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)
Methods inherited from class java.lang.Object |
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
NewAssembledSymbolList
public NewAssembledSymbolList()
setLength
public void setLength(int len)
putComponent
public void putComponent(ComponentFeature f)
removeComponent
public void removeComponent(ComponentFeature f)
getComponentLocationSet
public java.util.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