Skip to content

Add BioLocus methods and tests #10

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
hernanmd merged 1 commit into from
Mar 23, 2026
+301 −8
Merged

Add BioLocus methods and tests #10

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
80 changes: 80 additions & 0 deletions repository/BioTools-Tests/BioLocusTest.class.st
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,80 @@
"
Tests for BioLocus interval and coordinate behavior.
"
Class {
#name : 'BioLocusTest',
#superclass : 'TestCase',
#category : 'BioTools-Tests',
#package : 'BioTools-Tests'
}

{ #category : 'tests' }
BioLocusTest >> testContainsLocusAndUnion [
| outer inner disjoint union |
outer := BioLocus new
name: 'outer';
chrLocation: 'chr2';
from: 10 to: 100;
yourself.
inner := BioLocus new
name: 'inner';
chrLocation: 'chr2';
from: 25 to: 40;
yourself.
disjoint := BioLocus new
name: 'disjoint';
chrLocation: 'chr2';
from: 150 to: 200;
yourself.

self assert: (outer containsLocus: inner).
self deny: (inner containsLocus: outer).
self deny: (outer overlaps: disjoint).
self assert: (outer distanceTo: disjoint) equals: 50.

union := outer unionWith: disjoint.
self assert: union notNil.
self assert: union start equals: 10.
self assert: union end equals: 200
]

{ #category : 'tests' }
BioLocusTest >> testCoordinateConversionsAndNormalization [
| locus |
locus := BioLocus new
name: 'x';
chrLocation: 'chrX';
from: 30 to: 10;
yourself.

self deny: locus isValidRange.
locus normalizeBounds.
self assert: locus isValidRange.
self assert: locus start equals: 10.
self assert: locus end equals: 30.
self assert: locus length equals: 21.
self assert: locus asBedInterval equals: #(9 30).
self assert: locus asGffInterval equals: #(10 30)
]

{ #category : 'tests' }
BioLocusTest >> testOverlapIntersectionAndDistance [
| a b i |
a := BioLocus new
name: 'a';
chrLocation: 'chr1';
from: 100 to: 200;
yourself.
b := BioLocus new
name: 'b';
chrLocation: 'chr1';
from: 150 to: 250;
yourself.

self assert: (a overlaps: b).
i := a intersectionWith: b.
self assert: i notNil.
self assert: i start equals: 150.
self assert: i end equals: 200.
self assert: (a distanceTo: b) equals: 0
]
229 changes: 221 additions & 8 deletions repository/BioTools/BioLocus.class.st
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,21 +31,70 @@ Class {
{ #category : 'examples' }
BioLocus class >> example01 [

^ self class new
^ self new
name: 'BM1818';
chrLocation: 'D23S21';
beSimpleRepeat;
yourself

]

{ #category : 'instance creation' }
BioLocus class >> newFrom: aStart to: anEnd chr: aChr [
^ self new
start: aStart;
end: anEnd;
recomputeLength;
chrLocation: aChr;
yourself
]

{ #category : 'comparing' }
BioLocus >> < aBioLocus [
"Sort by chromosome then start then end then name."
self chrLocation = aBioLocus chrLocation ifFalse: [
^ (self chrLocation ifNil: [ '' ]) < (aBioLocus chrLocation ifNil: [ '' ]) ].
self start = aBioLocus start ifFalse: [ ^ (self start ifNil: [ 0 ]) < (aBioLocus start ifNil: [ 0 ]) ].
self end = aBioLocus end ifFalse: [ ^ (self end ifNil: [ 0 ]) < (aBioLocus end ifNil: [ 0 ]) ].
^ (self name ifNil: [ '' ]) < (aBioLocus name ifNil: [ '' ])
]

{ #category : 'comparing' }
BioLocus >> = anObject [
self == anObject ifTrue: [ ^ true ].
(self class = anObject class) ifFalse: [ ^ false ].
^ self name = anObject name
and: [ self chrLocation = anObject chrLocation
and: [ self start = anObject start
and: [ self end = anObject end
and: [ self value = anObject value ] ] ] ]
]

{ #category : 'converting' }
BioLocus >> asBedInterval [
"Answer a 0-based half-open interval pair suitable for BED-like exports.
Returns an Array {start0 . end0} or nil when no range is present."
self hasRange ifFalse: [ ^ nil ].
^ { self start - 1. self end }
]

{ #category : 'converting' }
BioLocus >> asGffInterval [
"Answer an Array with 1-based closed coordinates {start . end}."
self hasRange ifFalse: [ ^ nil ].
^ { self start. self end }
]

{ #category : 'converting' }
BioLocus >> asString [
" Answer a <String> representation of the receiver "

^ String streamContents: [ : stream |
stream nextPutAll: self name between: $[ and: $].
self printRangeOn: stream ]

^ String
streamContents: [ :stream |
stream
nextPutAll: self name
between: $[
and: $].
self printRangeOn: stream ]
]

{ #category : 'accessing - public' }
Expand All @@ -62,6 +111,54 @@ BioLocus >> chrLocation: aString [
chrLocation := aString
]

{ #category : 'testing' }
BioLocus >> containsLocus: aBioLocus [
"Answer true when aBioLocus is fully contained in receiver.
Chromosome must match when both are defined."

(aBioLocus isNil or: [ self hasRange not ]) ifTrue: [ ^ false ].
aBioLocus hasRange ifFalse: [ ^ false ].
((self chrLocation notNil
and: [ aBioLocus chrLocation notNil ])
and: [ self chrLocation ~= aBioLocus chrLocation ])
ifTrue: [ ^ false ].
^ self start <= aBioLocus start and: [ self end >= aBioLocus end ]
]

{ #category : 'testing' }
BioLocus >> containsPosition: aNumber [
"Alias for rangeIncludes: for a clearer API."
^ self rangeIncludes: aNumber
]

{ #category : 'copying' }
BioLocus >> copyFrom: aBioLocus [
"Copy relevant coordinates and metadata from aBioLocus."
self name: aBioLocus name.
self chrLocation: aBioLocus chrLocation.
self start: aBioLocus start.
self end: aBioLocus end.
self length: aBioLocus length.
self position: aBioLocus position.
self value: aBioLocus value.
^ self
]

{ #category : 'comparing' }
BioLocus >> distanceTo: aBioLocus [
"Answer distance in bases to aBioLocus.
0 when overlapping; nil when not comparable (missing range or chromosome mismatch)."

(self hasRange not or: [ aBioLocus isNil or: [ aBioLocus hasRange not ] ])
ifTrue: [ ^ nil ].
((self chrLocation notNil and: [ aBioLocus chrLocation notNil ])
and: [ self chrLocation ~= aBioLocus chrLocation ])
ifTrue: [ ^ nil ].
(self overlaps: aBioLocus) ifTrue: [ ^ 0 ].
self end < aBioLocus start ifTrue: [ ^ aBioLocus start - self end ].
^ self start - aBioLocus end
]

{ #category : 'accessing' }
BioLocus >> end [
" Answer a <Number> of the receiver's end "
Expand All @@ -74,6 +171,64 @@ BioLocus >> end: aNumber [
end := aNumber
]

{ #category : 'accessing' }
BioLocus >> from: aStart length: aLength [
"Set locus using start and length (inclusive coordinates)."
self start: aStart.
self length: aLength.
end := (aStart isNil or: [ aLength isNil ])
ifTrue: [ nil ]
ifFalse: [ aStart + aLength - 1 ].
^ self
]

{ #category : 'accessing' }
BioLocus >> from: aStart to: anEnd [
"Set start/end and derive length using inclusive coordinates."
self start: aStart.
self end: anEnd.
self recomputeLength.
^ self
]

{ #category : 'testing' }
BioLocus >> hasRange [
"Answer whether receiver has both start and end coordinates."
^ self start notNil and: [ self end notNil ]
]

{ #category : 'comparing' }
BioLocus >> hash [
^ { self class. self name. self chrLocation. self start. self end. self value } hash
]

{ #category : 'operations' }
BioLocus >> intersectionWith: aBioLocus [
"Answer a new BioLocus representing the interval intersection, or nil."
| newStart newEnd |
(self overlaps: aBioLocus) ifFalse: [ ^ nil ].
newStart := self start max: aBioLocus start.
newEnd := self end min: aBioLocus end.
^ self class new
name: (self name ifNil: [ aBioLocus name ]);
chrLocation: (self chrLocation ifNil: [ aBioLocus chrLocation ]);
value: (self value ifNil: [ aBioLocus value ]);
from: newStart to: newEnd;
yourself
]

{ #category : 'testing' }
BioLocus >> isPoint [
"Answer whether receiver represents a single-position locus."
^ self hasRange and: [ self start = self end ]
]

{ #category : 'testing' }
BioLocus >> isValidRange [
"Answer whether receiver range is well-formed (start <= end)."
^ self hasRange and: [ self start <= self end ]
]

{ #category : 'accessing' }
BioLocus >> length [
" Answer a <Number> of the length of this range "
Expand All @@ -88,6 +243,28 @@ BioLocus >> length: aNumber [
length := aNumber
]

{ #category : 'private' }
BioLocus >> normalizeBounds [
"Ensure start <= end by swapping when needed, then recompute length."
(start notNil and: [ end notNil and: [ start > end ] ]) ifTrue: [
| tmp |
tmp := start.
start := end.
end := tmp ].
self recomputeLength.
^ self
]

{ #category : 'testing' }
BioLocus >> overlaps: aBioLocus [
"Answer true if receiver overlaps aBioLocus.
Chromosome must match when both are defined."
(aBioLocus isNil or: [ self hasRange not or: [ aBioLocus hasRange not ] ]) ifTrue: [ ^ false ].
((self chrLocation notNil and: [ aBioLocus chrLocation notNil ])
and: [ self chrLocation ~= aBioLocus chrLocation ]) ifTrue: [ ^ false ].
^ self start <= aBioLocus end and: [ aBioLocus start <= self end ]
]

{ #category : 'accessing' }
BioLocus >> position [
^ position
Expand Down Expand Up @@ -136,11 +313,11 @@ BioLocus >> printNameOn: aStream [

{ #category : 'printing' }
BioLocus >> printOn: aStream [
" Private - See superimplementor's comment "
"Private - See superimplementor's comment"

super printOn: aStream.
self printNameOn: aStream.
self printRangeOn: aStream.
self hasRange ifTrue: [ self printRangeOn: aStream ].
self printChrOn: aStream.
self printLengthOn: aStream.
self printValueOn: aStream
Expand Down Expand Up @@ -187,6 +364,25 @@ BioLocus >> rangeIncludes: posNumber chrLocation: chrNumber [
^ (self start notNil and: [ self end notNil ]) and: [ self chrLocation = chrNumber and: [ self rangeIncludes: posNumber ] ]
]

{ #category : 'private' }
BioLocus >> recomputeLength [
"Recompute length from start/end using inclusive genomic coordinates."
(start isNil or: [ end isNil ])
ifTrue: [ length := nil ]
ifFalse: [ length := (end - start) + 1 ].
^ length
]

{ #category : 'operations' }
BioLocus >> shiftBy: anInteger [
"Shift range coordinates by anInteger bases."
self hasRange ifTrue: [
self start: self start + anInteger.
self end: self end + anInteger ].
position notNil ifTrue: [ position := position + anInteger ].
^ self
]

{ #category : 'accessing' }
BioLocus >> start [
" Answer a <Number> of the receiver's start "
Expand All @@ -200,6 +396,23 @@ BioLocus >> start: aNumber [
start := aNumber
]

{ #category : 'operations' }
BioLocus >> unionWith: aBioLocus [
"Answer a new BioLocus spanning receiver and aBioLocus.
Requires compatible chromosomes when both are defined."
| newStart newEnd |
(self hasRange not or: [ aBioLocus isNil or: [ aBioLocus hasRange not ] ]) ifTrue: [ ^ nil ].
((self chrLocation notNil and: [ aBioLocus chrLocation notNil ])
and: [ self chrLocation ~= aBioLocus chrLocation ]) ifTrue: [ ^ nil ].
newStart := self start min: aBioLocus start.
newEnd := self end max: aBioLocus end.
^ self class new
name: (self name ifNil: [ aBioLocus name ]);
chrLocation: (self chrLocation ifNil: [ aBioLocus chrLocation ]);
from: newStart to: newEnd;
yourself
]

{ #category : 'accessing' }
BioLocus >> value [
^ value
Expand Down
Loading