AbstractULAlignment (biojava-legacy 1.9.5 API)

AbstractULAlignment (biojava-legacy 1.9.5 API)

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`class`	`AbstractULAlignment.LeftRightLocationComparator<T>`	Orders by location left to right.
`class`	`AbstractULAlignment.SubULAlignment`

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
Modifier and Type Field Description

protected Alphabet alphabet
- 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
Constructor Description

AbstractULAlignment()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`debug(String s)`
`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
`Object`	`leftMost()`	leftMost and rightMost return labels.
`SortedSet<String>`	`orderedLables(Comparator<String> comp)`
`Object`	`rightMost()`
`Alignment`	`subAlignment(Set<String> labels, int min, int max)`	Retreives a subAlignment
`Alignment`	`subAlignment(Set<String> labels, Location loc)`	Retrieves a subalignment specified by the location.
`Symbol`	`symbolAt(int index)`	this will return the ambiguity symbol associated with all symbols in that column
`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.bio.alignment.Alignment
getLabels, symbolAt, symbolListForLabel

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, toList

Methods inherited from interface org.biojava.bio.alignment.UnequalLengthAlignment
locInAlignment