public class AbstractULAlignment.SubULAlignment extends AbstractSymbolList implements UnequalLengthAlignment
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
Alignment.SymbolListIterator
EDIT, EMPTY_LIST
Modifier | Constructor and Description |
---|---|
protected |
SubULAlignment(java.util.Set labels,
Location loc) |
Modifier and Type | Method and Description |
---|---|
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over.
|
java.util.List |
getLabels()
The list of SymbolLists in the alignment.
|
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
|
int |
length()
The number of symbols in this SymbolList.
|
protected java.util.List |
listIntersection(java.util.List s1,
java.util.List s2) |
Location |
locInAlignment(java.lang.Object label)
The location of an individual SymbolList relative to overall Alignment
|
Alignment |
subAlignment(java.util.Set labels,
Location loc)
Make a view onto this alignment.
|
Symbol |
symbolAt(int column)
Return the symbol at index, counting from 1.
|
Symbol |
symbolAt(java.lang.Object label,
int column)
Retrieve a symbol by label and column.
|
SymbolList |
symbolListForLabel(java.lang.Object label)
Retrieve a single row of the alignment by label.
|
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
edit, iterator, seqString, subList, subStr, toList
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
protected SubULAlignment(java.util.Set labels, Location loc) throws java.lang.IndexOutOfBoundsException
java.lang.IndexOutOfBoundsException
public int length()
SymbolList
length
in interface SymbolList
public Location locInAlignment(java.lang.Object label)
locInAlignment
in interface UnequalLengthAlignment
public Alignment subAlignment(java.util.Set labels, Location loc) throws java.util.NoSuchElementException
Alignment
Make a view onto this alignment.
If labels is null, then each label will be kept. Otherwise, only those in labels will be kept. If loc is null, then the entire length of the alignment will be kept. If loc is not null, then only the columns within the location will be kept.
subAlignment
in interface Alignment
labels
- the Set of sequences to include by labelloc
- the Location to includejava.util.NoSuchElementException
- if labels contains any item that is not a labelprotected java.util.List listIntersection(java.util.List s1, java.util.List s2)
public java.util.List labelsAt(int column) throws java.lang.IndexOutOfBoundsException
UnequalLengthAlignment
labelsAt
in interface UnequalLengthAlignment
java.lang.IndexOutOfBoundsException
public java.util.List labelsInRange(Location loc) throws java.lang.IndexOutOfBoundsException
UnequalLengthAlignment
labelsInRange
in interface UnequalLengthAlignment
java.lang.IndexOutOfBoundsException
public java.util.List getLabels()
Alignment
The list of SymbolLists in the alignment.
The index in the list is the same as the index in the alignment. Each SymbolList object will only be in the alignment once. However, a single underlying SymbolList may have more than one view within an alignment, each represented by a different GappedSymbolList.
public Symbol symbolAt(java.lang.Object label, int column) throws java.util.NoSuchElementException
Alignment
symbolAt
in interface Alignment
label
- the SymbolList to retrieve fromcolumn
- the index of the column to retrievejava.util.NoSuchElementException
- if there is no row for 'label'public Symbol symbolAt(int column) throws java.util.NoSuchElementException
SymbolList
symbolAt
in interface SymbolList
column
- the offset into this SymbolListjava.util.NoSuchElementException
public SymbolList symbolListForLabel(java.lang.Object label) throws java.util.NoSuchElementException
Alignment
symbolListForLabel
in interface Alignment
label
- the object from which to retrieve the symbol listjava.util.NoSuchElementException
- if there is no row for 'label'public Alphabet getAlphabet()
SymbolList
Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.
getAlphabet
in interface SymbolList
public java.util.Iterator symbolListIterator()
Alignment
symbolListIterator
in interface Alignment