AbstractULAlignment.SubULAlignment (biojava-legacy 1.9.5 API)

AbstractULAlignment.SubULAlignment (biojava-legacy 1.9.5 API)

Nested Class Summary
- Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
  AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
- 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

Constructor Summary

Constructors
Modifier Constructor Description

protected SubULAlignment(Set<String> labels, Location loc)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Alphabet`	`getAlphabet()`	The alphabet that this SymbolList is over.
`List<String>`	`getLabels()`	The list of SymbolLists in the alignment.
`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
`int`	`length()`	The number of symbols in this SymbolList.
`protected List<String>`	`listIntersection(List<String> s1, List<String> s2)`
`Location`	`locInAlignment(Object label)`	The location of an individual SymbolList relative to overall Alignment
`Alignment`	`subAlignment(Set<String> labels, Location loc)`	Make a view onto this alignment.
`Symbol`	`symbolAt(int column)`	Return the symbol at index, counting from 1.
`Symbol`	`symbolAt(String label, int column)`	Retrieve a symbol by label and column.
`SymbolList`	`symbolListForLabel(String label)`	Retrieve a single row of the alignment by label.
`Iterator<SymbolList>`	`symbolListIterator()`	Creates an Iterator over the SymbolLists in the alignment.

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

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