org.biojava.bio.symbol

Class AbstractSymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

All Implemented Interfaces:

SymbolList, Changeable

Direct Known Subclasses:

AbstractULAlignment, AbstractULAlignment.SubULAlignment, AssembledSymbolList, ChunkedSymbolList, DummySymbolList, NewAssembledSymbolList, PackedSymbolList, SimpleAlignment, SimpleGappedSymbolList, SimpleSymbolList

public abstract class AbstractSymbolList
extends AbstractChangeable
implements SymbolList

Abstract helper implementation of the SymbolList core interface. To produce a concrete SymbolList implementation, you need only implement the getAlphabet, length and symbolAt methods. Iterators and sublists are handled for you automatically.

This class makes many custom SymbolList implementations very quick to implement. See org.biojava.bio.seq.tools.ComplementSymbolList for an example of this.

To make a mutable SymbolList, override the implementation of edit to perform the apropreate edit. If your implementation of SymbolList is a view onto an underlying SymbolList, then you must forward any apropreate edit requests to that list, and forward all events from the underlying list to your listeners.

Author:

Thomas Down, Matthew Pocock

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	AbstractSymbolList.EditScreener This adapter screens all edit events to see if they overlap with a window of interest.
class	AbstractSymbolList.EditTranslater This translates edit events that fall within a window into window co-ordinates.

Field Summary

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

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractSymbolList()

Method Summary

Methods

Modifier and Type	Method and Description
void	edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
boolean	equals(Object o) Provides logical equality for two SymbolLists that share the same list of canonical symbols
int	hashCode()
Iterator<Symbol>	iterator() An Iterator over all Symbols in this SymbolList.
String	seqString() Stringify this symbol list.
SymbolList	subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
String	subStr(int start, int end) Return a region of this symbol list as a String.
List<Symbol>	toList() Returns a List of symbols.
String	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, finalize, getClass, notify, notifyAll, wait, wait, wait

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

getAlphabet, length, symbolAt

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

AbstractSymbolList

protected AbstractSymbolList()

Method Detail

iterator

public Iterator<Symbol> iterator()

Description copied from interface: SymbolList

An Iterator over all Symbols in this SymbolList.

This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.

Specified by:

iterator in interface SymbolList

Returns:

an iterator

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

Parameters:

start - the first symbol of the new SymbolList

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

toList

public List<Symbol> toList()

Description copied from interface: SymbolList

Returns a List of symbols.

This is an immutable list of symbols. Do not edit it.

Specified by:

toList in interface SymbolList

Returns:

a List of Symbols

seqString

public String seqString()

Description copied from interface: SymbolList

Stringify this symbol list.

It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.

Specified by:

seqString in interface SymbolList

Returns:

a string representation of the symbol list

subStr

public String subStr(int start,
            int end)

Description copied from interface: SymbolList

Return a region of this symbol list as a String.

This should use the same rules as seqString.

Specified by:

subStr in interface SymbolList

Parameters:

start - the first symbol to include

end - the last symbol to include

Returns:

the string representation

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

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

equals

public boolean equals(Object o)

Provides logical equality for two SymbolLists that share the same list of canonical symbols

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object