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Still requires some implementation of default behaviour, but depends on the discussion about API definitions. |
| * @author Daniel Gomez-Sanchez (magicDGS) | ||
| * @implSpec note that 0-length intervals are allowed in an implementation-dependent manner. | ||
| */ | ||
| public interface Locatable { |
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Maybe we should extend Comparable, but I think that it will be better to have a LocatableComparator instead to allow different comprators to be use
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I don't think this should be comparable because there's no single consistent comparator, it depends on how you want to sort he chromosomes.
| * @see #getStart() | ||
| * @see #getEnd() | ||
| */ | ||
| default OptionalLong getLengthOnReference() { |
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I thought about not implementing this in the interface, but an utility class instead which throws if no end is provided.
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Forget about this comment.
| * @implSpec should return {@code false} if {@code referenceMatch(other) == false}. | ||
| * @see #withinDistanceOf(Locatable, int) | ||
| */ | ||
| default boolean overlaps(Locatable other) { |
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We can add also more methods to pad/merge/etc. to make the interface complete...
| * with respect to a reference). | ||
| * </p> | ||
| * | ||
| * @author Daniel Gomez-Sanchez (magicDGS) |
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Do we want author's tags in the new code? My feeling has been that they rapidly become out of date and are handled better by git history. Do others feel differently?
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Was the default in my IDE - will remove!
| * > getEnd()}). | ||
| * @see #getStart() | ||
| */ | ||
| OptionalLong getEnd(); |
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Why make this optional? In a 1-based system a point just has end == start. Better to just require it I think and a point class can avoid storing it if they want. Adding an optional adds boxing overhead and complexity.
| @@ -0,0 +1,140 @@ | |||
| package org.samtools.htsjdk.core; | |||
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How do you feel by making a package that is called org.samtools.htsjdk.core.api for the core interfaces and then a implementation-specific package? For example (just care about the api name, the rest are just first idea of how to name specific implementations):
Readinterface in theapipackage, andSAMRecordimplementation inorg.samtools.htsjdk.core.samVariantinterface in theapipackage, andVCFRecordimplementation inorg.samtools.htsjdk.core.vcf
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Rebased into the latest master (build system parts are removed). |
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