org.biojavax.bio.seq

Class InfinitelyAmbiguousSymbolList

java.lang.Object

org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList

All Implemented Interfaces:

SymbolList, Changeable

public class InfinitelyAmbiguousSymbolList
extends Object
implements SymbolList

A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.

Since:

1.5

Author:

Richard Holland, MarkSchreiber

Field Summary

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

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
InfinitelyAmbiguousSymbolList(FiniteAlphabet fa) Creates a new instance of InfinitelyAmbiguousSymbolList

Method Summary

Methods

Modifier and Type	Method and Description
void	addChangeListener(ChangeListener cl) Add a listener that will be informed of all changes.
void	addChangeListener(ChangeListener cl, ChangeType ct) Add a listener that will be informed of changes of a given type.
void	edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
boolean	isUnchanging(ChangeType ct) A particular ChangeType can never be raised by this Changeable.
Iterator	iterator() An Iterator over all Symbols in this SymbolList.
int	length() The number of symbols in this SymbolList.
void	removeChangeListener(ChangeListener cl) Remove a listener that was interested in all types of changes.
void	removeChangeListener(ChangeListener cl, ChangeType ct) Remove a listener that was interested in a specific types of changes.
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.
Symbol	symbolAt(int index) Return the symbol at index, counting from 1.
List	toList() Returns a List of symbols.

Methods inherited from class java.lang.Object

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

Constructor Detail

InfinitelyAmbiguousSymbolList

public InfinitelyAmbiguousSymbolList(FiniteAlphabet fa)

Creates a new instance of InfinitelyAmbiguousSymbolList

Parameters:

fa - the finite alphabet to return ambiguous symbols from.

Method Detail

addChangeListener

public void addChangeListener(ChangeListener cl)

Add a listener that will be informed of all changes. IGNORED

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener to add

addChangeListener

public void addChangeListener(ChangeListener cl,
                     ChangeType ct)

Add a listener that will be informed of changes of a given type. IGNORED

Specified by:

addChangeListener in interface Changeable

Parameters:

cl - the ChangeListener

ct - the ChangeType it is to be informed of

edit

public void edit(Edit edit)
          throws IndexOutOfBoundsException,
                 IllegalAlphabetException,
                 ChangeVetoException

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());
 

IGNORED

Specified by:

edit in interface SymbolList

Parameters:

edit - the Edit to perform

Throws:

IndexOutOfBoundsException - if the edit does not lie within the SymbolList

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

getAlphabet

public Alphabet getAlphabet()

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

isUnchanging

public boolean isUnchanging(ChangeType ct)

A particular ChangeType can never be raised by this Changeable.

If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

ALWAYS RETURNS TRUE

Specified by:

isUnchanging in interface Changeable

Parameters:

ct - the ChangeType to check

Returns:

true if ChangeEvents of this type are guaranteed to never be fired

iterator

public Iterator iterator()

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. ALWAYS RETURNS AN ITERATOR OVER A SINGLE AMBIGUITY SYMBOL

Specified by:

iterator in interface SymbolList

Returns:

an iterator

length

public int length()

The number of symbols in this SymbolList. ALWAYS RETURNS Integer.MAX_VALUE

Specified by:

length in interface SymbolList

Returns:

the length

removeChangeListener

public void removeChangeListener(ChangeListener cl)

Remove a listener that was interested in all types of changes. IGNORED

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener to remove

removeChangeListener

public void removeChangeListener(ChangeListener cl,
                        ChangeType ct)

Remove a listener that was interested in a specific types of changes. IGNORED

Specified by:

removeChangeListener in interface Changeable

Parameters:

cl - a ChangeListener to remove

ct - the ChangeType that it was interested in

seqString

public String seqString()

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. ALWAYS RETURNS THE AMBIGUITY SYMBOL REPRESENTED AS A STRING

Specified by:

seqString in interface SymbolList

Returns:

a string representation of the symbol list

subList

public SymbolList subList(int start,
                 int end)
                   throws IndexOutOfBoundsException

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. ALWAYS RETURNS SELF

Specified by:

subList in interface SymbolList

Parameters:

start - the first symbol of the new SymbolList

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

Throws:

IndexOutOfBoundsException

subStr

public String subStr(int start,
            int end)
              throws IndexOutOfBoundsException

Return a region of this symbol list as a String.

This should use the same rules as seqString. ALWAYS RETURNS THE CORRECT LENGTH STRING MADE UP OF AMBIGUITY SYMBOLS

Specified by:

subStr in interface SymbolList

Parameters:

start - the first symbol to include

end - the last symbol to include

Returns:

the string representation

Throws:

IndexOutOfBoundsException - if either start or end are not within the SymbolList

symbolAt

public Symbol symbolAt(int index)
                throws IndexOutOfBoundsException

Return the symbol at index, counting from 1. ALWAYS RETURNS THE AMBIGUITY SYMBOL

Specified by:

symbolAt in interface SymbolList

Parameters:

index - the offset into this SymbolList

Returns:

the Symbol at that index

Throws:

IndexOutOfBoundsException - if index is less than 1, or greater than the length of the symbol list

toList

public List toList()

Returns a List of symbols.

This is an immutable list of symbols. Do not edit it. ALWAYS RETURNS A LIST CONTAINING THE AMBIGUITY SYMBOL

Specified by:

toList in interface SymbolList

Returns:

a List of Symbols