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JAL-1950 patch groovy bootstrap for importing hmmer3 json
author
Jim Procter
<j.procter@dundee.ac.uk>
Thu, 22 Jul 2021 19:37:51 +0000
(20:37 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Thu, 22 Jul 2021 19:37:51 +0000
(20:37 +0100)
examples/groovy/hmmertestimport.groovy
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diff --git
a/examples/groovy/hmmertestimport.groovy
b/examples/groovy/hmmertestimport.groovy
index
88bd0e1
..
9f0d34e
100644
(file)
--- 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))
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))