org.biojava.bio.symbol

Interface SymbolList

All Superinterfaces:

Changeable

All Known Subinterfaces:

Alignment, ARAlignment, GappedSequence, GappedSymbolList, RichSequence, Sequence, StatePath, UnequalLengthAlignment

All Known Implementing Classes:

AbstractSymbolList, AbstractULAlignment, AbstractULAlignment.SubULAlignment, AlignmentPair, AssembledSymbolList, ChunkedSymbolList, CircularView, DummySequence, DummySymbolList, FlexibleAlignment, InfinitelyAmbiguousSymbolList, NewAssembledSymbolList, NewSimpleAssembly, PackedSymbolList, PhredSequence, RelabeledAlignment, RevCompSequence, SimilarityPairFeature.EmptyPairwiseAlignment, SimpleAlignment, SimpleAssembly, SimpleGappedSequence, SimpleGappedSymbolList, SimpleRichSequence, SimpleSequence, SimpleStatePath, SimpleSymbolList, SubSequence, ThinRichSequence, ViewSequence

public interface SymbolList
extends Changeable

A sequence of symbols that belong to an alphabet.

This uses biological coordinates (1 to length).

Author:

Matthew Pocock, Mark Schreiber, Francois Pepin

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	EDIT Signals that the SymbolList is being edited.
static SymbolList	EMPTY_LIST A useful object that represents an empty symbol list, to avoid returning null.

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.
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
Iterator<Symbol>	iterator() An Iterator over all Symbols in this SymbolList.
int	length() The number of 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.
Symbol	symbolAt(int index) Return the symbol at index, counting from 1.
List<Symbol>	toList() Returns a List of symbols.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

EDIT

static final ChangeType EDIT

Signals that the SymbolList is being edited. The getChange field of the event should contain the SymbolList.Edit object describing the change.

EMPTY_LIST

static final SymbolList EMPTY_LIST

A useful object that represents an empty symbol list, to avoid returning null.

Method Detail

getAlphabet

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.

Returns:

the alphabet

length

int length()

The number of symbols in this SymbolList.

Returns:

the length

symbolAt

Symbol symbolAt(int index)
                throws IndexOutOfBoundsException

Return the symbol at index, counting from 1.

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

List<Symbol> toList()

Returns a List of symbols.

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

Returns:

a List of Symbols

iterator

Iterator<Symbol> 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.

Returns:

an iterator

subList

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.

Parameters:

start - the first symbol of the new SymbolList

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

Throws:

IndexOutOfBoundsException

seqString

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.

Returns:

a string representation of the symbol list

subStr

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.

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

edit

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());
 

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