org.biojava.bio.seq.impl
Class NewAssembledSymbolList
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbolList
org.biojava.bio.seq.impl.NewAssembledSymbolList
- All Implemented Interfaces:
- SymbolList, Changeable
public class NewAssembledSymbolList
- extends AbstractSymbolList
Support class for applications which need to patch together sections
of sequence into a single SymbolList. This class isn't intended
for direct use in user code -- instead, it is a helper for people
implementing the full BioJava assembly model. See SimpleAssembly
for an example.
- Since:
- 1.1
- Author:
- Thomas Down, Greg Cox, Matthew Pocock, David Huen (support for overlapped features)
NewAssembledSymbolList
public NewAssembledSymbolList()
setLength
public void setLength(int len)
putComponent
public void putComponent(ComponentFeature f)
removeComponent
public void removeComponent(ComponentFeature f)
getComponentLocationSet
public Set getComponentLocationSet()
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.
- Returns:
- the alphabet
length
public int length()
- Description copied from interface:
SymbolList
- The number of symbols in this SymbolList.
- Returns:
- the length
symbolAt
public Symbol symbolAt(int pos)
- Description copied from interface:
SymbolList
- Return the symbol at index, counting from 1.
- Parameters:
pos
- the offset into this SymbolList
- Returns:
- the Symbol at that index
subList
public SymbolList subList(int start,
int end)
- 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
- Overrides:
subList
in class AbstractSymbolList
- Parameters:
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolList