jalview

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Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)

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    /test/jalview/bin/CommandLineOperations.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763 release notes

Merge branch 'merge/develop_task/JAL-3763_newDatasetForCds' into develop

JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)

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    /test/jalview/bin/CommandLineOperations.java
Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/util/MapList.java

test/jalview/util/MapListTest.java

test/jalview/util/MappingUtilsTest.java

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/datamodel/SearchResults.java
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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)

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.

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 possible release date 1st Feb 2022

JAL-3746 Release notes for patch JAL-3702 JAL-3915

Merge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_fails' into develop

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-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

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    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

close filehandles straight after parse, without setting an error

JAL-3937 enable AIA download of intermediate certificates when needed

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 update release history for 2.11.1.5 and 2.11.1.6 patch releases

Merge branch 'critical/JAL-3933_log4j_update_for_develop_branch' into develop

Merge branch 'develop' into critical/JAL-3933_log4j_update_for_develop_branch

JAL-3934 updated log4j from 2.16.0 to 2.17.0

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    /j11lib/log4j-1.2-api-2.17.0.jar
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    /j11lib/log4j-api-2.17.0.jar
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    /j11lib/log4j-core-2.17.0.jar
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    /j11lib/log4j-slf4j18-impl-2.16.0.jar
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    /j11lib/log4j-slf4j18-impl-2.17.0.jar
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    /j8lib/log4j-1.2-api-2.17.0.jar
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    /j8lib/log4j-api-2.17.0.jar
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    /j8lib/log4j-core-2.17.0.jar
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    /j8lib/log4j-slf4j18-impl-2.16.0.jar
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    /j8lib/log4j-slf4j18-impl-2.17.0.jar
JAL-3933 updated THIRDPARTYLIBS