Build: #2 was successful Child of JB-GDB601-3
Code commits
Jalview Git
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Gitlab User 360177d2c0f4550de2be90b5f9536b991123e16f
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_4_0
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Ben Soares <b.soares@dundee.ac.uk> 68d58f205b96505c393bcf699db43dd586901233 m
JAL-4059 Updates to SwingJS and JmolJS
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Ben Soares <b.soares@dundee.ac.uk> 9ba4d4c0690650d114a7a772b902596f05daaa46 m
JAL-4059 JAL-4395 Updated closure-compiler. Added local_eclipse.properties for buildship
- .gitignore (version 9ba4d4c0690650d114a7a772b902596f05daaa46) (diffs)
- build.gradle (version 9ba4d4c0690650d114a7a772b902596f05daaa46) (diffs)
- gradle.properties (version 9ba4d4c0690650d114a7a772b902596f05daaa46) (diffs)
- tools/closure-compiler-v20230802.jar (version 9ba4d4c0690650d114a7a772b902596f05daaa46) (diffs)
- tools/closure-compiler-v20240317.jar (version 9ba4d4c0690650d114a7a772b902596f05daaa46) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> e41cdfd54ec09b75d7e26634c80215f8c7218a4f m
JAL-4059 Big improvements to jalviewjsProjectImport dependencies avoiding more unnecessary jalviewjsTranspiles
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Ben Soares <b.soares@dundee.ac.uk> 1674450cf970246a39009738cf913f633ee054c9 m
JAL-4059 Fixed Copy tasks merging site
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Ben Soares <b.soares@dundee.ac.uk> 625e3bca28ba06f4846f32e40bd34d06c045a878 m
JAL-4059 Fix jalviewjsLaunchTest for non-macos
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Ben Soares <b.soares@dundee.ac.uk> d4a6419783a9317edc0244fc867a5b5b23e50f1f m
JAL-4059 Fixed macOS timeoutscheduler and revert to --timeout for other OSes
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Ben Soares <b.soares@dundee.ac.uk> d886b22d795650c23c42dc94dabe9b29e8a9ad6f m
Merge branch 'bug/JAL-4375_annotation_not_redrawn_correctly_when_scrolling_left-right_via_trackpad_in_wrap_mode' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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Ben Soares <b.soares@dundee.ac.uk> 2cb06b103be32e40c74a0510789ea073adc73ca3 m
JAL-4380 Improved annotation tooltips especially secondary structure tooltips
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Ben Soares <b.soares@dundee.ac.uk> 0452a278049b8f71b7b7f1162cc3b9defe821ec1 m
JAL-4059 Updated SwingJS, JmolJS libraries
- build.gradle (version 0452a278049b8f71b7b7f1162cc3b9defe821ec1) (diffs)
- swingjs/SwingJS-site.zip (version 0452a278049b8f71b7b7f1162cc3b9defe821ec1) (diffs)
- swingjs/timestamp (version 0452a278049b8f71b7b7f1162cc3b9defe821ec1) (diffs)
- swingjs/ver/5.0.1/SwingJS-site.zip (version 0452a278049b8f71b7b7f1162cc3b9defe821ec1) (diffs)
- swingjs/ver/5.0.1/timestamp (version 0452a278049b8f71b7b7f1162cc3b9defe821ec1) (diffs)
- utils/jalviewjs/libjs/Jmol-SwingJS.zip (version 0452a278049b8f71b7b7f1162cc3b9defe821ec1) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> b2f01633bbdd3b0ca0de292314ab64a90b3ffaa6 m
JAL-4059 minor CSS fix
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Ben Soares <b.soares@dundee.ac.uk> 88b4327a871a9c732f9c5e94854bf8957fac905f m
Merge branch 'bug/JAL-4375_annotation_not_redrawn_correctly_when_scrolling_left-right_via_trackpad_in_wrap_mode' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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Ben Soares <b.soares@dundee.ac.uk> 32f5ed52602d35e1e2e218f06e7fa15094b032e9 m
JAL-4059 Updated SwingJS and JSmol (March 2024). Fix gradle to spot new SwingJS zip.
- build.gradle (version 32f5ed52602d35e1e2e218f06e7fa15094b032e9) (diffs)
- swingjs/SwingJS-site.zip (version 32f5ed52602d35e1e2e218f06e7fa15094b032e9) (diffs)
- swingjs/j2s.core.jar (version 32f5ed52602d35e1e2e218f06e7fa15094b032e9) (diffs)
- swingjs/timestamp (version 32f5ed52602d35e1e2e218f06e7fa15094b032e9) (diffs)
- swingjs/ver/5.0.1/SwingJS-site.zip (version 32f5ed52602d35e1e2e218f06e7fa15094b032e9) (diffs)
- swingjs/ver/5.0.1/timestamp (version 32f5ed52602d35e1e2e218f06e7fa15094b032e9) (diffs)
- utils/jalviewjs/libjs/Jmol-SwingJS.zip (version 32f5ed52602d35e1e2e218f06e7fa15094b032e9) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 80d58b8bdf6ca4cc38af10df2fcc9c05eb21dd00 m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> 19aa434e7ce0085dcb4f04173df53efa506533ae m
JAL-4320 Improve the inputs and outputs dependencies of jalviewjs build tasks
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Ben Soares <b.soares@dundee.ac.uk> 6ecb175edd7217d71160b3200819122e2595fd42 m
JAL-3225 Force gradle version in eclipse settings
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Ben Soares <b.soares@dundee.ac.uk> 068a88824face3da5b919d0abb47a59182989040 m
JAL-4381 Plausibly better division of line segment -- looks much better in SVG. Tidy of other methods.
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Ben Soares <b.soares@dundee.ac.uk> 4659f18e15f271145ade37cad2663e1335d32ace m
JAL-4381 For lineGraph line segments that should be one colour at one end and another colour at the other, only colour one half the line one colour and the other half of the line the other colour. For best results this is achieved through drawing the line twice but clipped one side and then the other.
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Ben Soares <b.soares@dundee.ac.uk> 2e94aeda7ce355d981651b76f42f43c8fb89ec7a m
JAL-4375 JAL-4381 Removal of AnnotationColouring and associated code
- src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouring.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouringI.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouringPLDDT.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouringRanges.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
- src/jalview/datamodel/annotations/AnnotationRowBuilder.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
- src/jalview/renderer/AnnotationRenderer.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
- src/jalview/datamodel/Annotation.java (version 2e94aeda7ce355d981651b76f42f43c8fb89ec7a) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> ae8edbda04dc4fabab67c71fe65c4b091b4b8073 m
JAL-4380 Added information to annotation tooltips when description is not present
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Ben Soares <b.soares@dundee.ac.uk> efd301320c3bd89d126980f661e4a7dbfca8bbfe m
JAL-4375 Add an AnnotationColouringI interface, and generic AnnotationColouringRanges to calculate changing colours between two values and specific AnnotationColouringPLDDT. Linegraph annotations can use this to drawSegmentedLine -- a line drawn multiple times clipped to different ranges in different colours. Calculations are cached.
- src/jalview/datamodel/Annotation.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
- src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouring.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouringI.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouringPLDDT.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
- src/jalview/datamodel/annotations/AnnotationColouringRanges.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
- src/jalview/datamodel/annotations/AnnotationRowBuilder.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
- src/jalview/renderer/AnnotationRenderer.java (version efd301320c3bd89d126980f661e4a7dbfca8bbfe) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> bfc58576f8b1bc505fbd27e5b573f26acd0f75b8 m
JAL-4375 Pass through a flag to AnnotationRenderer.drawComponent(...) so it knows when a full width render is required, adjusting the g2dCopy.setClip(...) width accordingly
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Ben Soares <b.soares@dundee.ac.uk> ab786bf36d2ffe1286c8b7e7802d7b9796b78f5d m
JAL-4375 This extra clip isn't necessary
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Ben Soares <b.soares@dundee.ac.uk> c8d59bf9932d6d54bd9d01d1569c7be8b186a1d6 m
JAL-4375 Clipped label text in annotations to annotation rectangle. Added property to change text antialias method. Changed translation/scaling of Graphics2D object more robust with a copy of the object.
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Ben Soares <b.soares@dundee.ac.uk> 0a20590a673993f11b664bf9d6747d1360ee54b5 m
JAL-4375 I don't think turning off antialiasing is necessary and possibly not appropriate
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Ben Soares <b.soares@dundee.ac.uk> 8b5ae15a094b5a90238bfe39ce10310ed92184d1 m
JAL-4375 Single width pixel artifacts appearing for PAE annotation now fixed for drawLine method. AnnotationRowRendererI adjusted to pass isVectorRendering boolean to ensure correct method to draw the matrix blocks in vector graphic export.
- src/jalview/renderer/AnnotationRenderer.java (version 8b5ae15a094b5a90238bfe39ce10310ed92184d1) (diffs)
- src/jalview/renderer/ContactMapRenderer.java (version 8b5ae15a094b5a90238bfe39ce10310ed92184d1) (diffs)
- src/jalview/renderer/api/AnnotationRowRendererI.java (version 8b5ae15a094b5a90238bfe39ce10310ed92184d1) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> cc90bba10bcf8748d174520f9aecac80a2ff4550 m
JAL-4375 fix typo in property name
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Ben Soares <b.soares@dundee.ac.uk> ad0b88e1b80d4b6b6dcb3448ec98e62aa0109149 m
JAL-4375 Improved trackpad user experience for wrapped format, with vertical scrolling thresholds for mousewheel/tackpad rotation and time-since-last-left-right-rotation reducing accidental up/down scrolls whilst using trackpad to scroll left/right. Thresholds can be adjusted in properties file.
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Ben Soares <b.soares@dundee.ac.uk> a0ccef9cc78fffa7be85f3b658a5768958a301ce m
JAL-4375 More consistent calculation for dashed threshold line
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Ben Soares <b.soares@dundee.ac.uk> 60cc481239cf33d711931d489a215185474e69a1 m
JAL-4375 Different way of getting mouse wheel movement for cross-platform (testing on macos and linux) sensitivity
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Ben Soares <b.soares@dundee.ac.uk> 98465614d8876f07bc43d8d5536feae8648b8ed9 m
JAL-4375 Fix big sideways scroll from trackpad at beginning and end of visible alignment.
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Ben Soares <b.soares@dundee.ac.uk> 27b122992f912988150a8c0fc1319f366d8d49ba m
JAL-4375 Fixed sensitivity of new more responsive left-right side scrolling
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Ben Soares <b.soares@dundee.ac.uk> b06a31dd0a0c0b187ef76ed44f59fd81c8c2f982 m
JAL-4375 Fixed the following when trackpad side-scrolling in wrap format: line-graph edge artifacts, ss sheet arrowhead artifact, boundary line overdraws, threshold dashed line overlay draws. Added half-line segments at both ends of line graph when neighbouring value exists, this applies to non-wrap format too.
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Ben Soares <b.soares@dundee.ac.uk> 5967236c2cc49ccc2ea8638caae778c17c41470e m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> 3e6ef3be69b763dcf917e2528be9c780fd1aec43 m
Merge branch 'bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> 1987cc04f6d1a002a3848b8e27ca4b65afcfd8a1 m
Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error
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Ben Soares <b.soares@dundee.ac.uk> 4a28fee3e0c129a01268d26e1396b045bd893fb8 m
Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail_on_eclipse_error
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Ben Soares <b.soares@dundee.ac.uk> 511db6ba69ae841f0a84188e3790476f7f842f82 m
JAL-4328 Example html 'form' launch in examples.html
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Ben Soares <b.soares@dundee.ac.uk> 50f7ec9ae3c5859e388f45e18ce4bcd75024a5eb m
JAL-4238 Marked where JalviewJS is hanging on 3DBeacons search.
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Ben Soares <b.soares@dundee.ac.uk> 3e912e689b988d1c8fe85f87a9374d7f7a40dbae m
JAL-4059 Added some more Platform.addJ2SDirectDatabaseCall web service URLs in static blocks in appropriate classes. Altered addJ2SDirectDatabaseCall to only add scheme://host:port and not path.
- src/jalview/ext/ensembl/EnsemblRestClient.java (version 3e912e689b988d1c8fe85f87a9374d7f7a40dbae) (diffs)
- src/jalview/fts/service/pdb/PDBFTSRestClient.java (version 3e912e689b988d1c8fe85f87a9374d7f7a40dbae) (diffs)
- src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java (version 3e912e689b988d1c8fe85f87a9374d7f7a40dbae) (diffs)
- src/jalview/util/Platform.java (version 3e912e689b988d1c8fe85f87a9374d7f7a40dbae) (diffs)
- src/jalview/ws/dbsources/TDBeacons.java (version 3e912e689b988d1c8fe85f87a9374d7f7a40dbae) (diffs)
- src/jalview/ws/dbsources/Uniprot.java (version 3e912e689b988d1c8fe85f87a9374d7f7a40dbae) (diffs)
- src/jalview/ws/ebi/EBIFetchClient.java (version 3e912e689b988d1c8fe85f87a9374d7f7a40dbae) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 5420b4add405969ebdff3959c203803783e21239 m
JAL-4328 Move the examples links to a sensible place. Add pae-example.jvp
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Ben Soares <b.soares@dundee.ac.uk> 831463516b5ae5c22a72a27194a57132ae73579e m
JAL-4059 Only run this once
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Ben Soares <b.soares@dundee.ac.uk> 736e66a7300ef13cb52dd643c9d22acb2ddc2bc7 m
JAL-4059 Use namespaced query parameters in preference to Info.args. Report what's being used.
- src/jalview/util/JalviewJSUtil.java (version 736e66a7300ef13cb52dd643c9d22acb2ddc2bc7) (diffs)
- utils/jalviewjs/site-resources/index.html (version 736e66a7300ef13cb52dd643c9d22acb2ddc2bc7) (diffs)
- utils/jalviewjs/site-resources/jalviewjs.html (version 736e66a7300ef13cb52dd643c9d22acb2ddc2bc7) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 58e9dd6622603ddbc8266912074689c3e0fcffbc m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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James Procter <j.procter@dundee.ac.uk> 38830e2f08245fe25064eb1c96869db51c5122ef m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> 9ed332c40312fc75fb64953066591f9c311c7907 m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> 740420bb36f9013a6e534787861589f072a661d2 m
JAL-4059 Improvement to launch indicator
- src/jalview/util/JalviewJSUtil.java (version 740420bb36f9013a6e534787861589f072a661d2) (diffs)
- utils/jalviewjs/site-resources/index.html (version 740420bb36f9013a6e534787861589f072a661d2) (diffs)
- utils/jalviewjs/site-resources/jalviewjs-core.html (version 740420bb36f9013a6e534787861589f072a661d2) (diffs)
- utils/jalviewjs/site-resources/jalviewjs.html (version 740420bb36f9013a6e534787861589f072a661d2) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27 m
JAL-4059 Updated swingjs and removed spare library .zip
- swingjs/SwingJS-site-3.1.1.zip (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
- swingjs/SwingJS-site-5.0.1.zip (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
- swingjs/SwingJS-site.zip (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
- swingjs/j2s.core.jar (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
- swingjs/timestamp (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
- swingjs/ver/5.0.1/SwingJS-site.zip (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
- swingjs/ver/5.0.1/timestamp (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
- utils/jalviewjs/libjs/Jmol-j2s-site.zip (version 806d0cb996bfb3fcb77caf5b6df20c4f97b41c27) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> 53f1b23374382066b9eb31e4850ffe5e9a1e408d m
JAL-4059 Attempts to set JalviewJS desktop geometry from Info hash
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Ben Soares <b.soares@dundee.ac.uk> 8881839853584ea4181e4f1600d5cb7b4da89bec m
JAL-4059 rename files from jsmol j2s zip from jsmol to swingjs
- build.gradle (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- swingjs/SwingJS-site-3.1.1.zip (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- swingjs/SwingJS-site-5.0.1.zip (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- swingjs/SwingJS-site.zip (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- swingjs/j2s.core.jar (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- swingjs/timestamp (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- swingjs/ver/5.0.1/timestamp (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- utils/jalviewjs/libjs/Jmol-SwingJS-16.1.40.zip (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- utils/jalviewjs/libjs/Jmol-SwingJS.zip (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- utils/jalviewjs/libjs/Jmol-j2s-site.zip (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-namespace.html (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_JalviewJS-corenamespace.html (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- utils/jalviewjs/site-resources/jalviewjs-core.html (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
- utils/jalviewjs/site-resources/jalviewjs.html (version 8881839853584ea4181e4f1600d5cb7b4da89bec) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> a7f3bd6355207ff46083e656badb6d9b073384f7 m
Merge branch 'bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square-FIXED_from_develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> d40eec66396ecc2590d76e24110d94da5e59f6c9 m
JAL-4059 Fixed a test for adding jalview.bin.JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> a6f547cb0d915cfaa5ae468428aef54c510c987c m
Merge branch 'bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS' into bug/JAL-4344_structureimage_cl_arg_only_creating_background_colour_square
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Ben Soares <b.soares@dundee.ac.uk> 54ac8fefd93757ecc1f69a91032381bea3cdabe7 m
JAL-4344 Some fixes of waiting blocks, and headless mode for export. Control logging of Jmol.
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Ben Soares <b.soares@dundee.ac.uk> fc10d42ea93d8c41a0a3a668074b1303d051f744 m
JAL-4238 minor errors fixed for JalviewJS structure colouring
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Ben Soares <b.soares@dundee.ac.uk> 0664ff257cacf018e31bf1b1b15753b28800e4f0 m
JAL-4059 Allow form-created querystring style values for boolean values
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Ben Soares <b.soares@dundee.ac.uk> c07cdd787ce23af4e965103256b22b23233c8d8c m
JAL-4059 Storing important thisApplet information in java. Some CSS loading indicators.
- src/jalview/gui/Desktop.java (version c07cdd787ce23af4e965103256b22b23233c8d8c) (diffs)
- src/jalview/util/JalviewJSUtil.java (version c07cdd787ce23af4e965103256b22b23233c8d8c) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-namespace.html (version c07cdd787ce23af4e965103256b22b23233c8d8c) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_JalviewJS-corenamespace.html (version c07cdd787ce23af4e965103256b22b23233c8d8c) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 487504e783d9292c8fad2813051ff7337eb47a0a m
JAL-4059 Made jalview.bin.JalviewJS to use new command-line args in querystring. See jalview_bin_JalviewJS-corenamespace.html for example.
- src/jalview/bin/Jalview.java (version 487504e783d9292c8fad2813051ff7337eb47a0a) (diffs)
- src/jalview/bin/JalviewJS.java (version 487504e783d9292c8fad2813051ff7337eb47a0a) (diffs)
- src/jalview/gui/Desktop.java (version 487504e783d9292c8fad2813051ff7337eb47a0a) (diffs)
- src/jalview/util/JalviewJSUtil.java (version 487504e783d9292c8fad2813051ff7337eb47a0a) (diffs)
- src/jalview/util/Platform.java (version 487504e783d9292c8fad2813051ff7337eb47a0a) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-corenamespace.html (version 487504e783d9292c8fad2813051ff7337eb47a0a) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_JalviewJS-corenamespace.html (version 487504e783d9292c8fad2813051ff7337eb47a0a) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> d4a298ce1c2227e2789da6cd6a1c2680ea4602eb m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> 5741a86e2baec7b85500f885419f32763a0bfd91 m
JAL-4059 rename vars to j2s_ this and that for clarity
- src/jalview/bin/Jalview.java (version 5741a86e2baec7b85500f885419f32763a0bfd91) (diffs)
- src/jalview/gui/Desktop.java (version 5741a86e2baec7b85500f885419f32763a0bfd91) (diffs)
- src/jalview/util/Platform.java (version 5741a86e2baec7b85500f885419f32763a0bfd91) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-corenamespace.html (version 5741a86e2baec7b85500f885419f32763a0bfd91) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-namespace.html (version 5741a86e2baec7b85500f885419f32763a0bfd91) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30 m
JAL-4059 Send bespoke Info hash parameters into jalview.bin.Jalview instance. Set 'splash' div exemplified in jalview_bin_Jalview-namespace.html. Add to core_jalview classlist.
- src/jalview/bin/Jalview.java (version 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30) (diffs)
- src/jalview/gui/Desktop.java (version 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30) (diffs)
- src/jalview/util/Platform.java (version 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30) (diffs)
- utils/jalviewjs/_j2sclasslist.txt (version 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30) (diffs)
- utils/jalviewjs/site-resources/images/jalview_logo_small.svg (version 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-corenamespace.html (version 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-namespace.html (version 4d5326a24a5d1a5ec45dffbfaf9cb2f63ca14a30) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 3cfc2d54b6d58df484be2dab494e09341c783d86 m
JAL-4238 an attempt to set JalviewJS desktop overflow to visible (not working)
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Ben Soares <b.soares@dundee.ac.uk> bf345c991a2b5403a0b53a31a55186b79f54808e m
JAL-4238 Changing visibility of locateInRange(int) bizarrely fixes a PAE viewing problem
-
Ben Soares <b.soares@dundee.ac.uk> 94ebe04bb31c86a385f72cd98fc1c127fa245fe4 m
JAL-4238 example file added to exmaples
-
Ben Soares <b.soares@dundee.ac.uk> 5d7f47edb99cb1bc3f9928e213a5b8b3adec6f1f m
JAL-4238 test files for PAE in jalviewjs
- utils/jalviewjs/site-resources/examples/pae-example.jvp (version 5d7f47edb99cb1bc3f9928e213a5b8b3adec6f1f) (diffs)
- utils/jalviewjs/site-resources/favicon.svg (version 5d7f47edb99cb1bc3f9928e213a5b8b3adec6f1f) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-namespace.html (version 5d7f47edb99cb1bc3f9928e213a5b8b3adec6f1f) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 7327c96c4f91dbe854759eb89a9088660944d402 m
JAL-4059 updated swingjs, Jmol-SwingJS.zip. Insignificantly altered build.gradle.
- build.gradle (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/j2s.core.jar (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/timestamp (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/ver/5.0.1/DEV_NOTES.txt (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/ver/5.0.1/Jmol-j2s-site.zip (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/ver/5.0.1/SwingJS-site.zip (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/ver/5.0.1/_j2sclasslist.txt (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/ver/5.0.1/differences.txt (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/ver/5.0.1/j2s.core.jar (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- swingjs/ver/5.0.1/timestamp (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- utils/jalviewjs/libjs/Jmol-SwingJS-16.1.40.zip (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
- utils/jalviewjs/libjs/Jmol-SwingJS.zip (version 7327c96c4f91dbe854759eb89a9088660944d402) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 00e3cf6993daba7e310af0bf75b4a64ba900f837 m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
-
Ben Soares <b.soares@dundee.ac.uk> cd96215b471f122ef03946d5683055332fa5a5b8 m
JAL-4238 ignore thread.sleeps in jalviewjs. Added a simple PAE example file.
-
Ben Soares <b.soares@dundee.ac.uk> 40d5a4dc2ed11b764836f3e4ede547a8ab8d3734 m
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
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Ben Soares <b.soares@dundee.ac.uk> 91fa082915888af61323703157e66347ed4067df m
JAL-4059 Revert libjs/MiGLayout as new miglayout transpile of 4.0 includes reference to java.beans.Beans which is not in swingjs. Settle on miglayout-4.2 jars.
- j11lib/miglayout-core-4.2.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- j11lib/miglayout-core-4.3-20121116.151612-3.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- j11lib/miglayout-swing-4.2.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- j11lib/miglayout-swing-4.3-20121116.151626-3.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- j8lib/miglayout-core-4.2.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- j8lib/miglayout-core-4.3-20121116.151612-3.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- j8lib/miglayout-swing-4.2.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- j8lib/miglayout-swing-4.3-20121116.151626-3.jar (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- utils/jalviewjs/libjs/MiGLayout-site.zip (version 91fa082915888af61323703157e66347ed4067df) (diffs)
- utils/jalviewjs/libjs/miglayout-core+swing-4.3-20121116.151612-3-site.zip (version 91fa082915888af61323703157e66347ed4067df) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> b19259b093196e2e3cc4796b6bfd60e45a9c40a8 m
Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
-
Ben Soares <b.soares@dundee.ac.uk> 065fef732147eadd0453d4dbb9b8081ad4a1d301 m
JAL-3836 Allow .ext.gz files to be recognised in the File Chooser if .ext is a recognised extension.
-
Ben Soares <b.soares@dundee.ac.uk> 2a9cd59afcaea81b72b7974a49ac9007c7faae04 m
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS
-
Ben Soares <b.soares@dundee.ac.uk> 29c562e835cc4e57ae4db15d643e62bab3b9468a m
JAL-4059 update intervalstore-1.2-site.zip transpiled with new j2s
-
Ben Soares <b.soares@dundee.ac.uk> fd746a963fe4742963c8bd898b03b6fb3af275cb m
Merge branch 'feature/JAL-3576intervalStore_1_2' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
-
Ben Soares <b.soares@dundee.ac.uk> 6aa776576a3976152872559d14d10385c6688253 m
JAL-4238 examples files for PAE
-
Ben Soares <b.soares@dundee.ac.uk> 410ef7be11683f0c2d797baa739e35b24fa40c1f m
JAL-4059 added test for <br/> break
-
Ben Soares <b.soares@dundee.ac.uk> 3a3a33716cc894b89ebdb5d965c20217d4ba9f77 m
Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' of https://source.jalview.org/git/jalview into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
-
Ben Soares <b.soares@dundee.ac.uk> d568795722af14d4cee9f2b155132a0f8b2d96ec m
JAL-4059 fix other PopupMenuTest
-
James Procter <j.procter@dundee.ac.uk> 78e5bd1e976a04afa6af36ba268866d11dc2f6c1 m
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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Ben Soares <b.soares@dundee.ac.uk> 3f5ab31c01cbf2e89b54144d7b6f94eaa1ba018a m
JAL-4059 revert to intervalstore 1.1 for VCFLoader
- j11lib/intervalstore-1.2.jar (version 3f5ab31c01cbf2e89b54144d7b6f94eaa1ba018a) (diffs)
- j11lib/intervalstore-v1.1.jar (version 3f5ab31c01cbf2e89b54144d7b6f94eaa1ba018a) (diffs)
- j8lib/intervalstore-1.2.jar (version 3f5ab31c01cbf2e89b54144d7b6f94eaa1ba018a) (diffs)
- j8lib/intervalstore-v1.1.jar (version 3f5ab31c01cbf2e89b54144d7b6f94eaa1ba018a) (diffs)
- utils/jalviewjs/libjs/intervalstore-1.1-site.zip (version 3f5ab31c01cbf2e89b54144d7b6f94eaa1ba018a) (diffs)
- utils/jalviewjs/libjs/intervalstore-1.2-site.zip (version 3f5ab31c01cbf2e89b54144d7b6f94eaa1ba018a) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 24e740c734e106a739dec7f31955f17103899641 m
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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Ben Soares <b.soares@dundee.ac.uk> 237dbac16def3207c09d903e1f508fe759238e3c m
JAL-4059 fixed a test that is now working as expected due to <br/>. Better calculation of long line with HTML tags.
-
Ben Soares <b.soares@dundee.ac.uk> 82c876a1b6312edb946dc98377dae0cd45837050 m
JAL-4059 Fix the tooltip formatting for when, e.g. enclose=false
-
Ben Soares <b.soares@dundee.ac.uk> c41f0715fd4f3c345c048a9ca558ee3e3364ffcd m
JAL-4059 redo these tests as TestNG asserts to add message
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Ben Soares <b.soares@dundee.ac.uk> 7d415d0b8bd5256c448f333a62023477b32f139c m
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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Ben Soares <b.soares@dundee.ac.uk> 70b8f731b0168c52c104e6a54d4c41c76d27f140 m
JAL-4059 Updates to miglayout, varna, intervalstore, with re-transpiled javascript libs. Some failing tests
- j11lib/miglayout-4.0-swing.jar (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- j11lib/miglayout-core-4.3-20121116.151612-3.jar (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- j11lib/miglayout-swing-4.3-20121116.151626-3.jar (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- j8lib/miglayout-4.0-swing.jar (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- j8lib/miglayout-core-4.3-20121116.151612-3.jar (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- j8lib/miglayout-swing-4.3-20121116.151626-3.jar (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- utils/jalviewjs/classlists/.gitkeep (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- utils/jalviewjs/libjs/MiGLayout-site.zip (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- utils/jalviewjs/libjs/VARNA-site.zip (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- utils/jalviewjs/libjs/intervalstore-1.2-site.zip (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- utils/jalviewjs/libjs/intervalstore-site.zip (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- utils/jalviewjs/libjs/miglayout-core+swing-4.3-20121116.151612-3-site.zip (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
- utils/jalviewjs/libjs/varna-3.93-site.zip (version 70b8f731b0168c52c104e6a54d4c41c76d27f140) (diffs)
-
James Procter <j.procter@dundee.ac.uk> 707df76dbeb3451d674bda26aaa5d82e040863df m
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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James Procter <j.procter@dundee.ac.uk> 3dae82ff491e1e112907a2f59707724feb9994ce m
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
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Ben Soares <b.soares@dundee.ac.uk> 5f474ea08d7102e8a27c7d04bb08e260a40c0e48 m
JAL-4059 updated intervalstore jars to match updating util/jalviewjs/libjs/intervalstore-site.zip
- j11lib/intervalstore-1.2.jar (version 5f474ea08d7102e8a27c7d04bb08e260a40c0e48) (diffs)
- j11lib/intervalstore-v1.1.jar (version 5f474ea08d7102e8a27c7d04bb08e260a40c0e48) (diffs)
- j8lib/intervalstore-1.2.jar (version 5f474ea08d7102e8a27c7d04bb08e260a40c0e48) (diffs)
- j8lib/intervalstore-v1.1.jar (version 5f474ea08d7102e8a27c7d04bb08e260a40c0e48) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 133dc2c227a23c5d06d05720400cdd77b8386591 m
JAL-4240 Remove unnecessary whitespace, being rendered in JalviewJS. Split on both <br> <br/>. Should make consistent at source, mea culpa.
-
Ben Soares <b.soares@dundee.ac.uk> 4a3612dad2aa178bb9f2d1ea4c2cb2f9e6073961 m
JAL-4059 tidyup
- Jmol-16.1.43.jar (version 4a3612dad2aa178bb9f2d1ea4c2cb2f9e6073961) (diffs)
- Jmol-NO_LOG4J-14.31.53.jar (version 4a3612dad2aa178bb9f2d1ea4c2cb2f9e6073961) (diffs)
- Jmol-NO_LOG4J-16.1.43.jar (version 4a3612dad2aa178bb9f2d1ea4c2cb2f9e6073961) (diffs)
- jsmol-swingjs-16.1.43.zip (version 4a3612dad2aa178bb9f2d1ea4c2cb2f9e6073961) (diffs)
- jsmol-swingjs.zip (version 4a3612dad2aa178bb9f2d1ea4c2cb2f9e6073961) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> 5ee06d5cc63936892adae84ccb3fdb2e9142a938 m
JAL-4059 Change long querystringnamespace to namespace as it's being used for more than query string now. Add a spinner image for proof of concept loading indicator.
- utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html (version 5ee06d5cc63936892adae84ccb3fdb2e9142a938) (diffs)
- utils/jalviewjs/coretemplate.html (version 5ee06d5cc63936892adae84ccb3fdb2e9142a938) (diffs)
- utils/jalviewjs/site-resources/images/jv.gif (version 5ee06d5cc63936892adae84ccb3fdb2e9142a938) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_Jalview-namespace.html (version 5ee06d5cc63936892adae84ccb3fdb2e9142a938) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html (version 5ee06d5cc63936892adae84ccb3fdb2e9142a938) (diffs)
- utils/jalviewjs/template.html (version 5ee06d5cc63936892adae84ccb3fdb2e9142a938) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> a9177efb4097815d9a8031aa22700c61a7d6260a m
JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance for retrieval within Java. If namespace exists when desktop appears, remove a div by id ns:jalviewSplash from the HTML page.
- src/jalview/bin/Jalview.java (version a9177efb4097815d9a8031aa22700c61a7d6260a) (diffs)
- src/jalview/gui/Desktop.java (version a9177efb4097815d9a8031aa22700c61a7d6260a) (diffs)
- src/jalview/gui/SeqPanel.java (version a9177efb4097815d9a8031aa22700c61a7d6260a) (diffs)
- src/jalview/util/Platform.java (version a9177efb4097815d9a8031aa22700c61a7d6260a) (diffs)
-
Ben Soares <b.soares@dundee.ac.uk> de2a523501376d27e85d08cdc38a47de3a082a39 m
JAL-4059 fix not merging html files to the final site from libs
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Ben Soares <b.soares@dundee.ac.uk> c87722ebb148446cf3528cdc287e91d8959b0d89 m
JAL-4059 SwingJS from java2script github repo. It works\!
- swingjs/README.txt (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/differences.txt (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/net.sf.j2s.core.jar (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/timestamp (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.1.1/SwingJS-site.zip (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.1.1/net.sf.j2s.core.3.1.1.jar (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.2.1/SwingJS-site.zip (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.2.1/net.sf.j2s.core_3.2.1.jar (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.2.10-j11/DEV_NOTES.txt (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.2.10-j11/SwingJS-site.zip (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.2.10-j11/_j2sclasslist.txt (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
- swingjs/ver/3.2.10-j11/differences.txt (version c87722ebb148446cf3528cdc287e91d8959b0d89) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> b8bbab1e3d858853b8d18087e0b94ac5deeaeff1 m
JAL-4059 Checked through and fixed build tasks
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Ben Soares <b.soares@dundee.ac.uk> 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d m
JAL-4059 Fix up Jsmol calls and delete html files from JS zips in build.gradle. Improve closure-compiler core creation with merged swingjs. Change startup file for core example page. Add querystringnamepspace to example pages. Remove unnecessary core lists.
- build.gradle (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- src/jalview/bin/JalviewJS2.java (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- utils/jalviewjs/_j2sclasslist.txt (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- utils/jalviewjs/chromium_test/jalview_bin_Jalview-stderr.html (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- utils/jalviewjs/classlists/jalview.txt (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- utils/jalviewjs/classlists/jvexamplefile.txt (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- utils/jalviewjs/coretemplate.html (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
- utils/jalviewjs/some_commands.txt (version 2a4a482c4d47f04849d6a6e304eadd56c70aeb3d) (diffs)
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Ben Soares <b.soares@dundee.ac.uk> f5c326f68b6fe17a0abb1336d9f291f934a5c891 m
JAL-4059 fix that boolean for non-value query string args
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Ben Soares <b.soares@dundee.ac.uk> afe4b88500a5d61bc8d312909cfdde2b7cdd53df m
Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
