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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

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

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

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
JAL-1950 patch groovy bootstrap for importing hmmer3 json

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

JAL-3748 test data for SplitFrameTest

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    ./testdata/MN908947.jvp
JAL-3641 allow protocol to be configured at top of script

JAL-3641 prototype FASTQ import via groovy script for 2.11.1

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    ./groovy/FastQParser.groovy
JAL-3445 JAL-3253 BSML bbb format test data - pox virus genomes

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
JAL-3407 add and document ComputePeptideVariants.groovy

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

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

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    ./groovy/exportconsensus.groovy
JAL-3536 failing test and test data

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    ./testdata/CantShowEnsemblCrossrefsTwice.jvp
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moving 10-poxgenomes.bbb and newer IdentifyFile.java to "unused"; revering IdentifyFile.

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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

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    ./testdata/10-poxgenomes.bbb
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JAL-3210 Barebones gradle/buildship/eclipse. See README

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JAL-3417 prototype sdppred calculation as groovy script

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    ./groovy/sdppred_testing.groovy
Test file relocated to test/jalview/io.

Test file relocated to test/jalview/io.

JAL-3141 test file in test folder not examples

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

JAL-3127 scripts updated for method signature change

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

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)

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.

JAL-2250 now done.

JAL-2250 now done.