jalview

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JAL-4059 update Jmol and JSmol to 15.2.69 - revised Jalview classes interating with Jmol API to handle double precision structure data

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JAL-3059 upgrade Jmol from 14.31.53 to 15.2.69 (double precision) - required patches to structure data related classes and Jmol API implementors for float->double

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JAL-4046 JAL-3993 imports reformatting

JAL-4046 JAL-3993 patch for 2.11.2.4 release

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Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup' into develop

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JAL-4034 show the loading spinner when switching between tabs

JAL-4055 quick patch to see how Jalview looks as a free-floating multiwindowed app rather than a Desktop contained app

JAL-4048 feature group filter

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    ./viewmodel/seqfeatures/IdColumns.java
JAL-4036 moved a comment block

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    ./fts/service/uniprot/UniProtFTSRestClient.java
JAL-4034 button looks better also on other OSes with the 0 vertical insets

JAL-4034 add round corners to 3DB confirmation button with icon on a mac

JAL-4036 Changes made from code review CR-JAL-265

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    ./fts/service/uniprot/UniprotFTSPanel.java
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-4048 fix disappearing sequence IDs, and non-positional feature descriptions

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    ./viewmodel/seqfeatures/IdColumns.java
JAL-4047 - proof of concept for JAL-4048 - display columns of info in sequence ID panel.

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    ./viewmodel/AlignmentViewport.java
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    ./viewmodel/seqfeatures/IdColumn.java
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    ./viewmodel/seqfeatures/IdColumns.java
after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a con...

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a convenient [search] button is shown so one doesn't have to click into the query field and press enter to trigger the search again.

should be Console.warn

should be Console.warn

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalvi...

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalview still work (up until legacy.uniprot.org goes away).

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

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    ./fts/service/uniprot/UniprotFTSPanel.java
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shouldn't this be a warn ?

shouldn't this be a warn ?

this comment block should really be after the imports ?

this comment block should really be after the imports ?

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
JAL-4036 removing the query field code from the dropdown indexes

JAL-4036 Don't autosearch changing index when autosearch is de-selected

JAL-4036 add search fieldname to dropdown list

JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API

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    ./fts/service/uniprot/UniProtFTSRestClient.java
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    ./fts/service/uniprot/UniprotFTSPanel.java
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JAL-4045 - don't apply distribution dependent scale factor to the axis lines!

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