Class SimpleStatePath

java.lang.Object
org.biojava.utils.Unchangeable
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:
  • Constructor Details

  • Method Details

    • 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

      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

      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

      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

      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

      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

      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 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

      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