public class SimpleStatePath extends Unchangeable implements StatePath, Serializable
Alignment.SymbolListIteratorEDIT, EMPTY_LIST| Constructor and Description |
|---|
SimpleStatePath(double score,
SymbolList sequence,
SymbolList states,
SymbolList scores) |
| 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 |
getLabels()
The list of SymbolLists in the alignment.
|
double |
getScore()
Return the overall score for this state-path and it's emissions.
|
Iterator<Symbol> |
iterator()
An Iterator over all Symbols in this SymbolList.
|
int |
length()
The number of symbols in this SymbolList.
|
String |
seqString()
Stringify this symbol list.
|
Alignment |
subAlignment(Set labels,
Location loc)
Make a view onto this alignment.
|
SymbolList |
subList(int start,
int end)
Return a new SymbolList for the symbols start to end inclusive.
|
String |
subStr(int start,
int end)
Return a region of this symbol list as a String.
|
Symbol |
symbolAt(int col)
Return the symbol at index, counting from 1.
|
Symbol |
symbolAt(String label,
int col)
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.
|
List<Symbol> |
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 SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores) throws IllegalArgumentException
IllegalArgumentExceptionpublic double getScore()
StatePathpublic 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 List 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 int length()
SymbolListlength in interface SymbolListpublic Alignment subAlignment(Set 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 Symbol symbolAt(int col) throws IndexOutOfBoundsException
SymbolListsymbolAt in interface SymbolListcol - the offset into this SymbolListIndexOutOfBoundsException - if index is less than 1, or greater than
the length of the symbol listpublic Symbol symbolAt(String label, int col) throws IndexOutOfBoundsException, NoSuchElementException
AlignmentsymbolAt in interface Alignmentlabel - the SymbolList to retrieve fromcol - the index of the column to retrieveNoSuchElementException - if there is no row for 'label'IndexOutOfBoundsExceptionpublic 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 Iterator<Symbol> iterator()
SymbolListThis is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
iterator in interface SymbolListpublic SymbolList subList(int start, int end)
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 SymbolListstart - the first symbol of the new SymbolListend - the last symbol (inclusive) of the new SymbolListpublic List<Symbol> toList()
SymbolListThis is an immutable list of symbols. Do not edit it.
toList in interface SymbolListpublic 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 start, int end) throws IndexOutOfBoundsException
SymbolListThis should use the same rules as seqString.
subStr in interface SymbolListstart - the first symbol to includeend - the last symbol to includeIndexOutOfBoundsException - if either start or end are not within the
SymbolListpublic void edit(Edit edit) throws IllegalAlphabetException, IndexOutOfBoundsException, 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 alphabetIndexOutOfBoundsException - if the edit does not lie within the
SymbolListChangeVetoException - if either the SymboList does not support the
edit, or if the change was vetoedpublic Iterator<SymbolList> symbolListIterator()
AlignmentsymbolListIterator in interface AlignmentCopyright © 2014 BioJava. All rights reserved.