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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-3808 example exonerate cdna2genome and coding2genome test data and test

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    ./test_cdna2genome_showquerygff.gff2
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    ./test_cdna2genome_showtargetgff.gff2
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    ./test_coding2genome_showquerygff.gff2
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    ./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

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

JAL-3536 failing test and test data

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

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    ./cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316
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JAL-3171 more complex project test - where sequences were copied from one alignment view into a new alignment and more views created.

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    ./projects/manyViews.jvp
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JAL-3171 failing test for legacy projects and fixing multiple dataset references

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    ./projects/twoViews.jvp
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JAL-3003 different coloured borders in demo annotation file

Update spike branch to latest (HMMSearch file chooser arg)

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Test added for original format

Test added for original format

done

done

added a no-numbers case to the unit test

added a no-numbers case to the unit test

Yes or revert the original (not sure I meant to commit that) for use in roundtrip unit tests and have the bespoke test for the other.

Yes or revert the original (not sure I meant to commit that) for use in roundtrip unit tests and have the bespoke test for the other.

Good question. The test seems to be to distinguish between sequence data lines (don't begin with whitespace) and conservation data lines (do begin with whitespace). So if ClustalO were to output co...

Good question. The test seems to be to distinguish between sequence data lines (don't begin with whitespace) and conservation data lines (do begin with whitespace).
So if ClustalO were to output consensus results with tabs this would fail.
Maybe recode like
boolean isConservation = line.startsWith(SPACE) || line.startsWith(TAB); // or line.matches("^
s.*") suitably tested!
if (!isConservation)

Unknown macro: { // parse sequence data }

else

Unknown macro: { // parse conservation data }
cf earlier comment - this test checks for tab/no tab versions of clustal file with numbers, but doesn't verify original clustal format. we should do both..

cf earlier comment - this test checks for tab/no tab versions of clustal file with numbers, but doesn't verify original clustal format. we should do both..

Possibly worth keeping both examples of Clustal output ?

Possibly worth keeping both examples of Clustal output ?

Seems a bit strange to first check for 0x20 and then have a tokenizer for all whitespace. Can a clustal file line include tabs only ?

Seems a bit strange to first check for 0x20 and then have a tokenizer for all whitespace. Can a clustal file line include tabs only ?

JAL-2997: Improve the Clustal format parser so that it can cope with numbers
JAL-2997: Improve the Clustal format parser so that it can cope with numbers
JAL-2997 handle tab-delimited trailing column number when parsing

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JAL-2944: Allow structures to be opened in a specific structure view
JAL-2944: Allow structures to be opened in a specific structure view
Updated with latest from mchmmer branch

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    ./4IM2_missing.pdb
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    ./4IM2_missing_noid.pdb
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