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java.lang.Object | +--org.biojava.bio.symbol.AbstractSymbolList
Abstract helper implementation of the SymbolList core interface.
To produce a concrete SymbolList implementation, you need only
implement the getAlphabet
, length
and
symbolAt
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.
Inner classes inherited from class org.biojava.bio.symbol.SymbolList |
SymbolList.EmptySymbolList |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
EMPTY_LIST |
Constructor Summary | |
protected |
AbstractSymbolList()
|
Method Summary | |
abstract Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
java.util.Iterator |
iterator()
An Iterator over all Symbols in this SymbolList. |
abstract 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. |
abstract 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 |
protected AbstractSymbolList()
Method Detail |
public abstract Alphabet getAlphabet()
Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.
public java.util.Iterator iterator()
This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
public abstract int length()
public abstract Symbol symbolAt(int index)
index
- the ofset into this SymbolListpublic SymbolList subList(int start, int end)
The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolListpublic java.util.List toList()
This is an immutable list of symbols. Do not edit it.
public java.lang.String seqString()
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.
public java.lang.String subStr(int start, int end)
This should use the same rules as seqString.
start
- the first symbol to includeend
- the last symbol to include
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