org.biojava.bio.symbol

Class ChunkedSymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.symbol.ChunkedSymbolList

All Implemented Interfaces:

Serializable, SymbolList, Changeable

public class ChunkedSymbolList
extends AbstractSymbolList
implements Serializable

SymbolList implementation using constant-size chunks. Each chunk provides the same number of symbols (except the last one, which may be shorter). When a request for symbols comes in, firstly the apropreate chunk is located, and then the symbols are extracted. This implementation is used in the IO package to avoid allocating and re-allocating memory when the total length of the symbol list is unknown. It can also be used when chunks are to be lazily fetched from some high-latency stoorage by implementing a single lazy-fetch SymbolList class and populating a ChunkedSymbolList with a complete tile-path of them.

Author:

David Huen, Matthew Pocock, George Waldon

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Field Summary

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)

Method Summary

Modifier and Type	Method and Description
void	edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
protected void	finalize()
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
int	length() The number of symbols in this SymbolList.
SymbolList	subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
Symbol	symbolAt(int pos) Return the symbol at index, counting from 1.

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList

equals, hashCode, iterator, seqString, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

ChunkedSymbolList

public ChunkedSymbolList(SymbolList[] chunks,
                         int chunkSize,
                         int length,
                         Alphabet alpha)

Method Detail

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolList

The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

symbolAt

public Symbol symbolAt(int pos)

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

pos - the offset into this SymbolList

Returns:

the Symbol at that index

subList

public SymbolList subList(int start,
                          int end)

Description copied from interface: SymbolList

Return a new SymbolList for the symbols start to end inclusive.

The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

Specified by:

subList in interface SymbolList

Overrides:

subList in class AbstractSymbolList

Parameters:

start - the first symbol of the new SymbolList

end - the last symbol (inclusive) of the new SymbolList

edit

public void edit(Edit edit)
          throws IllegalAlphabetException,
                 ChangeVetoException

Description copied from interface: SymbolList

Apply an edit to the SymbolList as specified by the edit object.

Description

All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

The pos and pos+length should always be valid positions on the SymbolList to:

• be edited (between 0 and symL.length()+1).
• To append to a sequence, pos=symL.length()+1, pos=0.
• To insert something at the beginning of the sequence, set pos=1 and length=0.

Examples

 SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
 System.out.println(seq.seqString());

 // delete 5 bases from position 4
 Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // delete one base from the start
 ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);

 // delete one base from the end
 ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // overwrite 2 bases from position 3 with "tt"
 ed = new Edit(3, 2, DNATools.createDNA("tt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 6 bases to the start
 ed = new Edit(1, 0, DNATools.createDNA("aattgg");
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 4 bases to the end
 ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // full edit
 ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
 seq.edit(ed);
 System.out.println(seq.seqString());
 

Specified by:

edit in interface SymbolList

Overrides:

edit in class AbstractSymbolList

Parameters:

edit - the Edit to perform

Throws:

IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet

ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed