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Basic implementation of an adapter for locatable. #569
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/* | ||
* The MIT License | ||
* | ||
* Copyright (c) 2020 Fulcrum Genomics LLC | ||
* | ||
* Permission is hereby granted, free of charge, to any person obtaining a copy | ||
* of this software and associated documentation files (the "Software"), to deal | ||
* in the Software without restriction, including without limitation the rights | ||
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
* copies of the Software, and to permit persons to whom the Software is | ||
* furnished to do so, subject to the following conditions: | ||
* | ||
* The above copyright notice and this permission notice shall be included in | ||
* all copies or substantial portions of the Software. | ||
* | ||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
* THE SOFTWARE. | ||
*/ | ||
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package com.fulcrumgenomics.util | ||
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import com.fulcrumgenomics.FgBioDef._ | ||
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import htsjdk.samtools.util.{CoordMath, Locatable} | ||
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/** | ||
* Trait that can be added to any class that defines chrom/start/end to implement Locatable | ||
*/ | ||
trait LocatableAdapter[A <: LocatableAdapter[A]] extends Locatable with Ordered[A] { | ||
def chrom: String | ||
def start: Int | ||
def end: Int | ||
def name: String | ||
def negativeStrand: Boolean | ||
def positiveStrand: Boolean = !negativeStrand | ||
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// Implementations of Locatable interface methods | ||
final override def getContig: String = chrom | ||
final override def getStart: Int = start | ||
final override def getEnd: Int = end | ||
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final def length: Int = getLengthOnReference | ||
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/** Calculates the overlap between two locatables assuming that they do in fact overlap. */ | ||
def overlap(other: Locatable): Int = CoordMath.getOverlap(start, end, other.getStart, other.getEnd) | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. This should probably be bullet-proofed to check for overlap first or return 0 if they don't overlap. |
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/** Provides a basic comparison that orders on chrom (lexicographically) and then start and end position. */ | ||
def compare(that: A): Int = { | ||
var result = this.chrom.compareTo(that.chrom) | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Should we have a trait |
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if (result == 0) result = this.start - that.start | ||
if (result == 0) result = this.end - that.end | ||
result | ||
} | ||
} |
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Should this be here? Should it have a default
= ""
or perhaps have typeOption[String] = None
? Or should we have aNamedLocatable
sub-trait?There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I don't think it needs a name at all. Things like
Variant
are locatable, but don't have a name (could default toid
).NamedLocatable
seems also overkill until we have sub-classes that could benefit from a commonNamedLocatable
trait. For the latter, what wouldNamedLocatable
help with? Would we have methods somewhere that operate onname
? That seems a bit kludgy until we have examples.