jalview

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Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch

JAL-3633 last minute refinement so password box doesn't get focus all the time

JAL-3633 Apply (proxy) button enabled when needed

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    /src/jalview/jbgui/GPreferences.java
JAL-3633 Help documentation updated

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    /help/help/html/features/preferences.html
JAL-3633 Small changes to allow future fitting with ApplicationSingletonI/Jalview-JS, Most NPE fixes for tests

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    /src/jalview/io/BackupFiles.java
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    /src/jalview/jbgui/GPreferences.java
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.

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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3675 update release note for JAL-2656

JAL-2656 recognise non-HTTP URI input streams as gzipped by detecting the gzip magic header

JAL-2656 recognise Gzipped file input streams by their content, not their filename

JAL-3615 update tests for Rfam/Pfam specific gzip endpoints

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    /test/jalview/ws/dbsources/PfamFullTest.java
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    /test/jalview/ws/dbsources/PfamSeedTest.java
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    /test/jalview/ws/dbsources/RfamFullTest.java
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    /test/jalview/ws/dbsources/RfamSeedTest.java
JAL-3633 Set proxy preferences before web calls in jalview.bin.Jalview. Fixed call to open Preferences->Connections with message when required.

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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3675 release notes for JAL-3615 and JAL-2656

Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch Conflict in way transparency slider was inited - followed HEAD's pattern here.

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    /src/jalview/gui/FeatureTypeSettings.java
JAL-3675 release notes for JAL-3621

JAL-3697 show total number of features not shown

JAL-3696 log the error message from the exception to the console

JAL-3695 htsjdk 2.12 -> 2.23 (library change only, no code change. needs gradle refresh in eclipse)

    • binary
    /j11lib/htsjdk-2.23.0.jar
    • binary
    /j8lib/htsjdk-2.23.0.jar
JAL-3633 Memory only proxy auth password storage. Open Preferences->Connection tab when proxy password needed

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3633 Added Proxy Authentication credentials in Preferences and set via java.net.Authenticator

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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3633 Added Preferences for Proxy Authentication. No jalview_properties yet

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    /resources/lang/Messages_es.properties
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    /src/jalview/jbgui/GPreferences.java
JAL-3633 label.proxy_server -> label.proxy_servers

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    /resources/lang/Messages_es.properties
JAL-3633 Remember system set proxy properties. Add options in Preferences for No proxy, system proxy, or custom proxy servers.

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
JAL-3609 JAL-3633 merged getdown jars

    • binary
    /getdown/lib/getdown-launcher-local.jar
Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch

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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/AlignFrame.java
JAL-3633 Compiled jars for pass getdown proxy settings in proxy.txt on to Jalview

    • binary
    /getdown/lib/getdown-launcher-local.jar
JAL-3633 pass getdown proxy settings in proxy.txt on to Jalview

JAL-3633 ensure check both http:// or https:// for urls

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/project/Jalview2XML.java
Merge branch 'bug/JAL-3541_cherry_pick_to_releases_Release_2_11_1_Branch' into task/JAL-3608_and_JAL-3609_merged_for_Release_2_11_1_Branch