public class RelabeledAlignment extends Unchangeable implements Alignment
Alignment.SymbolListIteratorEDIT, EMPTY_LIST| Constructor and Description |
|---|
RelabeledAlignment(Alignment delegate) |
| Modifier and Type | Method and Description |
|---|---|
void |
edit(Edit edit)
Apply an edit to the SymbolList as specified by the edit object.
|
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over.
|
List<String> |
getLabels()
The list of SymbolLists in the alignment.
|
Iterator |
iterator()
An Iterator over all Symbols in this SymbolList.
|
int |
length()
The number of symbols in this SymbolList.
|
protected String |
map(Object label) |
protected Set<String> |
map(Set<String> labels) |
String |
seqString()
Stringify this symbol list.
|
Alignment |
subAlignment(Set<String> labels,
Location loc)
Make a view onto this alignment.
|
SymbolList |
subList(int min,
int max)
Return a new SymbolList for the symbols start to end inclusive.
|
String |
subStr(int min,
int max)
Return a region of this symbol list as a String.
|
Symbol |
symbolAt(int pos)
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 |
symbolListIterator()
Creates an Iterator over the SymbolLists in the alignment.
|
List |
toList()
Returns a List of symbols.
|
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarderclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerpublic RelabeledAlignment(Alignment delegate)
public List<String> getLabels()
AlignmentThe 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(String label, int column) throws NoSuchElementException
AlignmentsymbolAt in interface Alignmentlabel - the SymbolList to retrieve fromcolumn - the index of the column to retrieveNoSuchElementException - if there is no row for 'label'public SymbolList symbolListForLabel(String label) throws NoSuchElementException
AlignmentsymbolListForLabel in interface Alignmentlabel - the object from which to retrieve the symbol listNoSuchElementException - if there is no row for 'label'public Alignment subAlignment(Set<String> labels, Location loc) throws NoSuchElementException
AlignmentMake 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 Alignmentlabels - the Set of sequences to include by labelloc - the Location to includeNoSuchElementException - if labels contains any item that is not a labelpublic String seqString()
SymbolListIt is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.
seqString in interface SymbolListpublic String subStr(int min, int max)
SymbolListThis should use the same rules as seqString.
subStr in interface SymbolListmin - the first symbol to includemax - the last symbol to includepublic 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 SymbolListpublic Iterator iterator()
SymbolListThis is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
iterator in interface SymbolListpublic int length()
SymbolListlength in interface SymbolListpublic List toList()
SymbolListThis is an immutable list of symbols. Do not edit it.
toList in interface SymbolListpublic SymbolList subList(int min, int max)
SymbolListThe resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
subList in interface SymbolListmin - the first symbol of the new SymbolListmax - the last symbol (inclusive) of the new SymbolListpublic Symbol symbolAt(int pos)
SymbolListsymbolAt in interface SymbolListpos - the offset into this SymbolListpublic void edit(Edit edit) throws IllegalAlphabetException, ChangeVetoException
SymbolListAll edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.
When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).
The pos and pos+length should always be valid positions on the SymbolList to:
SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
System.out.println(seq.seqString());
// delete 5 bases from position 4
Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
seq.edit(ed);
System.out.println(seq.seqString());
// delete one base from the start
ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
seq.edit(ed);
// delete one base from the end
ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
seq.edit(ed);
System.out.println(seq.seqString());
// overwrite 2 bases from position 3 with "tt"
ed = new Edit(3, 2, DNATools.createDNA("tt"));
seq.edit(ed);
System.out.println(seq.seqString());
// add 6 bases to the start
ed = new Edit(1, 0, DNATools.createDNA("aattgg");
seq.edit(ed);
System.out.println(seq.seqString());
// add 4 bases to the end
ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
seq.edit(ed);
System.out.println(seq.seqString());
// full edit
ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
seq.edit(ed);
System.out.println(seq.seqString());
edit in interface SymbolListedit - the Edit to performIllegalAlphabetException - if the SymbolList to insert has an
incompatible alphabetChangeVetoException - if either the SymboList does not support the
edit, or if the change was vetoedpublic Iterator symbolListIterator()
AlignmentsymbolListIterator in interface AlignmentCopyright © 2014 BioJava. All rights reserved.