jalview

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JAL-3633 label.proxy_server -> label.proxy_servers

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    /resources/lang/Messages_es.properties
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)

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    /resources/lang/Messages_es.properties
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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/util/MappingUtils.java
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    /src/jalview/ws/dbsources/EmblCdsSource.java
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    /src/jalview/ws/dbsources/EmblFlatfileSource.java
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    /src/jalview/ws/dbsources/EmblSource.java
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    /src/jalview/ws/dbsources/EmblXmlSource.java
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    /src/jalview/ws/ebi/EBIFetchClient.java
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    /test/jalview/util/MappingUtilsTest.java
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    /test/jalview/ws/dbsources/EmblXmlSourceTest.java
JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings) Conflicts: src/jalview/ws/dbsources/EmblXmlSource.java src/jalview/ws/ebi/EBIFetchClient.java

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    /resources/lang/Messages_es.properties
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    /src/jalview/io/EmblFlatFile.java
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    /src/jalview/util/MappingUtils.java
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    /src/jalview/ws/dbsources/EmblCdsSource.java
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    /src/jalview/ws/dbsources/EmblFlatfileSource.java
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    /src/jalview/ws/dbsources/EmblSource.java
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    /src/jalview/ws/dbsources/EmblXmlSource.java
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    /src/jalview/ws/ebi/EBIFetchClient.java
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    /test/jalview/util/MappingUtilsTest.java
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    /test/jalview/ws/dbsources/EmblXmlSourceTest.java
JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3597 slight tidying of code and Javadoc, passmark now heap <= 38MB

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3690 alternative servers menu fix

JAL-3690 alternative servers menu fix

JAL-3690 restore jws1 JPred

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    /src/jalview/gui/AlignFrame.java
JAL-3690 switching to CompletableFuture to allow chaining

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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-3690 mark JalviewChangeSupport as deprecated

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    /src/jalview/gui/JalviewChangeSupport.java
JAL-3690 refactoring web-services discovery

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws/ServiceChangeListener.java
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    /src/jalview/ws/jws1/Discoverer.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
JAL-1421 last change tidied up properly

JAL-1421 types added to nameHash and nodeHash maps

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    /src/jalview/gui/TreeCanvas.java
JAL-3597 additional references nulled, bug in test corrected

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    /test/jalview/gui/FreeUpMemoryTest.java
JAL-3597 additional references nulled, bug in test corrected

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    /test/jalview/gui/FreeUpMemoryTest.java
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-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

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    /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
Merge branch 'alpha/merge_212_JalviewJS_2112' into spike/JAL-3622_Scanner_swingjs_J212_merge

JAL-3633 Compiled jars for pass getdown proxy settings in proxy.txt on to Jalview

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

JAL-3633 pass getdown proxy settings in proxy.txt on to Jalview

Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/merge_212_JalviewJS_2112

Conflicts:

src/jalview/gui/Desktop.java

src/jalview/gui/Preferences.java

src/jalview/jbgui/GPreferences.java

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/ws/jws2/Jws2Discoverer.java
Merge branch 'feature/JAL-3686_slivka_client_js_update' into alpha/JAL-3066_Jalview_212_slivka-integration

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

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    /src/jalview/project/Jalview2XML.java
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

JAL-3683 retrieve job status to output stream