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Merged
hernanmd merged 1 commit into from
Mar 16, 2026
Merged

Add full frequency table for every possible k-mer #7

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78 changes: 42 additions & 36 deletions repository/BaselineOfBioSmalltalk/BaselineOfBioSmalltalk.class.st
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Original file line number Diff line number Diff line change
Expand Up @@ -20,33 +20,31 @@ Class {

{ #category : 'baselines' }
BaselineOfBioSmalltalk >> baseline: spec [
<baseline>

spec for: #'common' do: [
spec blessing: #'baseline'.

spec preLoadDoIt: #preLoad.
spec postLoadDoIt: #'postLoad'.

self
projectSpecForCommonUtils: spec;
projectSpecForDataDrameInspector: spec;
"projectSpecForProjectFramework: spec;"
projectSpecForStringExtensions: spec;
projectSpecForFileDialog: spec;
projectSpecForPolyMath: spec;
projectSpecForDataFrame: spec;
projectSpecForINIParser: spec;
projectSpecForPetitParser: spec;
projectSpecForNeedlemanWunsch: spec.
<baseline>
spec for: #common do: [
spec blessing: #baseline.

spec preLoadDoIt: #preLoad.
spec postLoadDoIt: #postLoad.

self
projectSpecForCommonUtils: spec;
projectSpecForDataDrameInspector: spec;
"projectSpecForProjectFramework: spec;"
projectSpecForStringExtensions: spec;
projectSpecForFileDialog: spec;
projectSpecForPolyMath: spec;
projectSpecForDataFrame: spec;
projectSpecForINIParser: spec;
projectSpecForPetitParser: spec;
projectSpecForNeedlemanWunsch: spec.
"projectSpecForRoassal2: spec."

self baselineOSDeps: spec.
self baselineCommonPackages: spec.
self baselineGroups: spec ].

self baselinePharo: spec.
self baselineCommonPackages: spec.
self baselineGroups: spec ].

self baselinePharo: spec
]

{ #category : 'groups' }
Expand Down Expand Up @@ -170,26 +168,34 @@ BaselineOfBioSmalltalk >> baselineOSDeps: spec [
{ #category : 'baselines' }
BaselineOfBioSmalltalk >> baselinePharo: spec [

spec for: #( #gtoolkit ) do: [
self projectSpecForXMLPharo12: spec.
self commonPackagesForPharo7onWards: spec ].

spec for: #( #'pharo4.x' #'pharo5.x' #'pharo6.x' ) do: [
self projectSpecForXMLPharo7: spec.
spec
package: 'BioTools' with: [ spec includes: #( 'BioPharo4' ) ];
package: 'BioPharo4' with: [ spec requires: #( 'BioTools' ) ];
group: 'Basic' with: #( 'BioPharo4' ) ].
self baselineOSDeps: spec.
self projectSpecForXMLPharo7: spec.
spec
package: 'BioTools' with: [ spec includes: #( 'BioPharo4' ) ];
package: 'BioPharo4' with: [ spec requires: #( 'BioTools' ) ];
group: 'Basic' with: #( 'BioPharo4' ) ].

spec for: #'pharo7.x' do: [
self projectSpecForXMLPharo7: spec.
self commonPackagesForPharo7onWards: spec ].
self baselineOSDeps: spec.
self projectSpecForXMLPharo7: spec.
self commonPackagesForPharo7onWards: spec ].

spec
for: #( #'pharo8.x' #'pharo9.x' #'pharo10.x' #'pharo11.x' )
do: [
self projectSpecForXMLPharo8: spec.
self commonPackagesForPharo7onWards: spec ].

spec for: #( #'pharo12.x' #'pharo13.x' #'pharo14.x') do: [
self projectSpecForXMLPharo12: spec.
self commonPackagesForPharo7onWards: spec ]
self baselineOSDeps: spec.
self projectSpecForXMLPharo8: spec.
self commonPackagesForPharo7onWards: spec ].

spec for: #( #'pharo12.x' #'pharo13.x' #'pharo14.x' ) do: [
self baselineOSDeps: spec.
self projectSpecForXMLPharo12: spec.
self commonPackagesForPharo7onWards: spec ]
]

{ #category : 'baselines' }
Expand Down
8 changes: 4 additions & 4 deletions repository/BioTools-Tests/BioAlphabetTest.class.st
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@@ -1,12 +1,12 @@
Class {
#name : 'BioAlphabetTest',
#superclass : 'BioAbstractTest',
#category : 'BioTools-Tests-Alphabets',
#package : 'BioTools-Tests',
#tag : 'Alphabets',
#instVars : [
'alphabet'
]
],
#category : 'BioTools-Tests-Alphabets',
#package : 'BioTools-Tests',
#tag : 'Alphabets'
}

{ #category : 'testing' }
Expand Down
38 changes: 31 additions & 7 deletions repository/BioTools-Tests/BioGenomicRangesTest.class.st
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Expand Up @@ -223,13 +223,15 @@ BioGenomicRangesTest >> testFromGFF [

{ #category : 'tests' }
BioGenomicRangesTest >> testIRangesRejectNegativeWidth [
self should: [ BioIRanges starts: #(5) ends: #(4) ] raise: Error

self should: [ BioIRanges starts: #( 5 ) ends: #( 4 ) ] raise: Error
]

{ #category : 'tests' }
BioGenomicRangesTest >> testIRangesWidth [

| ir |
ir := BioIRanges starts: #(2 10) ends: #(4 12).
ir := BioIRanges starts: #( 2 10 ) ends: #( 4 12 ).
self assert: (ir width at: 1) equals: 3.
self assert: (ir width at: 2) equals: 3
]
Expand All @@ -251,27 +253,49 @@ BioGenomicRangesTest >> testMetadataCanContainObjects [

{ #category : 'tests' }
BioGenomicRangesTest >> testOverlapWith [

| a b c |
a := BioGenomicRanges seqnames: #('chr1' 'chr1') starts: #(1 50) ends: #(10 60) strands: #('+' '+') metadata: Dictionary new.
b := BioGenomicRanges seqnames: #('chr1') starts: #(5) ends: #(15) strands: #('+') metadata: Dictionary new.
a := BioGenomicRanges
seqnames: #( 'chr1' 'chr1' )
starts: #( 1 50 )
ends: #( 10 60 )
strands: #( '+' '+' )
metadata: Dictionary new.
b := BioGenomicRanges
seqnames: #( 'chr1' )
starts: #( 5 )
ends: #( 15 )
strands: #( '+' )
metadata: Dictionary new.
c := a overlapWith: b.
self assert: c size equals: 1.
self assert: (c start at: 1) equals: 1
]

{ #category : 'tests' }
BioGenomicRangesTest >> testReduceKeepsStrandSeparate [

| gr red |
gr := BioGenomicRanges seqnames: #('chr1' 'chr1') starts: #(1 2) ends: #(5 6) strands: #('+' '-') metadata: Dictionary new.
gr := BioGenomicRanges
seqnames: #( 'chr1' 'chr1' )
starts: #( 1 2 )
ends: #( 5 6 )
strands: #( '+' '-' )
metadata: Dictionary new.
red := gr reduce.
self assert: red size equals: 2

]

{ #category : 'tests' }
BioGenomicRangesTest >> testReduceMergesAdjacent [

| gr red |
gr := BioGenomicRanges seqnames: #('chr1' 'chr1') starts: #(1 6) ends: #(5 10) strands: #('+' '+') metadata: Dictionary new.
gr := BioGenomicRanges
seqnames: #( 'chr1' 'chr1' )
starts: #( 1 6 )
ends: #( 5 10 )
strands: #( '+' '+' )
metadata: Dictionary new.
red := gr reduce.
self assert: red size equals: 1.
self assert: (red start at: 1) equals: 1.
Expand Down
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