Add parser changes

hernanmd · Aug 30, 2023 · 33c2012 · 33c2012
1 parent 8c34b6b
commit 33c2012
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Showing 10 changed files with 265 additions and 118 deletions.
diff --git a/repository/BioParserTests/BioAbstractFASTAParserTest.class.st b/repository/BioParserTests/BioAbstractFASTAParserTest.class.st
@@ -1,7 +1,7 @@
 Class {
 	#name : #BioAbstractFASTAParserTest,
 	#superclass : #BioAbstractParserTest,
-	#category : 'BioParserTests-Core'
+	#category : #'BioParserTests-Core'
 }
 
 { #category : #'samples-single' }
@@ -39,7 +39,8 @@ BioAbstractFASTAParserTest >> fastaSeq04 [
 	^ '>YAL068C-7235.2170 Putative promoter sequence
 TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAATTCGCA
 CAGTTTTCGTTAAGAGAACTTAACATTTTCTTATGACGTAAATGA
-AGTTTATATATAAATTTCCTTTTTATTGGA'
+AGTTTATATATAAATTTCCTTTTTATTGGA
+'
 ]
 
 { #category : #'samples-single' }

diff --git a/repository/BioParserTests/BioFASTAParserTest.class.st b/repository/BioParserTests/BioFASTAParserTest.class.st
diff --git a/repository/BioParsers/BioAbstractParser.class.st b/repository/BioParsers/BioAbstractParser.class.st
@@ -140,7 +140,7 @@ BioAbstractParser >> parseString: aString [
 	^ [ parser
 			parse:  aString
 			onError: [: failure | self error: failure message ] ]
-		on: Exception
+		on: Error
 		do: [: ex | 
 			self beFailed.
 			ex asString ].

diff --git a/repository/BioParsers/BioFASTABasicParser.class.st b/repository/BioParsers/BioFASTABasicParser.class.st
@@ -44,12 +44,14 @@ BioFASTABasicParser >> buildTokens: aCollection [
 BioFASTABasicParser >> fastaParser [
 
 	^ ( 
-		self parserForNonBreakingString , 
+		$> asPParser ,
+		(self noneOf: (Array with: Character cr with: Character lf)) plus flatten , 
 		#newline asPParser ,
-		(self perform: self fastaSequenceParser)
-		) plus end 
-
-
+			(
+				(self noneOf: (Array with: Character cr with: Character lf)) plus flatten , 
+				#newline asPParser star ==> [ :nodes | nodes copyWithoutAll: { Character cr asString . Character lf asString } ]
+			) plus
+		) plus end
 ]
 
 { #category : #initialization }
@@ -70,33 +72,33 @@ BioFASTABasicParser >> initializeWith: aString [
 	" Private - See superimplementor's comment "
 
 	super initializeWith: aString.
-	self fastaSequenceParser: #parserForSequence.
+	self fastaSequenceParser: #parserForSingleSequence.
 	parser := self fastaParser.
 
 ]
 
 { #category : #'accessing-parsers' }
 BioFASTABasicParser >> newLineParser [
 
-	^ #newline asPParser plus optional
+	^ #newline asPParser
 ]
 
 { #category : #'accessing-parsers' }
-BioFASTABasicParser >> parserForSequence [
+BioFASTABasicParser >> parserForSingleSequence [
 	" Answer a parser for parsing sequences as usually found in FASTA formatted files "
 
 	^ (
 			(
-			#word asPParser plus flatten , 
-			self newLineParser ==> self removeNewlinesBlock
-			) min: 1
-		) optimize
+				self parserForNonBreakingString , 
+				self newLineParser optional ==> self removeNewlinesBlock
+			) plus
+		)
 ]
 
 { #category : #removing }
 BioFASTABasicParser >> removeNewlinesBlock [
 
-	^ [ :nodes | nodes copyWithoutAll: { Character cr . Character lf } ]
+	^ [ :nodes | nodes copyWithoutAll: { Character cr asString . Character lf asString } ]
 ]
 
 { #category : #'accessing private' }

diff --git a/repository/BioParsers/BioFASTAMultiParser.class.st b/repository/BioParsers/BioFASTAMultiParser.class.st
@@ -8,7 +8,7 @@ Class {
 }
 
 { #category : #'instance creation' }
-BioFASTAMultiParser class >> onAmbigousGapped: anExpressionString [
+BioFASTAMultiParser class >> onAmbiguousGapped: anExpressionString [
 
 	^ self basicNew
 		fastaSequenceParser: #parserForAmbibuousGappedSequence;
@@ -49,6 +49,7 @@ BioFASTAMultiParser >> parseResultClass [
 BioFASTAMultiParser >> parserForAmbibuousGappedSequence [
 	" Configure the receiver's parser to parse DNA alignment (gaps are allowed) "
 
+	self halt.
 	^ (
 			(
 			#dnaAmbiguousLetterGapped asPParser plus flatten , 

diff --git a/repository/BioParsers/BioParser.class.st b/repository/BioParsers/BioParser.class.st
@@ -50,7 +50,7 @@ Class {
 BioParser class >> parseAccession: aString [
 	" Parse aString containing an accession number and answer an accession instance "
 
-	^ ( BioAccessionParser on: aString ) parse
+	^ (BioAccessionParser on: aString) parse
 ]
 
 { #category : #'instance creation' }
@@ -109,37 +109,28 @@ BioParser class >> parseMultiFasta: aFastaString [
 	" Parser aFastaString representing a MultiFASTA sequence.
 	Answer a FastaMultiRecord object "
 
-	^ (BioFASTAMultiParser onAmbigousGapped: aFastaString) parse
+	^ (BioFASTAMultiParser onAmbiguousGapped: aFastaString) parse
 ]
 
 { #category : #'parse-fasta' }
 BioParser class >> parseMultiFastaAlignment: aFastaString [
 	" Parser aFastaString representing a <String> containing multiple sequences in FASTA format.
 	Answer a <BioFastaMultiRecord> object "
 
-	^ (BioFASTAMultiParser onAmbigousGapped: aFastaString) parse
+	^ (BioFASTAMultiParser onAmbiguousGapped: aFastaString) parse
 ]
 
 { #category : #'parse-fasta' }
 BioParser class >> parseMultiFastaAlignmentFile: aFastaFullFileLocation [
 	" Parse aFastaFullFileLocation representing a <String> containing a file with multiple sequences in FASTA format. Answer a <BioAlignment> object "
-
-	^ (BioFASTAMultiParser onAmbigousGapped: 
-			(self openFullFileNamed: aFastaFullFileLocation) contents) parse asAlignment
-]
 
-{ #category : #'parse-fasta' }
-BioParser class >> parseMultiFastaAlignmentFileFast: aFastaFullFileLocation [
-	" Parse aFastaFullFileLocation representing a <String> containing a file with multiple sequences in FASTA format. Answer a <BioAlignment> object "
-
-	^ (BioFASTAMultiParser
-		onAmbigousGapped: (self openFullFileNamed: aFastaFullFileLocation)) parse asAlignment
+	^ (BioFASTAMultiParser onAmbiguousGapped: 
+			(self openFullFileNamed: aFastaFullFileLocation) contents) parse asAlignment
 ]
 
 { #category : #'parse-fasta' }
 BioParser class >> parseMultiFastaFile: aFastaFullFileLocation [
-	" Parser aFastaString representing a MultiFASTA sequence.
-	Answer a FastaMultiRecord object "
+	" Parse aFastaFullFileLocation (extensions .fa, .fasta, .fas, etc) representing a MultiFASTA sequence, i.e. a file which contains multiple fasta sequences. Answer a <BioFastaMultiRecord> object "
 
 	^ (BioFASTAMultiParser on: (self openFullFileNamed: aFastaFullFileLocation) contents) parse
 ]

diff --git a/repository/BioParsers/BioSAXParser.class.st b/repository/BioParsers/BioSAXParser.class.st
@@ -109,6 +109,12 @@ BioSAXParser >> current: anObject [
 	current := anObject
 ]
 
+{ #category : #accessing }
+BioSAXParser >> driver [
+
+	^ self parser driver
+]
+
 { #category : #private }
 BioSAXParser >> estimatedResultSize [
 	" Answer a <Number> of approximate found nodes in the receiver parsed file "
@@ -179,9 +185,7 @@ BioSAXParser >> parseDocument [
 	" Private - Parse receiver's input "
 
 	self bioLog: 'Start parsing document...' translated.
-	[ self driver reset ]
-		on: MessageNotUnderstood
-		do: [ :ex | self input reset ].
+	self input reset.
 	super parseDocument.
 	self bioLog: 'End parsing document' translated.
 	^ results

diff --git a/repository/BioTools/BioIUPACAmbiguousRNA.class.st b/repository/BioTools/BioIUPACAmbiguousRNA.class.st
@@ -1,7 +1,12 @@
+"
+It represents the IUPAC RNA alphabet for ambiguous bases.
+See class side for implementation details.
+
+"
 Class {
 	#name : #BioIUPACAmbiguousRNA,
 	#superclass : #BioIUPACRNA,
-	#category : 'BioTools-Alphabets'
+	#category : #'BioTools-Alphabets'
 }
 
 { #category : #accessing }

diff --git a/repository/BioTools/BioIUPACRNA.class.st b/repository/BioTools/BioIUPACRNA.class.st
@@ -1,7 +1,12 @@
+"
+Abstract class grouping codes for RNA alphabets.
+See subclasses for specific details.
+
+"
 Class {
 	#name : #BioIUPACRNA,
 	#superclass : #BioIUPACAlphabet,
-	#category : 'BioTools-Alphabets'
+	#category : #'BioTools-Alphabets'
 }
 
 { #category : #accessing }

diff --git a/repository/BioTools/BioIUPACUnambiguousRNA.class.st b/repository/BioTools/BioIUPACUnambiguousRNA.class.st
@@ -1,7 +1,11 @@
+"
+It represents the IUPAC RNA alphabet for unambiguous bases.
+See class side for implementation details.
+"
 Class {
 	#name : #BioIUPACUnambiguousRNA,
 	#superclass : #BioIUPACRNA,
-	#category : 'BioTools-Alphabets'
+	#category : #'BioTools-Alphabets'
 }
 
 { #category : #accessing }