From a012c2cde7ad7dbc155b17415227e163c5f20882 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 9 Nov 2015 06:59:39 +0000 Subject: [PATCH] JAL-1950 test positioning of posterior probability annotation on hit sequence --- test/jalview/ws/ebi/HmmerJSONProcessTest.java | 29 +++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/test/jalview/ws/ebi/HmmerJSONProcessTest.java b/test/jalview/ws/ebi/HmmerJSONProcessTest.java index 0c07584..291a5a3 100644 --- a/test/jalview/ws/ebi/HmmerJSONProcessTest.java +++ b/test/jalview/ws/ebi/HmmerJSONProcessTest.java @@ -1,6 +1,8 @@ package jalview.ws.ebi; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; import jalview.io.FileParse; import jalview.io.FormatAdapter; @@ -78,6 +80,33 @@ public class HmmerJSONProcessTest { HmmerJSONProcessor hjsp = new HmmerJSONProcessor(searchResult); hjsp.parseFrom(new FileParse(hmmerResultFile, FormatAdapter.FILE)); + AlignmentAnnotation[] aa = searchResult.getSequenceAt(5) + .getAnnotation(); + Assert.assertNotNull(aa); + Assert.assertEquals(aa.length, 3, + "didn't get expected set of annotation.\n"); + // DPTSERWFHGHLSGKEAEKLLTeKGKHGSFLVRESQSHPGDFVLSVRTgddkgesndgKSKVTHVMIR-CQELKYDVGGGERFDSLTDLVEHYKKNPmvet + // LGTVLQLKQP + // 5789*****************9799***********************999998888888********.99**************************9999 + // 899999*999 + // AlignmentAnnotation + // 101 == 8 + String seq = "tLGT"; + SequenceI s5 = searchResult.getSequenceAt(5); + Assert.assertEquals( + s5.getSubSequence(s5.findIndex(225), s5.findIndex(229)) + .getSequenceAsString(), + seq); + int pos = s5.findIndex(226); + for (AlignmentAnnotation an : aa) + { + if (an.label.startsWith("Posterior")) + { + Assert.assertEquals(an.annotations[pos].value, 8f); + + } + } + ; // check that // scores, posterior probabilities and stuff exist. } -- 1.7.10.2