From 327b70fcc535cee0098b53ebf928f453481be9d1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 22 Jul 2021 20:37:51 +0100 Subject: [PATCH] JAL-1950 patch groovy bootstrap for importing hmmer3 json --- examples/groovy/hmmertestimport.groovy | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/groovy/hmmertestimport.groovy b/examples/groovy/hmmertestimport.groovy index 88bd0e1..9f0d34e 100644 --- a/examples/groovy/hmmertestimport.groovy +++ b/examples/groovy/hmmertestimport.groovy @@ -1,5 +1,5 @@ -// def alv = new jalview.io.FileLoader().LoadFileWaitTillLoaded("examples/testdata/hmmer3/alignment_res.fa.gz","File").getViewport(); -def alv = jalview.bin.Jalview.getCurrentAlignFrame().getViewport(); + def alv = new jalview.io.FileLoader().LoadFileWaitTillLoaded("examples/testdata/hmmer3/alignment_res.fa.gz",jalview.io.DataSourceType.FILE).getViewport(); +//def alv = jalview.bin.Jalview.getCurrentAlignFrame().getViewport(); def al = alv.getAlignment(); def jproc = new jalview.ws.ebi.HmmerJSONProcessor(al) jproc.parseFrom(new jalview.io.FileParse("/Users/jprocter/git/jalview/examples/testdata/hmmer3/hmmeresult.json.gz",jalview.io.DataSourceType.FILE)) -- 1.7.10.2