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.alignment.Alignment

Alignment.SymbolListIterator

Field Summary

Fields inherited from interface org.biojava.bio.alignment.Alignment

CONTENT

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Method Summary

Methods

Modifier and Type	Method and Description
List<String>	labelsAt(int column) Returns a list labels, of all seqs that cover that column
List<String>	labelsInRange(Location loc) Returns list of all the labels that intersect that range
Location	locInAlignment(Object label) The location of an individual SymbolList relative to overall Alignment

Methods inherited from interface org.biojava.bio.alignment.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(Object label)

The location of an individual SymbolList relative to overall Alignment

labelsAt

List<String> labelsAt(int column)

Returns a list labels, of all seqs that cover that column

labelsInRange

List<String> labelsInRange(Location loc)

Returns list of all the labels that intersect that range