org.biojavax.bio.seq
Class InfinitelyAmbiguousSymbolList

java.lang.Object
  extended by org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
All Implemented Interfaces:
SymbolList, Changeable

public class InfinitelyAmbiguousSymbolList
extends java.lang.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
InfinitelyAmbiguousSymbolList(FiniteAlphabet fa)
          Creates a new instance of InfinitelyAmbiguousSymbolList
 
Method Summary
 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.
 java.util.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.
 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 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 java.lang.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:

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:
java.lang.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 java.util.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 java.lang.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 java.lang.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:
java.lang.IndexOutOfBoundsException

subStr

public java.lang.String subStr(int start,
                               int end)
                        throws java.lang.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:
java.lang.IndexOutOfBoundsException - if either start or end are not within the SymbolList

symbolAt

public Symbol symbolAt(int index)
                throws java.lang.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:
java.lang.IndexOutOfBoundsException - if index is less than 1, or greater than the length of the symbol list

toList

public java.util.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