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java.lang.Object | +--org.biojava.bridge.Biocorba.Seqcore.SymbolListAdapter
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 | |
SymbolListAdapter(AnonymousSeq anonymousSeq)
|
Method Summary | |
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
AnonymousSeq |
getAnonymousSeq()
|
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 java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public SymbolListAdapter(AnonymousSeq anonymousSeq) throws IllegalAlphabetException, IllegalSymbolException, BioException
Method Detail |
public AnonymousSeq getAnonymousSeq()
public 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 int length()
public Symbol symbolAt(int index) throws java.lang.IndexOutOfBoundsException
index
- the ofset into this SymbolListpublic 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 SymbolList subList(int start, int end) throws java.lang.IndexOutOfBoundsException
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.lang.String subStr(int start, int end) throws java.lang.IndexOutOfBoundsException
This should use the same rules as seqString.
start
- the first symbol to includeend
- the last symbol to includepublic java.util.List toList()
This is an immutable list of symbols. Do not edit it.
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