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Merge branch 'develop' into features/JAL-4219_extended_fasta_rna_ss
[jalview.git]
/
src
/
jalview
/
2024-06-06
Jim Procter
Merge branch 'develop' into features/JAL-4219_extended_...
tree
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commitdiff
2024-06-05
Ben Soares
Merge branch 'develop' into bug/JAL-4421_customise_volu...
tree
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commitdiff
2024-06-04
Jim Procter
Merge branch 'improvement/JAL-4409_implement_extra_sche...
tree
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commitdiff
2024-05-29
Ben Soares
JAL-4409 Allow more URI schemes (e.g. file) to be opene...
tree
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commitdiff
2024-05-29
Ben Soares
JAL-4409 Allow more URI schemes (e.g. file) to filter...
tree
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commitdiff
2024-05-29
Ben Soares
JAL-4414 Add SocketTimeoutException to exceptions that...
tree
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commitdiff
2024-05-28
Ben Soares
JAL-4409 JAL-4160 Don't let getdown turn jalviewX:...
tree
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commitdiff
2024-05-28
Ben Soares
JAL-4409 Don't insist on HttpURLConnection, allows...
tree
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commitdiff
2024-05-27
Ben Soares
Merge branch 'develop' into improvement/JAL-4409_implem...
tree
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commitdiff
2024-05-24
Jim Procter
JAL-4159 fix PairwiseAlignmentPanelTest - reinstate...
tree
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commitdiff
2024-05-24
Jim Procter
JAL-4159 peek in a Jalview project's PCA viewer's title...
tree
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commitdiff
2024-05-24
Jim Procter
JAL-4257 JAL-4159 JAL-789 tidy up passing of score...
tree
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commitdiff
2024-05-24
James Procter
JAL-789 pairwise alignment via calculations dialog...
tree
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commitdiff
2024-05-24
James Procter
JAL-4366 compute coverage on each side of the pairwise...
tree
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commitdiff
2024-05-24
Jim Procter
Merge branch 'jims/feature/JAL-4159_pasimap' into featu...
tree
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commitdiff
2024-05-23
Jim Procter
JAL-4159 fix sense of console/alignment output suppress...
tree
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commitdiff
2024-05-23
Jim Procter
JAL-4159 disable the score model combo box when pasimap...
tree
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commitdiff
2024-05-23
MorellThomas
Fix PaSiMap taking scoreModels input and allow AlignSeq...
tree
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commitdiff
2024-05-23
MorellThomas
Fix PaSiMap not having the eigenvalues saved
tree
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commitdiff
2024-05-22
MorellThomas
Save PaSiMap with Jalview Session
tree
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commitdiff
2024-05-22
MorellThomas
Rectanuglar selection changed to Mouse Button 3 drag
tree
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commitdiff
2024-05-21
Jim Procter
JAL-4259 set title using original alignment window...
spike/JAL-4159_pasimap_2114_series
tree
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commitdiff
2024-05-21
Jim Procter
JAL-4159 implement bounds for PASIMAP calculation ...
tree
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commitdiff
2024-05-21
Jim Procter
JAL-4159 connectivity should be computed for the sequen...
tree
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commitdiff
2024-05-21
Jim Procter
JAL-4159 PASiMap currently doesn't support different...
tree
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commitdiff
2024-05-21
Jim Procter
JAL-4159 sometimes the progress bar may not be availabl...
tree
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commitdiff
2024-05-21
Ben Soares
JAL-1054 Change one more (unused) url.openStream to...
tree
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commitdiff
2024-05-21
Ben Soares
JAL-1054 Change the rest of the url.openConnection...
tree
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commitdiff
2024-05-21
Ben Soares
JAL-4409 Make HttpUtils.equivalentJalviewUrlString...
tree
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commitdiff
2024-05-21
Jim Procter
Merge branch 'feature/JAL-4159_pasimap' into spike...
tree
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commitdiff
2024-05-20
Ben Soares
JAL-4409 Also interpret jalviewX:// URIs in Jalview...
tree
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commitdiff
2024-05-17
Ben Soares
JAL-4420 Add some debugging statements
tree
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commitdiff
2024-05-17
Ben Soares
JAL-4420 Allow preprocessing of arguments if they are...
tree
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commitdiff
2024-05-16
Jim Procter
Merge branch 'develop' into feature/JAL-4159_pasimap
tree
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commitdiff
2024-05-16
Jim Procter
Merge branch 'develop' into feature/JAL-4386_calculate_...
tree
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commitdiff
2024-05-15
Jim Procter
JAL-4416 TODO for fixing JAL-4415 JAL-3124 - need a...
bug/JAL-4416_sview_not_shown_for_local_strucfile
tree
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commitdiff
2024-05-15
Jim Procter
JAL-4416 ensure the structure view is shown and any...
tree
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commitdiff
2024-05-15
Jim Procter
JAL-4416 make sure the structure viewer is actually...
tree
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commitdiff
2024-05-15
Renia Correya
JAL-4386 Added preferences for secondary structure...
tree
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commitdiff
2024-05-15
Ben Soares
JAL-4409 Refactoring to allow easier reuse of classes...
tree
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commitdiff
2024-05-15
Jim Procter
Merge branch 'bug/JAL-4407_no_sec_str_from_draganddrop_...
tree
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commitdiff
2024-05-15
Renia Correya
JAL-4386 - Implementation of retrieving secondary structure
tree
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commitdiff
2024-05-14
Ben Soares
JAL-1054 Also recognise UnknownHostException as a file...
tree
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commitdiff
2024-05-14
Ben Soares
Merge branch 'bug/JAL-4397_failing_idWidth_tests' into...
tree
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commitdiff
2024-05-14
Ben Soares
Merge branch 'develop' into bug/JAL-4397_failing_idWidt...
bug/JAL-4397_failing_idWidth_tests
tree
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commitdiff
2024-05-14
Ben Soares
JAL-4414 Add a FileNotFoundException when identifying...
tree
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commitdiff
2024-05-13
Ben Soares
JAL-1054 Fix wrappers for following http->https redirects
tree
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commitdiff
2024-05-13
Jim Procter
JAL-518 better test coverage and support for case prese...
features/JAL-518_justify_seqs_in_region
tree
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commitdiff
2024-05-13
Ben Soares
JAL-1054 Add wrappers for URL.openConnection(), URL...
tree
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commitdiff
2024-05-13
Jim Procter
Merge branch 'develop' into features/JAL-518_justify_se...
tree
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commitdiff
2024-05-13
Renia Correya
Merge branch 'feature/JAL-4386_calculate_tree_using_sec...
tree
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commitdiff
2024-05-13
Renia Correya
JAL-4386 - Implementation of substitution matrix and...
tree
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commitdiff
2024-05-10
Jim Procter
JAL-4411 fix typo :(
tree
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commitdiff
2024-05-10
Jim Procter
JAL-4411 store class of provider in PDBEntry
tree
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commitdiff
2024-05-01
Renia Correya
Merge remote-tracking branch 'origin/bug/JAL-4407_no_se...
tree
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commitdiff
2024-05-01
Jim Procter
JAL-4407 don't transfer 'local' settings - leave as...
bug/JAL-4407_no_sec_str_from_draganddrop_to_msa
tree
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commitdiff
2024-04-30
Renia Correya
JAL-4392 Merging consensus secondary structure
tree
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commitdiff
2024-04-30
Renia Correya
JAL-4386 Comparing secondary structure similarity direc...
tree
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commitdiff
2024-04-26
Renia Correya
JAL-4386 Drop down for secondary structure sources...
tree
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commitdiff
2024-04-24
Renia Correya
JAL-4386 PCA/Tree Calculation for Secondary Structures...
tree
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commitdiff
2024-04-18
Ben Soares
JAL-4397 fixed testresetIdWidth() test on macos
tree
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commitdiff
2024-04-18
MorellThomas
Merge branch 'test/progressBar' into feature/JAL-4159_p...
tree
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commitdiff
2024-04-18
MorellThomas
Implemented ProgressBar for PaSiMap
tree
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commitdiff
2024-04-16
Renia Correya
JAL-4386 Calculate tree using secondary structure annot...
tree
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commitdiff
2024-04-12
MorellThomas
inlcude progress
tree
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commitdiff
2024-04-09
James Procter
JAL-4390 don't output alignment to text panel and stdou...
tree
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commitdiff
2024-03-15
MorellThomas
Fix output of all dimensions
tree
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commitdiff
2024-03-15
MorellThomas
Alogirthm working, but still giving slightly off results
tree
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commitdiff
2024-03-13
Renia Correya
JAL-4386_Added changes in similarity score calculation...
tree
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commitdiff
2024-03-08
Renia Correya
JAL-4386 Added further checks for sequences that have...
tree
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commitdiff
2024-03-08
Renia Correya
JAL-4386 Calculate tree using secondary structure annot...
tree
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commitdiff
2024-03-07
MorellThomas
Inlcude 8 dimensions
tree
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commitdiff
2024-03-06
MorellThomas
Fix PaSiMap on selected sequences
tree
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commitdiff
2024-03-06
MorellThomas
Test version to switch branches
tree
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commitdiff
2024-01-31
MorellThomas
Fix output points column labels
tree
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commitdiff
2024-01-23
James Procter
Merge branch 'develop' into bug/JAL-4290_headless_align...
tree
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commitdiff
2024-01-23
Ben Soares
JAL-4367 Limit right and top adjustments
tree
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commitdiff
2024-01-23
Ben Soares
JAL-4290 Fix image comparison between gui and headless...
tree
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commitdiff
2024-01-23
James Procter
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2024-01-23
James Procter
JAL-4369 invokeAndWait to avoid hang whilst calling...
tree
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commitdiff
2024-01-23
James Procter
JAL-4369 uniprotkb - try to avoid another redirect...
tree
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commitdiff
2024-01-23
James Procter
JAL-4369 use rest.uniprot.org as fetch domain
tree
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commitdiff
2024-01-23
James Procter
Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignor...
tree
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commitdiff
2024-01-19
Ben Soares
JAL-4373 Setting the jvmmempc and jvmmemmax strings...
bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch
tree
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commitdiff
2024-01-10
MorellThomas
Fixed PaSiMap output columns
tree
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commitdiff
2024-01-05
Ben Soares
JAL-4368 Only set a colour scheme if --colour is given...
bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately
tree
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commitdiff
2023-12-19
Ben Soares
JAL-4290 Fixed one test
tree
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commitdiff
2023-12-18
Ben Soares
JAL-4290 incorrect usage of main()
tree
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commitdiff
2023-12-15
Ben Soares
JAL-4290 Add method to allow for specific settings...
tree
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commitdiff
2023-12-15
Ben Soares
JAL-4290 Set structureSelectionManager settings more...
tree
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commitdiff
2023-12-15
Ben Soares
JAL-4290 Move some annotation visibility settings to...
tree
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commitdiff
2023-12-14
James Procter
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2023-12-14
James Procter
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2023-12-14
James Procter
Merge branch 'develop' into bug/JAL-2934proportionalScr...
bug/JAL-2934proportionalScrolling
tree
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commitdiff
2023-12-12
James Procter
JAL-4217 don’t try and export an image when Jmol is...
tree
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commitdiff
2023-12-12
Ben Soares
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2023-12-12
James Procter
Merge branch 'develop' into bug/JAL-4353_cannot_output_...
tree
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commitdiff
2023-12-12
James Procter
JAL-4217 close internal frame on the swing thread to...
tree
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commitdiff
2023-12-12
Ben Soares
JAL-4353 helper method and test for primary/secondary...
tree
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commitdiff
2023-12-12
James Procter
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
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