org.biojava.bio.dp
Class SimpleStatePath

java.lang.Object
  extended by org.biojava.utils.Unchangeable
      extended by org.biojava.bio.dp.SimpleStatePath
All Implemented Interfaces:
Serializable, Alignment, StatePath, SymbolList, Changeable

public class SimpleStatePath
extends Unchangeable
implements StatePath, Serializable

A no-frills implementation of StatePath.

Author:
Matthew Pocock, Nimesh Singh
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava.bio.alignment.Alignment
Alignment.SymbolListIterator
 
Field Summary
 
Fields inherited from interface org.biojava.bio.dp.StatePath
SCORES, SEQUENCE, STATES
 
Fields inherited from interface org.biojava.bio.alignment.Alignment
CONTENT
 
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
 
Constructor Summary
SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores)
           
 
Method Summary
 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.
 
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
 

Constructor Detail

SimpleStatePath

public SimpleStatePath(double score,
                       SymbolList sequence,
                       SymbolList states,
                       SymbolList scores)
                throws IllegalArgumentException
Throws:
IllegalArgumentException
Method Detail

getScore

public double getScore()
Description copied from interface: StatePath
Return the overall score for this state-path and it's emissions.

Specified by:
getScore in interface StatePath
Returns:
the score

getAlphabet

public Alphabet 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 interface SymbolList
Returns:
the alphabet

getLabels

public List 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.

Specified by:
getLabels in interface Alignment
Returns:
the List of all SymbolLists in the alignment

length

public int length()
Description copied from interface: SymbolList
The number of symbols in this SymbolList.

Specified by:
length in interface SymbolList
Returns:
the length

subAlignment

public Alignment subAlignment(Set labels,
                              Location loc)
                       throws NoSuchElementException
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 interface Alignment
Parameters:
labels - the Set of sequences to include by label
loc - the Location to include
Returns:
a sub Alignment
Throws:
NoSuchElementException - if labels contains any item that is not a label

symbolAt

public Symbol symbolAt(int col)
                throws IndexOutOfBoundsException
Description copied from interface: SymbolList
Return the symbol at index, counting from 1.

Specified by:
symbolAt in interface SymbolList
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

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 interface Alignment
Parameters:
label - the SymbolList to retrieve from
col - 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

symbolListForLabel

public SymbolList symbolListForLabel(String label)
                              throws NoSuchElementException
Description copied from interface: Alignment
Retrieve a single row of the alignment by label.

Specified by:
symbolListForLabel in interface Alignment
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'

iterator

public Iterator<Symbol> 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 interface SymbolList
Returns:
an iterator

subList

public SymbolList subList(int start,
                          int end)
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 interface SymbolList
Parameters:
start - the first symbol of the new SymbolList
end - the last symbol (inclusive) of the new SymbolList

toList

public List<Symbol> 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 interface SymbolList
Returns:
a List of Symbols

seqString

public String 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 interface SymbolList
Returns:
a string representation of the symbol list

subStr

public String subStr(int start,
                     int end)
              throws IndexOutOfBoundsException
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 interface SymbolList
Parameters:
start - the first symbol to include
end - the last symbol to include
Returns:
the string representation
Throws:
IndexOutOfBoundsException - if either start or end are not within the SymbolList

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:

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 interface SymbolList
Parameters:
edit - the Edit to perform
Throws:
IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet
IndexOutOfBoundsException - if the edit does not lie within the SymbolList
ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

symbolListIterator

public Iterator<SymbolList> 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 interface Alignment
Returns:
an Iterator


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