org.biojava.bio.seq.io

Class ChunkedSymbolListFactory

java.lang.Object

org.biojava.bio.seq.io.ChunkedSymbolListFactory

public class ChunkedSymbolListFactory
extends Object

class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.

The advantage is that those SymbolLists can be packed implementations.

You can build a SequenceBuilderFactory to create a packed chunked sequence from an input file without making an intermediate symbol list with:-

 public class PackedChunkedListFactory implements SequenceBuilderFactory
 {
   public SequenceBuilder makeSequenceBuilder()
   {
     return new SequenceBuilderBase() {
       private ChunkedSymbolListFactory chunker = new ChunkedSymbolListFactory(new PackedSymbolListFactory(true));

       // deal with symbols
       public void addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
         throws IllegalAlphabetException
       {
         chunker.addSymbols(alpha, syms, pos, len);
       }

       // make the sequence
       public Sequence makeSequence()
       {
         try {
           // make the SymbolList
           SymbolList symbols = chunker.makeSymbolList();
           seq = new SimpleSequence(symbols, uri, name, annotation);

           // call superclass method
           return super.makeSequence();
         }
         catch (IllegalAlphabetException iae) {
           throw new BioError("couldn't create symbol list");
         }
       }
     };
   }
 }
 

Then reading in FASTA files can be done with something like:-

 SequenceIterator seqI = new StreamReader(br, new FastaFormat(),
     DNATools.getDNA().getTokenization("token"),
     new PackedChunkedListFactory() );
 

Blend to suit taste.

Alternatively, you can input Symbols to the factory with addSymbols make the sequence eventually with makeSymbolList.

NOTE: An improvement has been introduced where an internal default SymbolList factory is used for small sequences. This implementation allows for faster SymbolList creation and access for small sequences while allowing a more space-efficient implementation to be selected for large sequences.

NOTE: This class is inherantly not threadsafe. You should create one instance for each symbol list you wish to manufacture, and then you should throw that instance away.

Author:

David Huen

Constructor Summary

Constructors

Constructor and Description
ChunkedSymbolListFactory(SymbolListFactory symListFactory)
ChunkedSymbolListFactory(SymbolListFactory userSymListFactory, int threshold)

Method Summary

Modifier and Type	Method and Description
void	addSymbols(Alphabet alfa, Symbol[] syms, int pos, int len) tool to construct the SymbolList by adding Symbols.
SymbolList	make(SymbolReader sr) Method to create a Sequence with a SymbolReader.
SymbolList	makeSymbolList() Converts accumulated Symbols to a SymbolList
void	useSuppliedSymListFactory() Call this to convert from default SymbolList implementation to user-supplied implementation.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ChunkedSymbolListFactory

public ChunkedSymbolListFactory(SymbolListFactory symListFactory)

Parameters:

symListFactory - class which produces the SymbolLists that are used to store the chunked symbols.

ChunkedSymbolListFactory

public ChunkedSymbolListFactory(SymbolListFactory userSymListFactory,
                                int threshold)

Parameters:

userSymListFactory - User-supplied class which produces the SymbolLists that are used to store the chunked symbols (only used when the chunked list to be created is larger than threshold.

threshold - the size of the SymbolList beyond which the userSymListFactory is used. Below that, the internal default SymbolList factory is used.

Method Detail

addSymbols

public void addSymbols(Alphabet alfa,
                       Symbol[] syms,
                       int pos,
                       int len)
                throws IllegalArgumentException,
                       IllegalAlphabetException

tool to construct the SymbolList by adding Symbols. Note that this class is not thread-safe. Also, it can only assemble one SymbolList at a time. And the composite formed by adding Symbols must not have interstitial missing Symbols.

Throws:

IllegalArgumentException

IllegalAlphabetException

useSuppliedSymListFactory

public void useSuppliedSymListFactory()

Call this to convert from default SymbolList implementation to user-supplied implementation.

makeSymbolList

public SymbolList makeSymbolList()
                          throws IllegalAlphabetException

Converts accumulated Symbols to a SymbolList

Throws:

IllegalAlphabetException

make

public SymbolList make(SymbolReader sr)
                throws IOException,
                       IllegalSymbolException,
                       IllegalAlphabetException,
                       BioException

Method to create a Sequence with a SymbolReader. (does anyone use this???> readme: As of 12/11/03, there are no references to this method in the codebase

Throws:

IOException

IllegalSymbolException

IllegalAlphabetException

BioException