String Formatter error when key or value of Qualifier has character "%"

feature.addQualifier("note", new Qualifier("note", "coding sequ%_ece", true));
GenbankWriterHelper.writeNucleotideSequence(......)

Exception in thread "main" java.util.UnknownFormatConversionException: Conversion = '_'
        at java.util.Formatter.checkText(Formatter.java:2579)
        at java.util.Formatter.parse(Formatter.java:2555)
        at java.util.Formatter.format(Formatter.java:2501)
        at java.io.PrintWriter.format(PrintWriter.java:905)
        at org.biojava.nbio.core.sequence.io.GenbankWriter.process(GenbankWriter.java:95)
        at org.biojava.nbio.core.sequence.io.GenbankWriterHelper.writeNucleotideSequence(GenbankWriterHelper.java:135)
        at GenBank.main(GenBank.java:41)

Have you tested doubling %% to scape % ?

I think it probably makes sense for BioJava to handle the escaping rather than forcing the user to do it.

Actually, I don't understand why format is getting called in GenbankWriter.java:95 as all. Does calling PrintWriter.format(s) have any effect without additional arguments? It seems like all the formatting (and escaping) should be done within GenericGenbankHeaderFormat.

IIRC, it converts %n to the platform default line separator. There are a few flags that don't require arguments.

…

On Fri, Sep 25, 2020, 3:36 AM Spencer Bliven ***@***.***> wrote: I think it probably makes sense for BioJava to handle the escaping rather than forcing the user to do it. Actually, I don't understand why format is getting called in GenbankWriter.java:95 <https://github.com/biojava/biojava/blob/b9519e4c568e8423dcfb9b5fdb06688935360dd7/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java#L95> as all. Does calling PrintWriter.format(s) <https://docs.oracle.com/javase/7/docs/api/java/io/PrintWriter.html#format(java.lang.String,%20java.lang.Object...)> have any effect without additional arguments? It seems like all the formatting (and escaping) should be done within GenericGenbankHeaderFormat. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#886 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLFC4EYNFQB4M6DU4ZQBT3SHRCBHANCNFSM4QHB4QXQ> .

@emckee2006

@emckee2006 Is there any reason why those couldn't be moved inside the HeaderFormat? It would still require escaping some sequences, but at least it only has to happen once.

Hello, I have recently come across this issue myself. Is anybody currently working on a fix for this problem?

If not I am happy to have a go at proposing a solution

@jamesmorris

Thanks @jamesmorris , I don't think anyone is working on it. We're always happy with pull requests :)

That might not be a bad idea...

…

On Fri, Sep 25, 2020, 5:23 AM Spencer Bliven ***@***.***> wrote: @emckee2006 <https://github.com/emckee2006> Is there any reason why those couldn't be moved inside the HeaderFormat? It would still require escaping some sequences, but at least it only has to happen once. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#886 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLFC4B3ZA4A7UGADWHA7N3SHROQ5ANCNFSM4QHB4QXQ> .

Merge pull request #1034 from jamesmorris/master

Fixed issue biojava#886 by escaping percent symbols when feature attr…

Added test for issue biojava#886

Merge pull request biojava#1034 from jamesmorris/master

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String Formatter error when key or value of Qualifier has character "%" #886

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String Formatter error when key or value of Qualifier has character "%" #886

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enilapb commented on Sep 23, 2020

sbliven commented on Sep 25, 2020

emckee2006 commented on Sep 25, 2020

sbliven commented on Sep 25, 2020

jamesmorris commented on Jul 1, 2021

josemduarte commented on Jul 1, 2021

emckee2006 commented on Jul 1, 2021

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