jalview

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I know the problems you had with close() - you mentioned in the comments on the issue. However, you might have noticed that FileParse.close() is not called from many places, so changing its behavio...

I know the problems you had with close() - you mentioned in the comments on the issue. However, you might have noticed that FileParse.close() is not called from many places, so changing its behaviour wouldn't have too many side effects.

The intended pattern for FileParse.close() was:

ParserThing pt;
try {
pt = new <? assignable to FileParse>(data spec..)
.. do whatever needed to trigger parsing
.. then check pt's error/warning status and report any problems.
} catch (IOException ..) {
.. handle read or parse errors 
}
finally {
if (pt!=null) {
pt.close();
} // catch and report any IOErrors if desired
}
I tried this first, but FileParse.close() deliberately leaves the FileParse in an error state, which caused problems later (I don't remember the specifics). I could not work out why the FileParse.c...

I tried this first, but FileParse.close() deliberately leaves the FileParse in an error state, which caused problems later (I don't remember the specifics). I could not work out why the FileParse.close() was designed to do this but suspect changing this methos so it's (in general) not left in an error state will cause bigger problems. Also, since Jalview is used to having dataIn for the lifetime of the alignment, I wasn't sure if nulling the object would cause unforeseen errors (in e.g. filename etc).

Maybe it would be best to overload FileParse.close() to pass in an error value/message, then it would essentially be calling FileParse.closeDataIn() instead of FileParse.dataIn.close()

Agree with the finally {} – forgot that (not been a java programmer for quite long enough!). Presumably that should go in FileParse and not AlignFile too.

Ideally, any low level file ops should happen in the base class (FileParse) rather than here. AlignFile should call the FileParse.close() method rather than directly manipulate dataIn, which is man...

Ideally, any low level file ops should happen in the base class (FileParse) rather than here. AlignFile should call the FileParse.close() method rather than directly manipulate dataIn, which is managed by FileParse. Note that FileParse.close() nulls the dataIn reference so the stream can be garbage collected properly.

It's also good practice to try to close() in a finally {} clause, catching and reporting exceptions if needed... this is actually what the FileParse.close() method's design was intended for, since the caller should have already checked 'error' and 'errormessage' for parsing problems. Exceptions/Errors on close are not fatal for file import.

file close error will trash import of project

file close error will trash import of project

close filehandles straight after parse, without setting an error
close filehandles straight after parse, without setting an error
JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped...
JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped...
Merge branch 'develop' into task/JAL-3911_getdown_improvements

JAL-3594 correct Jalview Develop logo SVG added in [not actually used in application]

JAL-3926 disable autosearch by default

JAL-3911 updated JARs for getdown

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    /getdown/lib/getdown-launcher-local.jar
JAL-3911 HiDPISetting update. jalview.bin.* update. Attempt to detect SHIFT key -- Order of app config and window appearance wrong. must create a window to click instead.

JAL-3855 verify pdb suffix is preserved when locally loaded file is saved in project and imported

JAL-3855 JAL-1731 reuse the StructureViewer.fetchPdbFile(PDBEntry) method in JmolBinding - avoid code duplication for retrieval and import of 3d data

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    /src/jalview/gui/AppJmolBinding.java
JAL-3855 try harder to ignore DNA/RNA only structures when deciding whether to download from SIFTS

JAL-3921 wait around until session file has been written

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    • +17
    /src/jalview/gui/StructureViewerBase.java
JAL-3829 remove duplicate IDs in 3DBeacons generated PDBFTS query and update mocks

JAL-3829 format and tidy up unused code

JAL-3919 use model format field to ensure we get the file extension correct when creating temp files for structure viewers

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    • +1
    /resources/fts/tdbeacons_data_columns.txt
JAL-3875 fully reset filter combo-box when fetch 3d-beacons button is pressed, and ensure first 3d-beacons option selected when structures are discovered even when cached structures are present.

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    /src/jalview/gui/StructureChooser.java
JAL-3746 Updated help docs for 3D-Beacons. Added and altered images and text.

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    /help/help/html/features/3dbeacons_button.png
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    /help/help/html/features/3dbeacons_structurechooser.png
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    /help/help/html/features/3dstructuredata_popupmenu.png
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    /help/help/html/features/schooser_main.png
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    /help/help/html/features/schooser_viewbutton.png
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    /help/help/html/features/selectfetchdb.gif
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    /help/help/html/features/seqfetch.html
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    /help/help/html/features/seqfetcher.gif
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    /help/help/html/features/structurechooser.html
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    /help/help/html/features/viewingpdbs.html
JAL-3915 JAL-3746 documentation for removed rnaview options

JAL-3916 TODO for improved selection of covering structures

JAL-3916 TODO for improved selection of covering structures

JAL-3915 remove RNAview opts from preferences. Still present in config file ready for when we have a new RNA structure processing service

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-3875 test case and patch to verify the query 3d beacons button is shown for proteins with uniprot ids but no canonical accessions

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    /src/jalview/gui/StructureChooser.java
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    /test/jalview/gui/StructureChooserTest.java