public abstract class AbstractULAlignment extends AbstractSymbolList implements UnequalLengthAlignment
Modifier and Type | Class and Description |
---|---|
class |
AbstractULAlignment.LeftRightLocationComparator
Orders by location left to right.
|
class |
AbstractULAlignment.SubULAlignment |
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
Alignment.SymbolListIterator
Modifier and Type | Field and Description |
---|---|
protected Alphabet |
alphabet |
EDIT, EMPTY_LIST
Constructor and Description |
---|
AbstractULAlignment() |
Modifier and Type | Method and Description |
---|---|
protected void |
debug(java.lang.String s) |
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
|
java.lang.Object |
leftMost()
leftMost and rightMost return labels.
|
java.util.SortedSet |
orderedLables(java.util.Comparator comp) |
java.lang.Object |
rightMost() |
Alignment |
subAlignment(java.util.Set labels,
int min,
int max)
Retreives a subAlignment
|
Alignment |
subAlignment(java.util.Set 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
|
java.util.Iterator |
symbolListIterator()
Creates an Iterator over the SymbolLists in the alignment.
|
edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
locInAlignment
getLabels, symbolAt, symbolListForLabel
edit, getAlphabet, iterator, length, seqString, subList, subStr, toList
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
protected Alphabet alphabet
public Symbol symbolAt(int index)
symbolAt
in interface SymbolList
index
- the offset into this SymbolListpublic java.util.List labelsAt(int column)
UnequalLengthAlignment
labelsAt
in interface UnequalLengthAlignment
public java.util.List labelsInRange(Location loc)
UnequalLengthAlignment
labelsInRange
in interface UnequalLengthAlignment
public java.util.Iterator symbolListIterator()
Alignment
symbolListIterator
in interface Alignment
protected void debug(java.lang.String s)
public java.lang.Object leftMost()
public java.lang.Object rightMost()
public Alignment subAlignment(java.util.Set labels, Location loc) throws java.lang.IndexOutOfBoundsException
WARNING: It is assumed that the location is contiguous. If the location is non-contiguous it may be preferable to use a block iterator to retrieve each sub location independently.
subAlignment
in interface Alignment
labels
- the Set of sequences to include by labelloc
- the Location to includejava.lang.IndexOutOfBoundsException
subAlignment(Set labels, int min, int max)
public Alignment subAlignment(java.util.Set labels, int min, int max) throws java.util.NoSuchElementException
labels
- the labels of the SymbolLists
to be in the Alignmentmin
- the left most coordinatemax
- the right most coordinatejava.util.NoSuchElementException
- if one of the values in labels
is not in the parent alignmentpublic java.util.SortedSet orderedLables(java.util.Comparator comp)