Ben Soares

JAL-4056 fixed tl;dr section of doc/building.md

JAL-4036 Fixed the virus_host_id query field

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    /resources/fts/uniprot_data_columns-2022.txt
JAL-4036 Added text to help about different number and date range acceptable formats

JAL-4036 updated help about new UniProt API

JAL-4036 moved a comment block

JAL-4034 button looks better also on other OSes with the 0 vertical insets

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    /src/jalview/jbgui/GStructureChooser.java
JAL-4034 add round corners to 3DB confirmation button with icon on a mac

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    /src/jalview/jbgui/GStructureChooser.java
JAL-4036 Changes made from code review CR-JAL-265

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace. This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses...

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace.
This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses. I notice that the new API server is sending back a 400 for bad input (including for non-existent query fields and wrong types for non-string query fields), which is invoking the warning triangle which puts the HTTP error message into the tooltip so this block is now getting more use!

The reason for wanting a full stacktrace in debug mode is that both the API and the changed client are new, so any errors in the next few months will be more quickly diagnosed if we can allow the user to easily obtain a stacktrace of the exception.

JAL-4036 Add getDbName to the GFTSPanelI and add an index code message to the index dropdown tooltip as appropriate

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    /resources/lang/Messages_es.properties
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    /src/jalview/fts/core/GFTSPanel.java
JAL-4036 removing the query field code from the dropdown indexes

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    /src/jalview/fts/core/FTSRestClient.java
JAL-4036 Don't autosearch changing index when autosearch is de-selected

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    /src/jalview/fts/core/GFTSPanel.java
JAL-4036 add search fieldname to dropdown list

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    /src/jalview/fts/core/FTSRestClient.java
JAL-4036 removed often duplicated pluralisation in message

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    /resources/lang/Messages_es.properties
JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API

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    /resources/fts/uniprot_data_columns-2022.txt
JAL-4034 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can moveToFront. Minor improvement to Search 3DB button appearance

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-4034 Allow request for non-modal JDialog, which puts the Runnable action into the button click listener (similar to JalviewJS)

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    /src/jalview/gui/JvOptionPane.java
JAL-4041 Use the new non-modal JDialog for 3DBeacons uniprot lookup confirmation. Link dialog to GStructureChooser's frame so it can be raised.

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    /src/jalview/gui/StructureChooser.java
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    /src/jalview/jbgui/GStructureChooser.java
JAL-4041 Allow request for non-modal JDialog, which puts the Runnable action into the button click listener (like JavliewJS)

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    /src/jalview/gui/JvOptionPane.java
JAL-4034 change to jalview property name

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    /src/jalview/gui/StructureChooser.java
JAL-4034 showConfirmDialog works for both desktop and jalviewjs

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    /src/jalview/gui/StructureChooser.java
JAL-4034 Non-blocking 3D Beacons query after warning dialog

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    /src/jalview/gui/StructureChooser.java
JAL-4034 allow a jalview_property to set the threshold level

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    /src/jalview/gui/StructureChooser.java
Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

JAL-1988 Don't put Quit in the File menu if there's a handler for it

Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

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    /src/jalview/jbgui/APQHandlers.java
JAL-1988 Check for setHandler capability to avoid About and Preferences menu options disappearing into a void

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    /src/jalview/jbgui/APQHandlers.java
JAL-3027 Avoid FlatLAF Desktop class is JalviewJS

JAL-1988 Hack to ensure Quit dialog box is moved to front

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    /src/jalview/jbgui/APQHandlers.java
JAL-1988 Moved APQHandlers to jalview.jbgui and called from jalview.jbgui.GDesktop. Use result to not add About and Preferences to normal menus.

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    /src/jalview/jbgui/APQHandlers.java