMappings(actualMapping, expectedMapping); } catch (Exception e) { @@ -388,6 +308,10 @@ public class Phyre2ClientTest // Test entry set for (int key : expectedMapping.keySet()) { + System.out.println(key + " ---> [" + expectedMapping.get(key)[0] + + ", " + expectedMapping.get(key)[1] + "] = [" + + actualMapping.get(key)[0] + ", " + + actualMapping.get(key)[1] + "]"); Assert.assertTrue(Arrays.equals(expectedMapping.get(key), actualMapping.get(key))); }