Class AbstractSymbolList
- java.lang.Object
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- org.biojava.utils.AbstractChangeable
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- org.biojava.bio.symbol.AbstractSymbolList
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- 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
andsymbolAt
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
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Nested Class Summary
Nested Classes Modifier and Type Class 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.
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Field Summary
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Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Constructor Summary
Constructors Modifier Constructor Description protected
AbstractSymbolList()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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 symbolsint
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()
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Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Methods inherited from interface org.biojava.bio.symbol.SymbolList
getAlphabet, length, symbolAt
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Constructor Detail
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AbstractSymbolList
protected AbstractSymbolList()
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Method Detail
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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 interfaceSymbolList
- Returns:
- an iterator
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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 interfaceSymbolList
- Parameters:
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolList
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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 interfaceSymbolList
- Returns:
- a List of Symbols
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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 interfaceSymbolList
- Returns:
- a string representation of the symbol list
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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 interfaceSymbolList
- Parameters:
start
- the first symbol to includeend
- the last symbol to include- Returns:
- the string representation
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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 interfaceSymbolList
- Parameters:
edit
- the Edit to perform- Throws:
IllegalAlphabetException
- if the SymbolList to insert has an incompatible alphabetChangeVetoException
- if either the SymboList does not support the edit, or if the change was vetoed
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equals
public boolean equals(Object o)
Provides logical equality for two SymbolLists that share the same list of canonical symbols
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