Add full frequency table for every possible k-mer (named integer vector or matrix with all 4^k entries). Similar to Biostrings (oligonucleotideFrequency family). (#7)

Add #gtoolkit baseline spec.

Author: hernanmd

repository/BaselineOfBioSmalltalk/BaselineOfBioSmalltalk.class.st

@@ -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' }
@@ -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' }

repository/BioTools-Tests/BioAlphabetTest.class.st

@@ -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' }

repository/BioTools-Tests/BioGenomicRangesTest.class.st

@@ -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
 ]
@@ -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.