Class SimpleStatePath
- All Implemented Interfaces:
Serializable
,Alignment
,StatePath
,SymbolList
,Changeable
- Author:
- Matthew Pocock, Nimesh Singh
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment
Alignment.SymbolListIterator
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Field Summary
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Constructor Summary
ConstructorsConstructorDescriptionSimpleStatePath
(double score, SymbolList sequence, SymbolList states, SymbolList scores) -
Method Summary
Modifier and TypeMethodDescriptionvoid
Apply an edit to the SymbolList as specified by the edit object.The alphabet that this SymbolList is over.The list of SymbolLists in the alignment.double
getScore()
Return the overall score for this state-path and it's emissions.iterator()
An Iterator over all Symbols in this SymbolList.int
length()
The number of symbols in this SymbolList.Stringify this symbol list.subAlignment
(Set labels, Location loc) Make a view onto this alignment.subList
(int start, int end) Return a new SymbolList for the symbols start to end inclusive.subStr
(int start, int end) Return a region of this symbol list as a String.symbolAt
(int col) Return the symbol at index, counting from 1.Retrieve a symbol by label and column.symbolListForLabel
(String label) Retrieve a single row of the alignment by label.Creates an Iterator over the SymbolLists in the alignment.toList()
Returns a List of symbols.Methods inherited from class org.biojava.utils.Unchangeable
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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SimpleStatePath
public SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores) throws IllegalArgumentException - Throws:
IllegalArgumentException
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Method Details
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getScore
Description copied from interface:StatePath
Return the overall score for this state-path and it's emissions. -
getAlphabet
Description copied from interface:SymbolList
The alphabet that this SymbolList is over.Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.- Specified by:
getAlphabet
in interfaceSymbolList
- Returns:
- the alphabet
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getLabels
Description copied from interface: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.
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length
Description copied from interface:SymbolList
The number of symbols in this SymbolList.- Specified by:
length
in interfaceSymbolList
- Returns:
- the length
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subAlignment
Description copied from interface: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.
- Specified by:
subAlignment
in interfaceAlignment
- Parameters:
labels
- the Set of sequences to include by labelloc
- the Location to include- Returns:
- a sub Alignment
- Throws:
NoSuchElementException
- if labels contains any item that is not a label
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symbolAt
Description copied from interface:SymbolList
Return the symbol at index, counting from 1.- Specified by:
symbolAt
in interfaceSymbolList
- Parameters:
col
- the offset into this SymbolList- Returns:
- the Symbol at that index
- Throws:
IndexOutOfBoundsException
- if index is less than 1, or greater than the length of the symbol list
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symbolAt
public Symbol symbolAt(String label, int col) throws IndexOutOfBoundsException, NoSuchElementException Description copied from interface:Alignment
Retrieve a symbol by label and column.- Specified by:
symbolAt
in interfaceAlignment
- Parameters:
label
- the SymbolList to retrieve fromcol
- the index of the column to retrieve- Returns:
- the symbol in the symbol list associated with the label at the given column
- Throws:
NoSuchElementException
- if there is no row for 'label'IndexOutOfBoundsException
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symbolListForLabel
Description copied from interface:Alignment
Retrieve a single row of the alignment by label.- Specified by:
symbolListForLabel
in interfaceAlignment
- Parameters:
label
- the object from which to retrieve the symbol list- Returns:
- a SymbolList that contains each token in a row of the alignment
- Throws:
NoSuchElementException
- if there is no row for 'label'
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iterator
Description copied from interface:SymbolList
An Iterator over all Symbols in this SymbolList.This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
- Specified by:
iterator
in interfaceSymbolList
- Returns:
- an iterator
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subList
Description copied from interface:SymbolList
Return a new SymbolList for the symbols start to end inclusive.The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
- Specified by:
subList
in interfaceSymbolList
- Parameters:
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolList
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toList
Description copied from interface:SymbolList
Returns a List of symbols.This is an immutable list of symbols. Do not edit it.
- Specified by:
toList
in interfaceSymbolList
- Returns:
- a List of Symbols
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seqString
Description copied from interface:SymbolList
Stringify this symbol list.It 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.
- Specified by:
seqString
in interfaceSymbolList
- Returns:
- a string representation of the symbol list
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subStr
Description copied from interface:SymbolList
Return a region of this symbol list as a String.This should use the same rules as seqString.
- Specified by:
subStr
in interfaceSymbolList
- Parameters:
start
- the first symbol to includeend
- the last symbol to include- Returns:
- the string representation
- Throws:
IndexOutOfBoundsException
- if either start or end are not within the SymbolList
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edit
public void edit(Edit edit) throws IllegalAlphabetException, IndexOutOfBoundsException, ChangeVetoException Description copied from interface:SymbolList
Apply an edit to the SymbolList as specified by the edit object.Description
All 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:
- be edited (between 0 and symL.length()+1).
- To append to a sequence, pos=symL.length()+1, pos=0.
- To insert something at the beginning of the sequence, set pos=1 and length=0.
Examples
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());
- Specified by:
edit
in interfaceSymbolList
- Parameters:
edit
- the Edit to perform- Throws:
IllegalAlphabetException
- 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 vetoed
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symbolListIterator
Description copied from interface:Alignment
Creates an Iterator over the SymbolLists in the alignment. This should be similar to iterating over the labels and then fetching each SymbolList, but the order is not guaranteed to be the same.- Specified by:
symbolListIterator
in interfaceAlignment
- Returns:
- an Iterator
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