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JAL-629 change --renderer to --textrenderer to be more specific
[jalview.git]
/
src
/
jalview
/
2023-02-27
James Procter
Merge branch 'develop' into features/JAL-4134_treeviewe...
tree
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commitdiff
2023-02-26
Ben Soares
JAL-629 PAE matrix file guesstimate from filename
tree
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commitdiff
2023-02-24
Ben Soares
JAL-629 Position GUI widgets for PDF file options....
tree
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commitdiff
2023-02-24
James Procter
JAL-629 JAL-4124 JAL-3855 test to check we can import...
tree
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commitdiff
2023-02-24
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-24
Ben Soares
JAL-629 add widgets to StructureChooser for tempfac...
tree
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commitdiff
2023-02-24
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
features/JAL-3858_PAEsInProjects
tree
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commitdiff
2023-02-24
Ben Soares
JAL-629 helper function for getting sensible structure...
tree
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commitdiff
2023-02-24
Ben Soares
JAL-629 Made ArgValuesMap helper class, simplifies...
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 group columns using a tree cut - seems to...
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 - brutal hack to build a tree clustering colum...
tree
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commitdiff
2023-02-23
Ben Soares
JAL-629 bootstrap args and properties. Remember index...
tree
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commitdiff
2023-02-23
Ben Soares
JAL-629 fix a PAEMatrix casting error
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 tidied up refactoring and fix compilation...
tree
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commitdiff
2023-02-23
James Procter
Merge branch 'features/JAL-3858_PAEsInProjects' into...
tree
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commitdiff
2023-02-23
James Procter
JAL-3858 new MatrixType JAX-RI POJO
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 - refactor tree calculation code to work with...
tree
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commitdiff
2023-02-23
James Procter
JAL-4133 update validChar width when font is changed...
tree
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commitdiff
2023-02-22
James Procter
JAL-4133 store/restore alignment view’s charWidth and...
tree
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commitdiff
2023-02-22
James Procter
JAL-3858 persist PAE matrix (only so far) as serialised...
tree
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commitdiff
2023-02-22
James Procter
JAL-3858 construct a PAE direct from float array
tree
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commitdiff
2023-02-22
James Procter
JAL-629 make sure we show GUI when not driven programma...
tree
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commitdiff
2023-02-22
James Procter
JAL-4095 slightly better threshold setting and todos...
tree
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commitdiff
2023-02-22
James Procter
JAL-4095 magic fill behaviour is PAE specific
tree
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commitdiff
2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-02-22
James Procter
JAL-3858 JAL-2381 allow different linear shading scheme...
tree
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commitdiff
2023-02-22
James Procter
JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MAT...
tree
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commitdiff
2023-02-20
Ben Soares
JAL-3416 Turn off (partial) flatlaf scaling for HiDPI...
tree
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commitdiff
2023-02-20
Ben Soares
JAL-4128 Catch RasterFormatException caused whilst...
bug/JAL-4128_resizing_overview_with_solid_drags_causes_exception
tree
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commitdiff
2023-02-20
Ben Soares
Merge branch 'develop' into bug/JAL-4125_flatlaf_quitha...
bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_properly
tree
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commitdiff
2023-02-16
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
tree
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commitdiff
2023-02-16
James Procter
JAL-1713 don’t close an automatically created overview...
tree
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commitdiff
2023-02-13
Ben Soares
Merge branch 'develop' into bug/JAL-4125_flatlaf_quitha...
tree
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commitdiff
2023-02-13
Ben Soares
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
tree
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commitdiff
2023-02-13
Ben Soares
JAL-4125 Move confirmation of closing external viewer...
tree
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commitdiff
2023-02-13
James Procter
Merge branch 'develop' into feature/JAL-1713_overviewIn...
tree
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commitdiff
2023-02-10
James Procter
Fix for JAL-4126 - don’t automatically create a thresho...
tree
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commitdiff
2023-02-09
Ben Soares
JAL-4125 Additions to JvOptionPane and QuitHandler...
tree
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commitdiff
2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
tree
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commitdiff
2023-02-03
James Procter
JAL-1551 remove temp file in src
tree
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commitdiff
2023-02-03
James Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2023-01-31
James Procter
JAL-1713 update from Jalview 2.11.3 develop
tree
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commitdiff
2023-01-30
Ben Soares
JAL-1988 Make sensible choices if only the opening...
merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
tree
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commitdiff
2023-01-26
Ben Soares
JAL-4118 fix a small buglet in BackupFiles exhibited...
tree
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commitdiff
2023-01-26
Ben Soares
JAL-629 adjust arg type for tempfac-shading -- was...
tree
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commitdiff
2023-01-25
James Procter
JAL-4116 relegate the failed to promote warning to...
tree
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commitdiff
2023-01-25
James Procter
Merge branch 'new_feature/JAL-4019_ambiguous_base_colou...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 hacked in --tempfac-shading - hardcoded to...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 suggest not breaking out of the structure proce...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 need to delay call to AlignFile.parse() if...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 don’t carry on Jalview.main if we’ve already...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 don’t trash user’s system property file when...
tree
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commitdiff
2023-01-24
James Procter
JAL-629 don’t complain for Unary args
tree
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commitdiff
2023-01-24
James Procter
JAL-629 labelled breaks are frowned upon by everyone
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
tree
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commitdiff
2023-01-24
James Procter
Merge branch 'develop' (JAL-4102 2.11.2.6 patch release...
features/r2_11_2_alphafold/JAL-2349_JAL-3855
tree
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commitdiff
2023-01-23
Ben Soares
JAL-629 Attempts to add PAE to structure. --headless...
tree
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commitdiff
2023-01-20
Jim Procter
Merge branch 'patch/JAL-4114_updated_3dbeacons_api...
tree
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commitdiff
2023-01-20
Jim Procter
JAL-4114 model_page_url not required in v2.0 response
patch/JAL-4114_updated_3dbeacons_api
tree
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commitdiff
2023-01-20
Jim Procter
Merge branch 'patch/JAL-4114_updated_3dbeacons_api...
tree
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commitdiff
2023-01-20
Jim Procter
Merge branch 'patch/Release_2_11_2_6_Branch' into develop
tree
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commitdiff
2023-01-20
Jim Procter
JAL-2353 primary ref candidates that should be promoted...
patch/Release_2_11_2_6_Branch
tree
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commitdiff
2023-01-20
Jim Procter
JAL-4114 only rank model qualities that are computed...
tree
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commitdiff
2023-01-20
Jim Procter
JAL-4114 alphafold now marked as AB-INITIO so adjust...
tree
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commitdiff
2023-01-20
Jim Procter
JAL-4114 additional warnings when PDBe doesn’t return...
tree
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commitdiff
2023-01-20
Jim Procter
JAL-4114 patch REST client for changed JSON schema...
tree
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commitdiff
2023-01-20
Jim Procter
JAL-4114 formatting
tree
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commitdiff
2023-01-18
Ben Soares
JAL-629 make sequence id key 'seqid'
tree
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commitdiff
2023-01-17
Ben Soares
JAL-3416 No longer needed
tree
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commitdiff
2023-01-17
Ben Soares
Merge branch 'develop' into merge/JAL-1988_JAL-3772...
tree
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commitdiff
2023-01-16
Ben Soares
JAL-3416 More tweaking of FlatLaf. Problem with macOS...
tree
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commitdiff
2023-01-11
Ben Soares
JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as...
tree
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commitdiff
2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
tree
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commitdiff
2023-01-06
Ben Soares
JAL-3416 More explicit setting of FlatLaf macOS theme
tree
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commitdiff
2023-01-06
Ben Soares
JAL-3416 Upgraded FlatLaf to 3.0 and added macOS theme...
tree
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commitdiff
2023-01-06
Ben Soares
JAL-3416 remove a missed panel titlebar icon in TreePanel
tree
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commitdiff
2022-12-19
Ben Soares
JAL-629 Add image output and quit
tree
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commitdiff
2022-12-15
Ben Soares
JAL-629 move SubId to more logical place. Attempt remov...
tree
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commitdiff
2022-12-14
Ben Soares
JAL-629 Open Structure Viewer from cmdline
tree
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commitdiff
2022-12-09
Ben Soares
JAL-629 null check, fixed tests!
tree
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commitdiff
2022-12-08
Ben Soares
JAL-629 fix opening files
tree
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commitdiff
2022-12-08
Ben Soares
JAL-629 stray code deleted
tree
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commitdiff
2022-12-08
Ben Soares
JAL-629 Allow attachment of pAE file to a particular...
tree
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
tree
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commitdiff
2022-11-30
Ben Soares
JAL-4101 Updated DEFAULT_RFAM_BASEURL
tree
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commitdiff
2022-11-30
Jim Procter
JAL-2353 patch for Ensembl refs from uniprot - needs...
tree
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commitdiff
2022-11-29
Ben Soares
JAL-4101 Updated DEFAULT_RFAM_BASEURL
tree
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commitdiff
2022-11-23
Ben Soares
JAL-629 Doing things with the command line arguments
tree
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commitdiff
2022-11-16
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
tree
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commitdiff
2022-11-16
Ben Soares
JAL-3416 make flatlaf default for linux
improvement/JAL-3416_default_to_LIVE_DRAG_MODE_for_flatlaf
tree
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commitdiff
2022-11-16
Ben Soares
JAL-4019 finalised a boolean option and tidied some...
tree
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commitdiff
2022-11-14
Ben Soares
JAL-4019 Make diagnostic message debug level
tree
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commitdiff
2022-11-13
Ben Soares
JAL-4019 small but important corrections to array order...
tree
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commitdiff
2022-11-13
Ben Soares
JAL-4019 improvement to short sequence nucleotide detec...
tree
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commitdiff
2022-11-10
Ben Soares
JAL-4019 Nucleotide Ambiguity Colour Scheme added....
tree
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commitdiff
2022-11-09
Ben Soares
JAL-3416 Add necessary logo to non-internal Frames
tree
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commitdiff
2022-11-09
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
tree
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commitdiff
2022-11-09
Ben Soares
JAL-3416 Add necessary logo to non-internal Frames
tree
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commitdiff
2022-11-09
Ben Soares
Merge branch 'improvement/JAL-3416_default_to_LIVE_DRAG...
tree
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commitdiff
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