org.biojava.bio.symbol
Class TranslatedSymbolList
java.lang.Object
|
+--org.biojava.bio.symbol.AbstractSymbolList
|
+--org.biojava.bio.symbol.TranslatedSymbolList
- public class TranslatedSymbolList
- extends AbstractSymbolList
- implements SymbolList
Provides a 'translated' view of an underlying SymbolList.
This class allows you to translate from one alphabet into another, so
for example, you could translate from DNA-triplets into amino-acids. You
could also translate from DNA-dinucleotide into the 'twist' structural
metric, or any other translation that takes your fancy.
The actual mapping from source to view Symbol is encapsulated in a
TranslationTable object.
The TranslatedSymbolList will be the same length as the source, and each
Symbol in the view will correspond to a single Symbol in the source.
- Author:
- Matthew Pocock
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
TranslatedSymbolList
public TranslatedSymbolList(SymbolList source,
TranslationTable transTable)
throws IllegalAlphabetException
getTranslationTable
public TranslationTable getTranslationTable()
- Obtain the translation table associated with this symbol list
getSource
public SymbolList getSource()
- Returns the symbol list associated with this translated symbol list.
length
public int length()
- Description copied from interface: SymbolList
- The number of symbols in this SymbolList.
- Specified by:
- length in interface SymbolList
- Overrides:
- length in class AbstractSymbolList
- Tags copied from interface: SymbolList
- Returns:
- the length
symbolAt
public Symbol symbolAt(int indx)
- Description copied from interface: SymbolList
- Return the symbol at index, counting from 1.
- Specified by:
- symbolAt in interface SymbolList
- Overrides:
- symbolAt in class AbstractSymbolList
- Tags copied from interface: SymbolList
- Parameters:
index
- the ofset 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
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
- Overrides:
- getAlphabet in class AbstractSymbolList
- Tags copied from interface: SymbolList
- Returns:
- the alphabet