org.biojava.bio.symbol
Class SymbolList.EmptySymbolList

java.lang.Object
  extended byorg.biojava.utils.Unchangeable
      extended byorg.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
Throws:
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:

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:
java.lang.IndexOutOfBoundsException - if the edit does not lie within the SymbolList
ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed