JAL-3608 cherry pick of 92cb745e7

Activity

CR-JAL-244 4

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    Participant Role Time Spent Comments Latest Comment
    Author 32m 2 Agreed. I seem to remember (this was a while ago now) tha...
    Reviewer - 0% reviewed      
    Total   32m 4  
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    Objectives

    • JAL-3608 cherry pick of 92cb745e7
    • JAL-3609 Added a -DforceHiDPISetting=true option mainly for testing, and updated getdown HiDPISetting
    • JAL-3609 system properties to force a scale, or automatically choose based on OS, Screen DPI and Screen height in pixels
    • JAL-3609 changed property names to something more palatable and catered for portrait screens
    • JAL-3609 removed debugging prints
    • JAL-3609 corrected maxdimension to mindimension. Adjusted tallscreen limit
    • JAL-3609 New auto-scale 'formula' for linux HiDPI. Tested to work for UHD screen in various OS display settings.
    • JAL-3609 Report when scale setting used.
    • JAL-3609 Allow pass-through of setHiDPIScale property to tests via (e.g.) gradle test -Ptest_HiDPIScale=2
    • JAL-3609 formatting save after cherry-picks
    • JAL-3628 Changed all file1.renameTo(file2) calls to Files.move(path1,path2,REPLACE_EXISTING) in jalview.io.BackupFiles. This fixes a problem in Windows with renameTo when destination file already exists.
    • JAL-3628 Changed other calls to renameTo to use BackupFiles.moveFileToFile
    • JAL-3628 More Cache.log.debug statements
    • JAL-3628 Even more Cache.log.debug statements
    • JAL-3628 Fix for slightly incorrect boolean usage to determine success when rolling backup files
    • JAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console
    • JAL-3676 code review – added non-listed Level into dropdown list
    • JAL-3676 improvement for visual selection of console text - fg color change if required
    • JAL-3628 Fixed oddly worded and non-formatted error popups when saving fails
    • JAL-3676 Removed BACKUPFILESPRESETENTRY logging for opening the file browser. Changed most BACKUPFILES logging from DEBUG to TRACE level. Minor wording changes.
    • JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.
    • JAL-3628 Error when saving alert box has been moved in develop for JS, adding Platform.isHeadless test to new isSaveAlignmentSuccessful method.
    • JAL-3633 ensure check both http:// or https:// for urls
    • JAL-3633 pass getdown proxy settings in proxy.txt on to Jalview
    • JAL-3633 Remember system set proxy properties. Add options in Preferences for No proxy, system proxy, or custom proxy servers.
    • JAL-3633 label.proxy_server -> label.proxy_servers
    • JAL-3633 Added Preferences for Proxy Authentication. No jalview_properties yet
    • JAL-3633 Added Proxy Authentication credentials in Preferences and set via java.net.Authenticator
    • JAL-3633 Memory only proxy auth password storage. Open Preferences->Connection tab when proxy password needed
    • JAL-3633 Set proxy preferences before web calls in jalview.bin.Jalview. Fixed call to open Preferences->Connections with message when required.
    • JAL-3275 JAL-3633: JAL-3275 Turned Preferences into a Singleton that checks renews if it's been closed. Removed some debugging for JAL-3633. Added focus/highlight to proxy password box when needed. Forced WS lookup wheb proxy settings changed.
    • JAL-3633 Small changes to allow future fitting with ApplicationSingletonI/Jalview-JS, Most NPE fixes for tests
    • JAL-3633 Help documentation updated
    • JAL-3633 Apply (proxy) button enabled when needed
    • JAL-3633 last minute refinement so password box doesn't get focus all the time
    • JAL-3775 Eclipse re-formatting commit
    • JAL-3775 Re-compiled Getdown jars
    • JAL-3757 JAL-3689 Fixed checks for URLs by adding checks for https:// as well as http://
    • JAL-3757 JAL-3689 use AppletFormat.checkProtocol to resolve startup file’s retrieval protocol (sorry @benzoid for finessing you !)
    • JAL-3530 Added a -nowebservicediscovery command line argument.
    • JAL-3660 Fix for specified output format when using command line arg to convert a file
    • JAL-3775 Adding Mockito jars for tests. Needed for HiDPISettingTest1
    • JAL-3609 JAL-3775 Refactoring a bit of jalview.bin.HiDPISetting so screen display can be mocked in tests by Mockito
    • JAL-3609 JAL-3775 Tests for jalview.bin.HiDPISetting
    • JAL-3609 JAL-3775 Updated getdown with re-factored HiDPISetting and ScreenInfo. No real functionality change.
    • Merge branch 'develop' into merge/develop_and_rebase_squashed_merge_JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    Jim Procter

    I think there are lots of things that could be tidied up (particularly the ov...

    I think there are lots of things that could be tidied up (particularly the overloading and additional logging functions via Cache which don't really reduce code at point of use, but are certainly useful in spirit), but now is most definitely not the time to optimise and beautify code.

    Ben Soares

    Agree this is just touching on a much bigger task. However... The reason I /n...

    Agree this is just touching on a much bigger task.
    However...
    The reason I /needed/ to do this rather than just /wanted/ to do this is that several of the classes I've been working on (e.g. jalview.bin.Launcher, jalview.bin.HiDPISetting, jalview.bin.MemorySetting) run very early on (especially jalview.bin.Launcher!). This means Cache.log has perhaps not yet been initialised, so a Cache.log.debug doesn't log (unless you count reams of NullPointerExceptions as logging!).

    In the case of HiDPISetting and MemorySetting that also get used in Getdown, where there is no jalview.bin.Cache, they currently have to use System.out and System.err [or maybe I could stub jalview.bin.Cache too]. I'd prefer them to use Cache.log when they can so this is an attempt at starting to decouple jalview.bin.Cache from other jalview things so it can be used standalone within Getdown. The main reason for wanting to do that is to have shared code to read the preferences between Jalview and Getdown.

    /getdown/lib/FJVL_VERSION Changed
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    /getdown/lib/JVL_VERSION Changed
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    /getdown/lib/getdown-core.jar Changed
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    /getdown/lib/getdown-launcher-local.jar Changed
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    /getdown/lib/getdown-launcher.jar Changed
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    /getdown/src/getdown/ant/pom.xml Changed
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    /getdown/src/.../getdown/data/Application.java Changed
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    /getdown/src/.../jalview/bin/GetMemory.java Changed
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    /getdown/src/.../jalview/bin/HiDPISetting.java Changed
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    /getdown/src/.../bin/MemorySetting.java Changed
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    /getdown/src/.../jalview/bin/ScreenInfo.java Added
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    /getdown/src/getdown/core/pom.xml Changed
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    /getdown/src/getdown/launcher/pom.xml Changed
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    /getdown/src/getdown/mvn_cmd Changed
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    /getdown/src/getdown/pom.xml Changed
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    /help/help/html/features/preferences.html Changed
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    /j11lib/getdown-core.jar Changed
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    /j8lib/getdown-core.jar Changed
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    /resources/lang/Messages.properties Changed
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    /resources/lang/Messages_es.properties Changed
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    /src/jalview/bin/Cache.java Changed
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    /src/jalview/bin/HiDPISetting.java Changed
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    /src/jalview/bin/Jalview.java Changed 2
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    /src/jalview/bin/Launcher.java Changed
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    /src/jalview/bin/MemorySetting.java Changed
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    /src/jalview/bin/ScreenInfo.java Added
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    /src/jalview/gui/AlignFrame.java Changed
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    /src/jalview/gui/Console.java Changed
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    /src/jalview/gui/Desktop.java Changed
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    /src/jalview/gui/Preferences.java Changed
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    /src/jalview/gui/WsPreferences.java Changed
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    /src/jalview/io/BackupFiles.java Changed
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    /src/.../io/BackupFilesPresetEntry.java Changed
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    /src/jalview/jbgui/GPreferences.java Changed
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    /src/jalview/project/Jalview2XML.java Changed
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    /src/jalview/util/HttpUtils.java Changed
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    /src/jalview/ws/sifts/SiftsClient.java Changed
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    /test/jalview/bin/HiDPISettingTest1.java Added
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    /test/jalview/bin/HiDPISettingTest2.java Added
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    /test/jalview/bin/hidpiTestProps.jvprops Added
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    /utils/testnglibs/byte-buddy-1.10.15.jar Added
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    /utils/testnglibs/byte-buddy-agent-1.10.15.jar Added
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    /utils/testnglibs/mockito-core-3.6.0.jar Added
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    /utils/testnglibs/objenesis-3.1.jar Added
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    /build.gradle Changed

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