[Biojava-dev] binary compatibility policy

[Andreas Prlic]

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)
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