ChemoJunSdFileReader

ChemoJun050 (2006/08/08) Copyright 2002-2006 National Institute of Informatics, Research Organization of Information and Systems.

category:

• ChemoJun-File-IO

inheritance:

• Object
  • ChemoJunAbstractFile
    • ChemoJunAbstractFileReader
      • ChemoJunSdFileReader

instance variables:

• molFileReaders

class instance variables:

class variables:

pool variables:

instance methods:

1. initialize [initialize-release]
   

   	super initialize.
   	molFileReaders := nil

2. moleculeObjects [accessing]
   

   	^self molFileReaders 
   		collect: [:aReader | self class defaultMoleculeObjectClass fromReader: aReader]

3. molFileReaders [accessing]
   

   	molFileReaders ifNil: [molFileReaders := OrderedCollection new].
   	^molFileReaders

4. readDataItemFrom: aStream [reading]
   

    
   	^self

5. readDataItemsFrom: aStream [reading]
   

    
   	^self

6. readDelimiterFrom: aStream [reading]
   

    
   	[aStream atEnd not] whileTrue: 
   			[| aString aCollection |
   			aString := self getLine: aStream.
   			aCollection := self separate: aString.
   			(aCollection size >= 1 and: [aCollection first = '$$$$']) ifTrue: [^self]].
   	^self

7. readFrom: aStream [reading]
   

    
   	[aStream atEnd not] whileTrue: 
   			[self readMolfileFrom: aStream.
   			self readNonStructuredDataFrom: aStream.
   			self readDelimiterFrom: aStream]

8. readMolfileFrom: aStream [reading]
   

    
   	| molFileReader |
   	molFileReader := self class defaultMolFileReaderClass new.
   	molFileReader readFrom: aStream.
   	self molFileReaders add: molFileReader

9. readNonStructuredDataFrom: aStream [reading]
   

    
   	[aStream atEnd not] whileTrue: 
   			[| aString |
   			self readDataItemFrom: aStream.
   			self readDataItemsFrom: aStream.
   			aString := self getLine: aStream.
   			aString = (String with: Character cr) ifTrue: [^self]].
   	^self

class methods:

1. copyright [copyright]
   

   	^'ChemoJun050 (2006/08/08) Copyright 2002-2006 National Institute of Informatics, Research Organization of Information and Systems.'

2. defaultFileDescriptions [defaults]
   

   	^Array with: (Array 
   				with: (#chemoJun_SD_files >> 'SD files') asString)
   		with: (Array with: (#jun_All_files >> 'All files') asString)

3. defaultFilePatterns [defaults]
   

   	^Array with: #('*.sd' '*.SD') with: #('*')

4. defaultMoleculeObjectClass [defaults]
   

   	^ChemoJunMoleculeObject

5. defaultMolFileReaderClass [defaults]
   

   	^ChemoJunMolFileReader

6. defaultRequestMessageString [defaults]
   

   	^(#chemoJun_Select_a_SD_file_ >> 'Select a SD file.') asString

7. example1 [examples]
   

   	"ChemoJunSdFileReader example1."
   
   	| aReader |
   	aReader := ChemoJunSdFileReader request.
   	aReader isNil ifTrue: [^nil].
   	^aReader

8. example2 [examples]
   

   	"ChemoJunSdFileReader example2."
   
   	| aReader |
   	aReader := ChemoJunSdFileReader request.
   	aReader isNil ifTrue: [^nil].
   	aReader moleculeObjects 
   		do: [:moleculeObject | (ChemoJunMoleculeViewer moleculeObject: moleculeObject) open]

9. system [copyright]
   

   	^'ChemoJun'

10. version [copyright]
    

    	^'050'