org.biojava.bio.alignment
Interface UnequalLengthAlignment

All Superinterfaces:
Alignment, Changeable, SymbolList
All Known Implementing Classes:
AbstractULAlignment, AbstractULAlignment.SubULAlignment, FlexibleAlignment

public interface UnequalLengthAlignment
extends Alignment

UnequalLengthAlignment has the following behavior. Two or more SymbolLists may align in such a way that their ends do not overlap.

      example
         1         aaaaaatttcttt
         2               tttgtttggggggc
 

length returns ??
symbolAt(1,1) returns 20
symbolAt(2,1) returns null -- NOT an exception
symbolAt(2,99) throws NoSuchElementException
leftMost returns 1
rightMost returns 2
locInAlignment (1) returns (1,13)
locInAlignment (2) returns (7,20)
alignmentRange() returns (7,13)

Author:
David Waring

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava.bio.symbol.Alignment
Alignment.SymbolListIterator
 
Field Summary
 
Fields inherited from interface org.biojava.bio.symbol.Alignment
CONTENT
 
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
 
Method Summary
 java.util.List labelsAt(int column)
          Returns a list labels, of all seqs that cover that column
 java.util.List labelsInRange(Location loc)
          Returns list of all the labels that intersect that range
 Location locInAlignment(java.lang.Object label)
          The location of an individual SymbolList relative to overall Alignment
 
Methods inherited from interface org.biojava.bio.symbol.Alignment
getLabels, subAlignment, symbolAt, symbolListForLabel, symbolListIterator
 
Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Method Detail

locInAlignment

Location locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment


labelsAt

java.util.List labelsAt(int column)
Returns a list labels, of all seqs that cover that column


labelsInRange

java.util.List labelsInRange(Location loc)
Returns list of all the labels that intersect that range