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java.lang.Object | +--org.biojava.bio.symbol.AbstractSymbolList | +--org.biojava.bio.symbol.SimpleSymbolList
Basic implementation of SymbolList. This is currently backed by a normal Java array. This is a new implementation which no longer uses the Java ArrayLists. I hope that eventually it can be made immutable, but for now the legacy addSymbol method is implemented.
Constructor Summary | |
SimpleSymbolList(Alphabet alpha)
Construct an empty SimpleSymbolList. |
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SimpleSymbolList(Alphabet alpha,
java.util.List rList)
Construct a SymbolList containing the symbols in the specified list. |
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SimpleSymbolList(SymbolList sl)
Construct a copy of an existing SymbolList. |
Method Summary | |
void |
addSymbol(Symbol sym)
Deprecated. Can we make SimpleSymbolList immutable [Thomas Down] |
Alphabet |
getAlphabet()
Get the alphabet of this SymbolList. |
int |
length()
Get the length of this SymbolList. |
Symbol |
symbolAt(int pos)
Find a symbol at a specified offset in the SymbolList. |
Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList |
iterator,
seqString,
subList,
subStr,
toList |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public SimpleSymbolList(Alphabet alpha)
alpha
- The alphabet of legal symbols in this list.public SimpleSymbolList(Alphabet alpha, java.util.List rList) throws IllegalSymbolException
alpha
- The alphabet of legal symbols for this list.rList
- A Java List of symbols.public SimpleSymbolList(SymbolList sl)
The
- list to copy.Method Detail |
public Alphabet getAlphabet()
public int length()
public Symbol symbolAt(int pos)
pos
- Position in biological coordinates (1..length)public void addSymbol(Symbol sym) throws IllegalSymbolException
sym
- Symbol to add
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