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JAL-3761 extra check that VCF feature is fully mappable to sequence

Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

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JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations

  1. … 8 more files in changeset.
JAL-3691 toUpperCase(Locale.ROOT) for all standard file format operations

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JAL-3696 log the error message from the exception to the console

JAL-3696 log the error message from the exception to the console

Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

  1. … 19 more files in changeset.

changeset discussion

  1. Jim Procter: relevant issue is JAL-3626
JAL-3407 add GPL license to Jalview source files

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3253-omnibus save

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Merge branch 'develop' into Jalview-JS/develop

Conflicts:

.gitignore

build.gradle

gradle.properties

src/jalview/gui/AlignFrame.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureSettings.java

src/jalview/gui/JvSwingUtils.java

src/jalview/util/MessageManager.java

test/jalview/gui/AlignmentPanelTest.java

test/jalview/gui/JvSwingUtilsTest.java

test/jalview/gui/PopupMenuTest.java

utils/eclipse/org.eclipse.jdt.core.jalview.prefs

  1. … 33 more files in changeset.
OK - careful reading of spec suggests this might only be an issue for 'TARGET' ID resolution where if the sequence ID specified via the target attribute contains spaces, they must be encoded as %20.

OK - careful reading of spec suggests this might only be an issue for 'TARGET' ID resolution where if the sequence ID specified via the target attribute contains spaces, they must be encoded as %20.

could consider using the jalview.io.FileParse error and warning flags (plus associated String fields) to pass messages back to the user.

could consider using the jalview.io.FileParse error and warning flags (plus associated String fields) to pass messages back to the user.

JAL-3375: Better VCF numeric data field validation while parsing (e.g. AF* attributes)
JAL-3375: Better VCF numeric data field validation while parsing (e.g. AF* attributes)
JAL-3376: Record 'fixed column' values from VCF
JAL-3376: Record 'fixed column' values from VCF
Tab and % characters added to those encoded/decoded, and to StringUtilsTest

Tab and % characters added to those encoded/decoded, and to StringUtilsTest

I propose to leave this as it is: *StringUtils.urlEncode() uses java.net.URLEncoder() which encodes space as '+' *but GFF processing does not encode or decode space characters

I propose to leave this as it is:

  • StringUtils.urlEncode() uses java.net.URLEncoder() which encodes space as '+'
  • but GFF processing does not encode or decode space characters
Maybe... problem being that URLEncoder does the encoding. see rants at https://stackoverflow.com/questions/4737841/urlencoder-not-able-to-translate-space-character

Maybe... problem being that URLEncoder does the encoding. see rants at
https://stackoverflow.com/questions/4737841/urlencoder-not-able-to-translate-space-character

Will drop in favour of your suggestion e.g. CSQ=POLYPHEN=benign,damaging,SIFT=tolerated

Will drop in favour of your suggestion e.g. CSQ=POLYPHEN=benign,damaging,SIFT=tolerated

GffHelperI.GFF_ENCODABLE = ",=;"; specifies the characters to encode/decode for GFF. Doesn't include space so no issue here (other than adding tab and % to this list). Can change to encode to %20 a...

GffHelperI.GFF_ENCODABLE = ",=;";
specifies the characters to encode/decode for GFF. Doesn't include space so no issue here (other than adding tab and % to this list).
Can change to encode to %20 anyway.

Encoding ' ' as '+' has been deprecated in GFF3 - https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md Could mark as defect for release if %20 encoding can't be implemented ...

Encoding ' ' as '+' has been deprecated in GFF3 -
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md

Could mark as defect for release if %20 encoding can't be implemented easily

this jalview specific extension to GFF3 needs to be documented clearly. See also comments in the issue re interoperability

this jalview specific extension to GFF3 needs to be documented clearly. See also comments in the issue re interoperability

GFF3 spec requires tab characters to also be url-encoded - it doesn't look like there are test cases for this in StringUtilsTest.java: https://github.com/The-Sequence-Ontology/Specifications/blob/m...

GFF3 spec requires tab characters to also be url-encoded - it doesn't look like there are test cases for this in StringUtilsTest.java:
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md

GFF2 spec is different/less stringent (C-style escaping - presumably like \t \n \r
): http://gmod.org/wiki/GFF2#Column_9:_Group_.2F_Attributes

JAL-3121: Allow export/import of map-value feature attributes via GFF3
JAL-3121: Allow export/import of map-value feature attributes via GFF3
JAL-3375: Better VCF data validation while parsing
JAL-3375: Better VCF data validation while parsing