Merge 8e9f94c

hernanmd · Aug 16, 2023 · 21c0f48 · 21c0f48
2 parents d0154fa + 8e9f94c
commit 21c0f48
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Showing 3 changed files with 16 additions and 41 deletions.
diff --git a/repository/BioNCBI/BioNCBIChrGD.class.st b/repository/BioNCBI/BioNCBIChrGD.class.st
@@ -170,6 +170,7 @@ BioNCBIChrGD >> downloadChromosomes: chrInterval [
 BioNCBIChrGD >> initialize [
 	" Private - See superimplementor's comment "
 
+	super initialize.
 	self beChrFileZeroPrefixed.
 	self beChrDirZeroPrefixed.
 ]

diff --git a/repository/BioPlots/BioSequence.extension.st b/repository/BioPlots/BioSequence.extension.st
@@ -44,44 +44,18 @@ BioSequence >> plotGcSkewInt [
 BioSequence >> plotGcSkewInt: extentPoint x: xLabel y: yLabel [
 	" Plot receiver's GC skew "
 
-	| b values ds |
-	b := RTGrapher new.
-	values := self gcSkewInt.
-	b 
-		extent: extentPoint.
-" if: [:value | value < 0 ] fillColor: (Color red alpha: 0.3). 
-		if: [ :v | v < 0 ] fillColor: Color red;
-		if: [ :v | v > 0 ] fillColor: Color green.
-"
-	ds := RTData new.
-	ds interaction popup.
-	ds points: values.
-	ds connectColor: Color red.
-"	ds y: #yourself."
-
-	b add: ds.
-
-	" Configure axis settings "
-	b axisY 
-		minValue: values min;
-		title: yLabel;
-		color: Color black;
-		noDecimal.
-	self size > 80
-		ifTrue: [
-			ds noDot. 
-			b axisX 
-				numberOfTicks: 10;
-				noLabel ]
-		ifFalse: [ 
-			b axisX
-				numberOfTicks: self size;
-				numberOfLabels: self size ].
-	b axisX
-		noDecimal;
-		color: Color black;
-		title: xLabel.		
-
-"	b build."
-	b open
+	| chart  positionsInSequence |
+
+	positionsInSequence := (1 to: self sequence size) asArray.
+	chart := RSCompositeChart new.
+	chart horizontalTick integer.
+	chart
+		extent: extentPoint;
+		title: 'GC Skew (' , self size asString , ' bp)';
+		xlabel: xLabel;
+		ylabel: yLabel;
+		add: (RSLinePlot new 
+			x: positionsInSequence y: self gcSkewInt allButFirst;
+			color: Color blue);
+		open
 ]
diff --git a/repository/BioTools/BioDownloader.trait.st b/repository/BioTools/BioDownloader.trait.st
@@ -127,7 +127,7 @@ BioDownloader >> prvDownloadFileNamed: fileName binary: boolean [
 
 	self bioLog: 'Started download of ' , fileName.			
 	stream := [ self newFileNamed: fileName ]
-	on: FileExistsException
+	on: FileAlreadyExistsException  
 	do: [ : ex | ^ self ].
 	boolean ifTrue: [ stream binary ].
 	self flag: #needsWork. " on: TelnetProtocolError  ....: Could not enter passive mode: 421 Idle timeout (420 seconds): closing control connection "