org.biojava.bio.symbol
Class SymbolList.EmptySymbolList

java.lang.Object
  |
  +--org.biojava.utils.Unchangeable
        |
        +--org.biojava.bio.symbol.SymbolList.EmptySymbolList

All Implemented Interfaces:

Changeable, java.io.Serializable, SymbolList

Enclosing class:

SymbolList

public static class SymbolList.EmptySymbolList

extends Unchangeable

implements SymbolList, java.io.Serializable

The empty immutable implementation.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biojava.bio.symbol.SymbolList

SymbolList.EmptySymbolList

Field Summary

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

EDIT, EMPTY_LIST

Constructor Summary

SymbolList.EmptySymbolList()

Method Summary

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.
java.util.Iterator	iterator() An Iterator over all Symbols in this SymbolList.
int	length() The number of symbols in this SymbolList.
java.lang.String	seqString() Stringify this symbol list.
SymbolList	subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
java.lang.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.
java.util.List	toList() Returns a List of symbols.

Methods inherited from class org.biojava.utils.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SymbolList.EmptySymbolList

public SymbolList.EmptySymbolList()

Method Detail

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 index)
                throws java.lang.IndexOutOfBoundsException

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

index - the offset into this SymbolList

Returns:

the Symbol at that index

Throws:

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

toList

public java.util.List 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

iterator

public java.util.Iterator 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)
                   throws java.lang.IndexOutOfBoundsException

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

java.lang.IndexOutOfBoundsException

seqString

public java.lang.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 java.lang.String subStr(int start,
                               int end)
                        throws java.lang.IndexOutOfBoundsException

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

Throws:

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

edit

public void edit(Edit edit)
          throws java.lang.IndexOutOfBoundsException,
                 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:

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

java.lang.IndexOutOfBoundsException - if the edit does not lie within the SymbolList