From a28768a635abf715690fe991326dc7e650f37049 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 16 Jun 2016 18:29:40 +0100 Subject: [PATCH] tests for validating start-end number/sequence length, annotation and metadata for retrieval from PDB via mmCIF and PDB JAL-2007 JAL-2005 JAL-1919 --- test/jalview/ws/PDBSequenceFetcherTest.java | 35 +++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java index d020173..b560f01 100644 --- a/test/jalview/ws/PDBSequenceFetcherTest.java +++ b/test/jalview/ws/PDBSequenceFetcherTest.java @@ -76,4 +76,39 @@ public class PDBSequenceFetcherTest } } + @Test(groups = { "Network" }, enabled = true) + public void testPdbSeqRetrieve() throws Exception + { + Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", + Boolean.TRUE.toString()); + testRetrieveProteinSeqFromPDB(); + } + + @Test(groups = { "Network" }, enabled = true) + public void testmmCifSeqRetrieve() throws Exception + { + Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", + Boolean.FALSE.toString()); + testRetrieveProteinSeqFromPDB(); + } + + private void testRetrieveProteinSeqFromPDB() throws Exception + { + List sps = sf.getSourceProxy("PDB"); + AlignmentI response = sps.get(0).getSequenceRecords("1QIP"); + assertTrue(response != null); + assertTrue(response.getHeight() == 4); + for (SequenceI sq : response.getSequences()) + { + assertTrue("No annotation transfered to sequence.", + sq.getAnnotation().length > 0); + assertTrue("No PDBEntry on sequence.", + sq.getAllPDBEntries().size() > 0); + org.testng.Assert + .assertEquals(sq.getEnd() - sq.getStart() + 1, + sq.getLength(), + "Sequence start/end doesn't match number of residues in sequence"); + } + } + } -- 1.7.10.2