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jalview.git
2024-06-21
Jim Procter
JAL-4414 clean up code for handling FileNotFound except...
jims/review_JAL-4409_implement_extra_schemes_in_getdown
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2024-06-21
Jim Procter
Merge remote-tracking branch 'origin/jims/review_JAL...
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2024-06-21
Ben Soares
JAL-4409 Don't merge JVL configs when changing appbase
improvement/JAL-4409_implement_extra_schemes_in_getdown
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2024-06-20
Ben Soares
JAL-4409 Use fixed 'latest' artifact URL
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2024-06-20
Ben Soares
JAL-4409 Changes in BUILD channel appbase to tie in...
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2024-06-07
Ben Soares
Merge branch 'develop' into improvement/JAL-4409_implem...
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2024-06-06
Ben Soares
JAL-4420 Added some more filename extensions
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2024-06-06
Ben Soares
JAL-4072 Add zip-slip check in getdown
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2024-06-06
Jim Procter
Merge branch 'bug/JAL-4421_customise_volume_name_of_DMG...
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2024-06-06
Ben Soares
JAL-4358 Add the JALVIEW: CREATED DESKTOP line to java...
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2024-06-05
Ben Soares
JAL-4420 Allow associated files to be dragged on separa...
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2024-06-05
Ben Soares
JAL-4409 Small refactoring of ArgParserUtils to allow...
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2024-06-05
Jim Procter
JAL-4414 propagate the URL cannot be read error message...
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2024-06-05
Jim Procter
JAL-1551 formatting
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2024-06-05
Jim Procter
JAL-4281 - JAL-4397 - tidy up unused variable. could...
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2024-06-05
Jim Procter
JAL-1054 JAL-1551 formatting and javadoc
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2024-06-05
Jim Procter
JAL-4414 fix logic for local file paths that cannot...
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2024-06-05
Ben Soares
Merge branch 'develop' into bug/JAL-4421_customise_volu...
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2024-06-05
Ben Soares
JAL-4421 Downgrading ds_store to 1.3.0 for build server...
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2024-06-05
Ben Soares
JAL-4421 Configuration for positioning icons in DMG
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2024-06-05
Ben Soares
JAL-4421 Add --appname --appxpos --appypos to position...
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2024-06-04
Ben Soares
JAL-4421 Remove the disk_image_alias from the backgroun...
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2024-06-04
Ben Soares
JAL-4421 Allow JSON config file to be options (no icon...
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2024-06-04
Jim Procter
Merge branch 'improvement/JAL-4409_implement_extra_sche...
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2024-06-04
Jim Procter
JAL-4409 don't ignore gitignore !
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2024-06-04
Jim Procter
JAL-4418 first development release for 2.11.4.0 - relea...
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2024-06-04
Jim Procter
Merge branch 'feature/JAL-4159_pasimap' into develop
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2024-06-04
Jim Procter
Merge branch 'releases/Release_2_11_3_Branch' into...
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2024-06-04
Ben Soares
JAL-4421 Put correct VolumeIcon.icns file onto DMG...
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2024-06-03
Ben Soares
JAL-4421 Icns to use as .VolumeIcon.icns in DMG volumes...
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2024-06-03
Ben Soares
JAL-4421 Also add DMG filename to python script. Necess...
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2024-05-31
Ben Soares
JAL-4421 Add DS_Store customisation to gradle. Add...
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2024-05-31
Ben Soares
JAL-4421 Python script for customising DS_Store. Separ...
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2024-05-29
Ben Soares
JAL-4409 Allow more URI schemes (e.g. file) to be opene...
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2024-05-29
Ben Soares
JAL-4409 Allow more URI schemes (e.g. file) to filter...
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2024-05-29
Ben Soares
JAL-4414 Add SocketTimeoutException to exceptions that...
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2024-05-29
Ben Soares
JAL-3196 Need more memory for the install4j process...
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2024-05-28
Ben Soares
JAL-4409 JAL-4160 Don't let getdown turn jalviewX:...
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2024-05-28
Ben Soares
JAL-4417 Use a specified props file for consistent...
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2024-05-28
Ben Soares
JAL-4409 TEMPORARY don't clean up image files from...
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2024-05-28
Ben Soares
JAL-4409 Ensure the specific scheme jalviewx is only...
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2024-05-28
Ben Soares
JAL-4409 Don't insist on HttpURLConnection, allows...
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2024-05-27
Ben Soares
Merge branch 'develop' into improvement/JAL-4409_implem...
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2024-05-24
Jim Procter
JAL-4159 fix up test for applicable filters for pasimap
feature/JAL-4159_pasimap
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2024-05-24
Jim Procter
JAL-4159 fix PairwiseAlignmentPanelTest - reinstate...
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2024-05-24
Jim Procter
JAL-4159 peek in a Jalview project's PCA viewer's title...
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2024-05-24
Jim Procter
JAL-4257 JAL-4159 JAL-789 tidy up passing of score...
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2024-05-24
James Procter
JAL-789 pairwise alignment via calculations dialog...
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2024-05-24
James Procter
JAL-4366 compute coverage on each side of the pairwise...
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2024-05-24
Jim Procter
Merge branch 'jims/feature/JAL-4159_pasimap' into featu...
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2024-05-24
Jim Procter
Merge branch 'features/JAL-4257_adjustablegapparams_nw...
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2024-05-23
Jim Procter
JAL-4159 fix sense of console/alignment output suppress...
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2024-05-23
Jim Procter
JAL-4159 disable the score model combo box when pasimap...
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2024-05-23
MorellThomas
mend
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2024-05-23
MorellThomas
Fix PaSiMap taking scoreModels input and allow AlignSeq...
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2024-05-23
MorellThomas
Fix PaSiMap not having the eigenvalues saved
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2024-05-22
MorellThomas
revert build.gradle changes
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2024-05-22
MorellThomas
Save PaSiMap with Jalview Session
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2024-05-22
MorellThomas
Rectanuglar selection changed to Mouse Button 3 drag
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2024-05-21
Jim Procter
JAL-4259 set title using original alignment window...
spike/JAL-4159_pasimap_2114_series
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2024-05-21
Jim Procter
JAL-4159 implement bounds for PASIMAP calculation ...
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2024-05-21
Jim Procter
JAL-4159 connectivity should be computed for the sequen...
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2024-05-21
Jim Procter
JAL-4159 PASiMap currently doesn't support different...
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2024-05-21
Jim Procter
JAL-4159 sometimes the progress bar may not be availabl...
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2024-05-21
Ben Soares
JAL-1054 Change one more (unused) url.openStream to...
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2024-05-21
Ben Soares
JAL-1054 Change the rest of the url.openConnection...
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2024-05-21
Ben Soares
JAL-4409 Adjust usage of HttpUtils.equivalentJalviewURL...
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2024-05-21
Ben Soares
JAL-4409 Make HttpUtils.equivalentJalviewUrlString...
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2024-05-21
Jim Procter
Merge branch 'feature/JAL-4159_pasimap' into spike...
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2024-05-21
Jim Procter
JAL-4356 release date for 2.11.3.3 is 22nd May 2025
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2024-05-21
Jim Procter
JAL-4356 release date for 2.11.3.3 is 22nd May 2025
releases/Release_2_11_3_Branch
Release_2_11_3_3
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2024-05-20
Ben Soares
JAL-4409 Also interpret jalviewX:// URIs in Jalview...
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2024-05-20
Ben Soares
JAL-4397 Another fix on linux
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2024-05-17
Ben Soares
JAL-4420 Add some debugging statements
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2024-05-17
Ben Soares
JAL-4420 Tests for new FileUtils methods
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2024-05-17
Ben Soares
JAL-4420 Allow preprocessing of arguments if they are...
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2024-05-17
Ben Soares
JAL-4409 Checking getdown jars up to date
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2024-05-17
Ben Soares
JAL-3409 Add newline back into Buffered Reader in getdo...
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2024-05-17
Ben Soares
JAL-4409 corrected the umount of dmg to hdiutil detach...
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2024-05-16
Ben Soares
JAL-4409 Added remote JVL files for Linux/Windows
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2024-05-16
Ben Soares
JAL-4409 Added multiple file open to getdown. Added...
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2024-05-16
Jim Procter
JAL-4356 release notes for JAL-3978 patch
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2024-05-16
Jim Procter
JAL-4356 release notes for JAL-3978 patch
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2024-05-16
Ben Soares
JAL-3978 Add the bin dir to be copied from website...
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2024-05-16
Jim Procter
Merge branch 'bug/JAL-3978_copy_bin_dir_to_getdownArchi...
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2024-05-16
Ben Soares
JAL-3978 Add the bin dir to be copied from website...
bug/JAL-3978_copy_bin_dir_to_getdownArchiveBuild_task
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2024-05-16
Ben Soares
JAL-4409 Easier full install from source for macOS
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2024-05-16
Ben Soares
JAL-4409 more places to check for jalviewd://
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2024-05-16
Jim Procter
JAL-4418 bump release to 2.11.4.0
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2024-05-16
Jim Procter
Merge branch 'develop' into feature/JAL-4159_pasimap
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2024-05-16
Jim Procter
Merge branch 'feature/JAL-4386_calculate_tree_using_sec...
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2024-05-16
Jim Procter
Merge branch 'develop' into feature/JAL-4386_calculate_...
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2024-05-16
Jim Procter
Merge branch 'develop' into releases/Release_2_11_3_Branch
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2024-05-16
Jim Procter
JAL-4356 bump release date to today, release notes...
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2024-05-15
Ben Soares
JAL-4397 IdWidth tests slightly less restrictive for...
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2024-05-15
Ben Soares
JAL-4409 extra schemes now opening correctly in macos
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2024-05-15
Renia Correya
JAL-4386 Fixed failed test case
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2024-05-15
Jim Procter
Merge branch 'bug/JAL-4416_sview_not_shown_for_local_st...
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2024-05-15
Renia Correya
JAL-4386 Fixed failed test cases
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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
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