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Implement MSA, scoring and counting the connections
[jalview.git]
/
src
/
2023-07-22
MorellThomas
Implement MSA, scoring and counting the connections
tree
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commitdiff
2023-07-09
MorellThomas
Copied PCA files to PaSiMap analogues and changed all...
tree
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commitdiff
2023-07-08
MorellThomas
Includes the PaSiMap button in the CalculationChooser
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
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
2022-10-25
Ben Soares
JAL-3416 Making FlatLaF default for macs due to a probl...
tree
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commitdiff
2022-10-11
Jim Procter
JAL-4073 fix PEBCAK failure
tree
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commitdiff
2022-10-06
Jim Procter
stable url for PFAM retrieval via interpro api :) JAL...
tree
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commitdiff
2022-10-06
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2022-10-06
Jim Procter
JAL-4073 Pfam retrieval now works via a template includ...
tree
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commitdiff
2022-10-06
Jim Procter
Patch for JAL-4074 - any content ending in ‘gzip’ recog...
tree
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commitdiff
2022-09-14
Jim Procter
Merge branch 'bug/JAL-3612_overviewFeatureOrdering...
tree
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commitdiff
2022-08-08
Jim Procter
JAL-4046 JAL-3993 imports reformatting
tree
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commitdiff
2022-08-08
Jim Procter
JAL-4046 JAL-3993 patch for 2.11.2.4 release
tree
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commitdiff
2022-08-08
Jim Procter
Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
tree
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commitdiff
2022-08-08
Jim Procter
Merge branch 'improvement/JAL-4014_gecos_colour_schemes...
tree
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commitdiff
2022-08-08
Jim Procter
Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoin...
tree
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commitdiff
2022-08-08
Jim Procter
JAL-4034 show the loading spinner when switching betwee...
tree
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commitdiff
2022-08-08
Jim Procter
Merge branch 'features/JAL-4034_improve_3dbeacons_butto...
tree
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commitdiff
2022-07-25
Ben Soares
JAL-4036 moved a comment block
tree
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commitdiff
2022-07-25
Ben Soares
JAL-4034 button looks better also on other OSes with...
tree
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commitdiff
2022-07-24
Ben Soares
JAL-4034 add round corners to 3DB confirmation button...
tree
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commitdiff
2022-07-22
Ben Soares
JAL-4036 Changes made from code review CR-JAL-265
tree
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commitdiff
2022-07-22
Ben Soares
JAL-4036 Add getDbName to the GFTSPanelI and add an...
tree
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commitdiff
2022-07-22
Ben Soares
JAL-4036 removing the query field code from the dropdow...
tree
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commitdiff
2022-07-21
Ben Soares
JAL-4036 Don't autosearch changing index when autosearc...
tree
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commitdiff
2022-07-21
Ben Soares
JAL-4036 add search fieldname to dropdown list
tree
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commitdiff
2022-07-21
Ben Soares
JAL-4036 New configuration, target and pagination proce...
tree
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commitdiff
2022-07-20
Jim Procter
JAL-4045 - don't apply distribution dependent scale...
tree
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commitdiff
2022-07-15
Ben Soares
JAL-4034 Use the new non-modal JDialog for 3DBeacons...
tree
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commitdiff
2022-07-15
Ben Soares
JAL-4034 Allow request for non-modal JDialog, which...
tree
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commitdiff
2022-07-12
Ben Soares
JAL-4034 change to jalview property name
tree
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commitdiff
2022-07-12
Ben Soares
JAL-4034 showConfirmDialog works for both desktop and...
tree
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commitdiff
2022-07-11
Ben Soares
JAL-4034 Non-blocking 3D Beacons query after warning...
tree
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commitdiff
2022-07-11
Ben Soares
JAL-4034 allow a jalview_property to set the threshold...
tree
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commitdiff
2022-07-04
Jim Procter
JAL-4034 fix #3 change uniprot ref fetch dialog to...
tree
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commitdiff
2022-07-04
Jim Procter
JAL-4034 Fix #2 show an icon and a button to press...
tree
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commitdiff
2022-06-30
Jim Procter
JAL-4036 use the legacy endpoint (and report the FTS...
tree
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commitdiff
2022-06-28
Ben Soares
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
tree
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commitdiff
2022-06-28
Ben Soares
JAL-1988 Don't put Quit in the File menu if there's...
tree
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commitdiff
2022-06-23
Ben Soares
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
tree
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commitdiff
2022-06-23
Ben Soares
JAL-1988 Check for setHandler capability to avoid About...
tree
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commitdiff
2022-06-17
Ben Soares
JAL-3027 Avoid FlatLAF Desktop class is JalviewJS
tree
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commitdiff
2022-06-15
Jim Procter
JAL-1988 JAL-3416 avoid unnecessary static flag
tree
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commitdiff
2022-06-15
Jim Procter
JAL-3418 JAL-1988 don’t need java version check anymore
tree
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commitdiff
2022-06-13
Ben Soares
JAL-1988 Hack to ensure Quit dialog box is moved to...
tree
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commitdiff
2022-06-13
Ben Soares
JAL-1988 Moved APQHandlers to jalview.jbgui and called...
tree
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commitdiff
2022-06-13
Jim Procter
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
tree
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commitdiff
2022-06-13
Ben Soares
JAL-3416 remove flat as default for linux
tree
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commitdiff
2022-06-13
Ben Soares
JAL-1988 JAL-3416 Using the flatlaf-extras About, Prefe...
tree
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commitdiff
2022-06-13
Ben Soares
JAL-3416 Added some mac specific FlatLAF settings....
tree
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commitdiff
2022-06-09
Jim Procter
Merge branch 'bug/JAL-4020_add_pymolwin_paths' into...
tree
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commitdiff
2022-06-09
Jim Procter
JAL-4026 ignore StructureSelectionManager events if...
tree
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commitdiff
2022-06-09
Jim Procter
JAL-4026 update the viewport’s wrapped width after...
tree
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commitdiff
2022-06-08
Jim Procter
Merge branch 'improvement/JAL-4023_snotation_for_trees...
tree
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commitdiff
2022-06-08
Jim Procter
Merge branch 'patch/JAL-4024_jumpScrollHang' into develop
tree
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commitdiff
2022-06-08
Jim Procter
JAL-4024 only render partially when new view overlaps...
patch/JAL-4024_jumpScrollHang
tree
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commitdiff
2022-06-07
Ben Soares
JAL-4020 class formatting
tree
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commitdiff
2022-06-07
Ben Soares
JAL-4020 added the \Scripts\pymol.exe. to the pathList
tree
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commitdiff
2022-06-06
Ben Soares
JAL-4020 Added the +2 arg for PyMOLWin.exe allowing...
tree
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commitdiff
2022-06-06
Ben Soares
JAL-4020 class reformatting
tree
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commitdiff
2022-06-06
Ben Soares
JAL-4020 Added path search for global installation...
tree
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commitdiff
2022-06-06
Jim Procter
JAL-4023 use %g for distances (scientific notation...
improvement/JAL-4023_snotation_for_trees
tree
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commitdiff
2022-06-06
Ben Soares
JAL-4020 Added search for PyMOLWinWithConsole.bat ...
tree
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commitdiff
2022-06-06
Jim Procter
JAL-4023 store distances as doubles
tree
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commitdiff
2022-05-12
Ben Soares
JAL-4014 4 gecos colour schemes added
tree
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commitdiff
2022-04-21
Ben Soares
Merge branch 'develop' into merge/JAL-3978+JAL-3553...
tree
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commitdiff
2022-04-21
Ben Soares
Merge branch 'develop' into task/JAL-3991_check_actual_...
tree
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commitdiff
2022-04-19
Jim Procter
Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into...
tree
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commitdiff
2022-04-18
Jim Procter
JAL-3997 check for tooltip being null before checking...
bug/JAL-3997_NPE_in_wrapped_mode
tree
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commitdiff
2022-04-16
Jim Procter
JAL-3365 expand range of allowed DSSP secondary structu...
tree
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commitdiff
2022-04-06
Ben Soares
JAL-3991 Made info displayed only when needed (Java...
tree
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commitdiff
2022-04-06
Ben Soares
JAL-3991 Added information output about the slightly...
tree
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commitdiff
2022-04-06
Ben Soares
JAL-3991 JAVA_COMPILE_VERSION put into build_properties...
tree
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commitdiff
2022-04-05
Jim Procter
JAL-3981 patch tests and remove errant imports
tree
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commitdiff
2022-04-05
Jim Procter
JAL-3990 gradle spotlessApply
tree
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commitdiff
2022-04-05
Jim Procter
Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_d...
tree
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commitdiff
2022-03-31
Ben Soares
Merge branch 'develop' into improvement/JAL-3978_add_gr...
tree
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commitdiff
2022-03-31
Jim Procter
JAL-3985 formatting
tree
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commitdiff
2022-03-31
Jim Procter
JAL-3985 split PDB id queries into multiple queries...
tree
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commitdiff
2022-03-30
Jim Procter
Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop
tree
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commitdiff
2022-03-30
Jim Procter
JAL-360 JAL-3975 update parent for text colour dialog...
tree
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commitdiff
2022-03-30
Ben Soares
JAL-360 JAL-3975 make AlignFrame the parent of FeatureE...
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3980 JAL-3979 TODOs
bug/JAL-3980_JAL-3981_tooltips_sequence_details
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3980 defensive copy - inefficient but fixes bug
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3981 Additional line breaks - sort of helps
tree
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commitdiff
2022-03-24
Jim Procter
JAL-3981 strategic newlines to help speed up Java's...
tree
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commitdiff
2022-03-23
Jim Procter
JAL-3976 skip entries with null values when analyzing
tree
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commitdiff
2022-03-18
Ben Soares
JAL-3978 Using getdowninstanceappdir and getdowninstanc...
tree
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commitdiff
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