Ben Soares

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

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    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

    • -0
    • +93
    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

close filehandles straight after parse, without setting an error

Conflicts:

src/jalview/project/Jalview2XML.java

(locale aware PDBID string compare)

close filehandles straight after parse, without setting an error

JAL-3937 update releases.html

JAL-3937 enable AIA download of intermediate certificates when needed

JAL-3937 enable AIA download of intermediate certificates when needed

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

JAL-3934 updated log4j from 2.16.0 to 2.17.0

    • binary
    /j11lib/log4j-1.2-api-2.17.0.jar
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    /j11lib/log4j-api-2.17.0.jar
    • binary
    /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
    • binary
    /j8lib/log4j-1.2-api-2.17.0.jar
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    /j8lib/log4j-api-2.17.0.jar
    • binary
    /j8lib/log4j-core-2.17.0.jar
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    /j8lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/log4j-slf4j18-impl-2.17.0.jar
JAL-3934 updated log4j from 2.16.0 to 2.17.0

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

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 updated THIRDPARTYLIBS

JAL-3933 updated log4j and slf4j jars with log4j1.2 compatibility API jar. Removed log4j from jabaws-min-client and Jmol jars

    • binary
    /j11lib/Jmol-NO_LOG4J-14.31.53.jar
    • binary
    /j11lib/jabaws-min-client-2.2.0.jar
    • binary
    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j11lib/log4j-1.2-api-2.16.0.jar
    • binary
    /j11lib/log4j-api-2.16.0.jar
    • binary
    /j11lib/log4j-core-2.16.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j11lib/slf4j-api-1.7.32.jar
    • binary
    /j11lib/slf4j-log4j12-1.7.32.jar
    • binary
    /j8lib/Jmol-NO_LOG4J-14.31.53.jar
  1. … 13 more files in changeset.
JAL-3933 updated slf4j to 1.7.32

    • binary
    /j11lib/slf4j-api-1.7.32.jar
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    /j11lib/slf4j-log4j12-1.7.32.jar
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    /j8lib/slf4j-api-1.7.32.jar
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    /j8lib/slf4j-log4j12-1.7.32.jar
JAL-3933 Updated log4j jars with log4j-2.16.0 and compatibility API log4j-1.2-api-2.16.0. Stripped log4j classes from jabaws-min-client jar. Updated sl4j jars in j8lib

    • binary
    /j11lib/jabaws-min-client-2.2.0.jar
    • binary
    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j11lib/log4j-1.2-api-2.16.0.jar
    • binary
    /j11lib/log4j-api-2.16.0.jar
    • binary
    /j11lib/log4j-core-2.16.0.jar
    • binary
    /j11lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j8lib/log4j-1.2-api-2.16.0.jar
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    /j8lib/log4j-api-2.16.0.jar
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    /j8lib/log4j-core-2.16.0.jar
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    /j8lib/log4j-slf4j18-impl-2.16.0.jar
    • binary
    /j8lib/slf4j-api-1.7.26.jar
  1. … 4 more files in changeset.
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations. Better for response.varfile installation of Jalview

    • -25
    • +25
    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/file_associations_template-install4j8.xml
Merge branch 'develop' into task/JAL-3911_getdown_improvements

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

JAL-3553 added filesize to json

JAL-3066 Vastly updated testng libs

    • binary
    /utils/testnglibs/testng-7.4.0-sources.jar
    • binary
    /utils/testnglibs/testng-7.4.0.jar
    • binary
    /utils/testnglibs/testng-sources.jar
JAL-3553 now creating a json file for use on website. It's easier to parse all the info here than on the website!

JAL-3553 copy sha256sums to a versioned filename too when created

JAL-3553 added customized labels for install4j output.txt

JAL-3553 improve the labels in install4j's output.txt and make a versioned filename output-JALVIEW_VERSION.txt