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JAL-3365 the correct Pfam ID

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JAL-3365 per-sequence secondary structure symbol ‘X’ is not properly exported and reimported

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Merge branch 'master' into releases/Release_2_11_2_Branch

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JAL-3417 groovy script enables per group consensus and sequence logos for all so the sdppred calculation actually has something to work on

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