Class InfinitelyAmbiguousSymbolList

java.lang.Object
org.biojavax.bio.seq.InfinitelyAmbiguousSymbolList
All Implemented Interfaces:
SymbolList, Changeable

public class InfinitelyAmbiguousSymbolList extends Object implements SymbolList
A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
Since:
1.5
Author:
Richard Holland, MarkSchreiber
  • Constructor Details

    • InfinitelyAmbiguousSymbolList

      Creates a new instance of InfinitelyAmbiguousSymbolList
      Parameters:
      fa - the finite alphabet to return ambiguous symbols from.
  • Method Details

    • addChangeListener

      Add a listener that will be informed of all changes. IGNORED
      Specified by:
      addChangeListener in interface Changeable
      Parameters:
      cl - the ChangeListener to add
    • addChangeListener

      Add a listener that will be informed of changes of a given type. IGNORED
      Specified by:
      addChangeListener in interface Changeable
      Parameters:
      cl - the ChangeListener
      ct - the ChangeType it is to be informed of
    • edit

      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());
       
      IGNORED
      Specified by:
      edit in interface SymbolList
      Parameters:
      edit - the Edit to perform
      Throws:
      IndexOutOfBoundsException - if the edit does not lie within the SymbolList
      IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet
      ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed
    • getAlphabet

      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
    • isUnchanging

      public boolean isUnchanging(ChangeType ct)

      A particular ChangeType can never be raised by this Changeable.

      If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

      ALWAYS RETURNS TRUE
      Specified by:
      isUnchanging in interface Changeable
      Parameters:
      ct - the ChangeType to check
      Returns:
      true if ChangeEvents of this type are guaranteed to never be fired
    • iterator

      public Iterator iterator()
      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. ALWAYS RETURNS AN ITERATOR OVER A SINGLE AMBIGUITY SYMBOL

      Specified by:
      iterator in interface SymbolList
      Returns:
      an iterator
    • length

      public int length()
      The number of symbols in this SymbolList. ALWAYS RETURNS Integer.MAX_VALUE
      Specified by:
      length in interface SymbolList
      Returns:
      the length
    • removeChangeListener

      Remove a listener that was interested in all types of changes. IGNORED
      Specified by:
      removeChangeListener in interface Changeable
      Parameters:
      cl - a ChangeListener to remove
    • removeChangeListener

      Remove a listener that was interested in a specific types of changes. IGNORED
      Specified by:
      removeChangeListener in interface Changeable
      Parameters:
      cl - a ChangeListener to remove
      ct - the ChangeType that it was interested in
    • seqString

      public String seqString()
      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. ALWAYS RETURNS THE AMBIGUITY SYMBOL REPRESENTED AS A STRING

      Specified by:
      seqString in interface SymbolList
      Returns:
      a string representation of the symbol list
    • subList

      public SymbolList subList(int start, int end) throws IndexOutOfBoundsException
      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. ALWAYS RETURNS SELF

      Specified by:
      subList in interface SymbolList
      Parameters:
      start - the first symbol of the new SymbolList
      end - the last symbol (inclusive) of the new SymbolList
      Throws:
      IndexOutOfBoundsException
    • subStr

      public String subStr(int start, int end) throws IndexOutOfBoundsException
      Return a region of this symbol list as a String.

      This should use the same rules as seqString. ALWAYS RETURNS THE CORRECT LENGTH STRING MADE UP OF AMBIGUITY SYMBOLS

      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
    • symbolAt

      public Symbol symbolAt(int index) throws IndexOutOfBoundsException
      Return the symbol at index, counting from 1. ALWAYS RETURNS THE AMBIGUITY SYMBOL
      Specified by:
      symbolAt in interface SymbolList
      Parameters:
      index - 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
    • toList

      public List toList()
      Returns a List of symbols.

      This is an immutable list of symbols. Do not edit it. ALWAYS RETURNS A LIST CONTAINING THE AMBIGUITY SYMBOL

      Specified by:
      toList in interface SymbolList
      Returns:
      a List of Symbols