[Biojava-dev] biojava-legacy 1.8.2 release plan
George Waldon
gwaldon at geneinfinity.org
Thu Mar 8 18:35:30 UTC 2012
Hi Michael,
All this sounds very good and I am looking forward to it. When you are
ready to move to the official release, I'll be happy to help you
updating the website.
Regards,
George
Quoting Michael Heuer <heuermh at gmail.com>:
> All,
>
> I propose then to create a biojava-legacy 1.8.2 release shortly; the
> changes since 1.8.1 will include commits
>
> Adjustment to Entrez update to EFetch 2.0
> Bug fix for one-ambiguous-symbol motif
> Added new constructor for RestrictionMapper using
> java.util.concurrent.ExecutorService
> specifying all Date formats to either Locale.US or Locale.ENGLISH, to
> avoid Arabic months names induced problems
> Some fixes for Division in EMBL and GenBank formats
> add some generics to biojavax
> Added generic for biojavax Note
> More fix with circularity
> Added circularity for locations
> Section parser now accepts tags not followed by white space.
> Fix ordering of sublocations on complementary strand
>
> and this diff to AbstractFastqParser.java
>
> @@ -70,6 +70,7 @@
> /**
> * Validate the specified description.
> *
> + * @deprecated to be removed in version 1.9
> * @param builder FASTQ formatted sequence builder, will not be null
> * @param description description to validate, will not be null
> * @param lineNumber current line number in input stream
> @@ -81,6 +82,7 @@
> /**
> * Validate the specified sequence.
> *
> + * @deprecated to be removed in version 1.9
> * @param builder FASTQ formatted sequence builder, will not be null
> * @param sequence sequence to validate, will not be null
> * @param lineNumber current line number in input stream
> @@ -92,6 +94,7 @@
> /**
> * Validate the specified repeat description.
> *
> + * @deprecated to be removed in version 1.9
> * @param builder FASTQ formatted sequence builder, will not be null
> * @param repeatDescription repeat description to validate, will
> not be null
> * @param lineNumber current line number in input stream
> @@ -103,6 +106,7 @@
> /**
> * Validate the specified quality scores.
> *
> + * @deprecated to be removed in version 1.9
> * @param builder FASTQ formatted sequence builder, will not be null
> * @param quality quality scores to validate, will not be null
> * @param lineNumber current line number in input stream
>
>
> After the 1.8.2 release, I will commit the remainder of my fastq
> changes in preparation for a version 1.9 release. Alternatively, if
> there is no concern about the binary incompatibilities described
> below, I could skip the mark as @deprecated in 1.8.2 step and commit
> my changes before a 1.8.2 release.
>
>
> I assume the documentation on cutting a release at
>
> http://biojava.org/wiki/BioJava:Make_release
>
> is still relevant?
>
> michael
>
>
>> On Tue, Mar 6, 2012 at 6:18 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> both 1.8.1. and 1.9 are good names IMHO... Did you do the changes also
>>> in the 3.X copy of this?
>>>
>>> Andreas
>>>
>>> On Tue, Mar 6, 2012 at 2:44 PM, Michael Heuer <heuermh at gmail.com> wrote:
>>>> Hello,
>>>>
>>>> I was wondering what the policy is with regards to binary
>>>> compatibility between releases. I have some changes to FASTQ support
>>>> in mind which result in the following binary incompatible changes.
>>>>
>>>> Is it ok to make such changes? I would argue that it is:
>>>> FastqVariant is final and an enum, so it should not possible for
>>>> client code to be effected. Likewise, IlluminaFastqReader,
>>>> SangerFastqReader, SolexaFastqReader are all final classes.
>>>>
>>>> If ok, should the next version of biojava-legacy be 1.8.2, 1.9 or 2.0?
>>>> I would prefer marking the validateXxx methods as @deprecated in
>>>> 1.8.2 and then releasing 1.9 with the new changes.
>>>>
>>>> michael
>>>>
>>>>
>>>> The results of clirr between my working directory and version 1.8.1 are
>>>>
>>>> Error Added abstract modifier to
>>>> class org.biojava.bio.program.fastq.FastqVariant
>>>> Error Abstract method 'public double
>>>> errorProbability(int)' has been
>>>> added org.biojava.bio.program.fastq.FastqVariant
>>>> public double
>>>> errorProbability(int)
>>>> Error Abstract method 'public int maximumQualityScore()' has been
>>>> added org.biojava.bio.program.fastq.FastqVariant
>>>> public int
>>>> maximumQualityScore()
>>>> Error Abstract method 'public int minimumQualityScore()' has been
>>>> added org.biojava.bio.program.fastq.FastqVariant
>>>> public int
>>>> minimumQualityScore()
>>>> Error Abstract method 'public int qualityScore(char)' has been
>>>> added org.biojava.bio.program.fastq.FastqVariant
>>>> public int
>>>> qualityScore(char)
>>>> Error Method 'protected void
>>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader
>>>> protected
>>>> void validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader
>>>> protected
>>>> void validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader
>>>> protected
>>>> void validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.IlluminaFastqReader
>>>> protected
>>>> void validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SangerFastqReader protected void
>>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>>> validateDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>>> validateQuality(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>>> validateRepeatDescription(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> Error Method 'protected void
>>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)' has been
>>>> removed org.biojava.bio.program.fastq.SolexaFastqReader protected void
>>>> validateSequence(org.biojava.bio.program.fastq.FastqBuilder,
>>>> java.lang.String, int)
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
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--------------------------------
George Waldon
Gene Infinity LLC
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