UnequalLengthAlignment (biojava-legacy 1.9.5 API)

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

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	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.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList

- 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