jalview

examples

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Monday 23 Aug
4:52 pm

Jim Procter

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

4:49 pm

Jim Procter

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

4:48 pm

Jim Procter

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

4:43 pm

Jim Procter

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
Thursday 22 Jul
8:37 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-1950 patch groovy bootstrap for importing hmmer3 json

Options
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    ./groovy/hmmertestimport.groovy
Tuesday 06 Jul
5:42 pm

Jim Procter

5:42 pm

Jim Procter

WIP
WIP
Wednesday 03 Feb
4:33 pm

Jim Procter

JAL-3808 example exonerate cdna2genome and coding2genome test data and test

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    ./testdata/test_cdna2genome_showquerygff.gff2
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    ./testdata/test_cdna2genome_showtargetgff.gff2
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    ./testdata/test_coding2genome_showquerygff.gff2
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    ./testdata/test_coding2genome_showtargetgff.gff2
  5. … 1 more file in changeset.
Tuesday 27 Oct 2020
12:58 pm

Jim Procter

update test for JAL-3763 redact shared DS sequences for contiguous CDS

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    • binary
    ./testdata/MN908947.jvp
Tuesday 22 Sep 2020
3:30 pm

Jim Procter

JAL-3748 test data for SplitFrameTest

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    ./testdata/MN908947.jvp
Monday 08 Jun 2020
11:22 am

Jim Procter

JAL-3641 allow protocol to be configured at top of script

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    ./groovy/FastQParser.groovy
11:08 am

Jim Procter

JAL-3641 prototype FASTQ import via groovy script for 2.11.1

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    ./groovy/FastQParser.groovy
Tuesday 02 Jun 2020
8:16 pm

Bob Hanson

JAL-3445 JAL-3253 BSML bbb format test data - pox virus genomes

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    ./testdata/10-poxgenomes.bbb
Friday 29 May 2020
6:25 pm

Jim Procter

JAL-518 quick and dirty groovy script implementing undo/redo left justify (or right if the flag is disabled)

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    ./groovy/justifyRegionQuick.groovy
Tuesday 21 Apr 2020
5:39 pm

Jim Procter

JAL-3407 add and document ComputePeptideVariants.groovy

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    ./groovy/ComputePeptideVariants.groovy
  2. … 3 more files in changeset.
Thursday 05 Mar 2020
12:14 pm

Jim Procter

JAL-3548 start an http server for posting gene ids to retrieve from ensembl and display in Jalview

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    • +45
    ./groovy/simpleHttpServlet.groovy
  2. … 4 more files in changeset.
Tuesday 03 Mar 2020
9:06 am

Jim Procter

JAL-3547 groovy script to get the conservation sequence and output it as fasta

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    ./groovy/exportconsensus.groovy
Monday 17 Feb 2020
4:08 pm

Jim Procter

JAL-3536 failing test and test data

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    ./testdata/CantShowEnsemblCrossrefsTwice.jvp
  2. … 1 more file in changeset.
Monday 30 Sep 2019
1:39 am

hansonr <hansonr@STO24954W.ad.stolaf.edu>

moving 10-poxgenomes.bbb and newer IdentifyFile.java to "unused"; revering IdentifyFile.

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    ./testdata/10-poxgenomes.bbb
  2. … 3 more files in changeset.
Saturday 28 Sep 2019
1:55 pm

hansonr <hansonr@STO24954W.ad.stolaf.edu>

JAL-3445 preliminary BSML reader

- only dna type

- only GENE class features

- only primary strand reading, not complement

- test file put into examples/testdata

- uses javax.xml.parsers.DocumentBuilder

- seems to work in Java; needs TestNG test

- not tested in JavaScript

- for discussion only

Options
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    • +8457
    ./testdata/10-poxgenomes.bbb
  2. … 3 more files in changeset.
Tuesday 27 Aug 2019
10:20 pm

Ben Soares

JAL-3210 Barebones gradle/buildship/eclipse. See README

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    ./1gaq.txt
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    ./2GIS.pdb
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    ./3W5V.pdb
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    ./PF00111_seed.stk
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    ./RF00031_folded.stk
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    ./appletDeployment.html
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    ./appletParameters.html
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    ./applets.html
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    ./backupfilestest.fa
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    ./biojson-doc/.gitignore
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    ./biojson-doc/LICENSE
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    ./biojson-doc/README.md
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    ./biojson-doc/biojson_uml.png
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    ./biojson-doc/biojsonschema.json
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    ./biojson-doc/bower.json
  16. … 1976 more files in changeset.
Friday 23 Aug 2019
4:16 pm

Jim Procter

JAL-3417 prototype sdppred calculation as groovy script

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    ./groovy/sdppred_testing.groovy
Monday 27 May 2019
9:16 am

Mungo Carstairs

Test file relocated to test/jalview/io.

Test file relocated to test/jalview/io.

9:16 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3141 test file in test folder not examples

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    ./backupfilestest.fa
  2. … 2 more files in changeset.
Friday 26 Apr 2019
12:34 pm

Jim Procter

JAL-3150 examples/exampleFile.jvp for updated manual/tutorial exercises

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    ./exampleFile.jvp
Monday 25 Mar 2019
8:57 am

gmungoc <g.m.carstairs@dundee.ac.uk>

JAL-3127 scripts updated for method signature change

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    ./groovy/colourConserved.groovy
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    ./groovy/colourSchemes.groovy
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    ./groovy/colourUnconserved.groovy
Thursday 14 Mar 2019
10:38 am

Mungo Carstairs

May be worth adding temp.deleteOnExit() in case anything goes wrong with renaming later

May be worth adding temp.deleteOnExit() in case anything goes wrong with renaming later

10:37 am

Mungo Carstairs

Needs Javadoc; in particular to highlight the side-effect (that a file is written)

Needs Javadoc; in particular to highlight the side-effect (that a file is written)

Wednesday 13 Mar 2019
11:08 am

Mungo Carstairs

Use '.' (test/jalview/io) rather than examples (which should be kept for real user data files). Or better if possible, use File.createTempFile to save files to a system-managed temporary folder.

Use '.' (test/jalview/io) rather than examples (which should be kept for real user data files).
Or better if possible, use File.createTempFile to save files to a system-managed temporary folder.

Monday 11 Mar 2019
11:04 am

Mungo Carstairs

JAL-2250 now done.

JAL-2250 now done.