Package org.biojavax.bio.seq

Class InfinitelyAmbiguousSymbolList

    • Constructor Detail

      • InfinitelyAmbiguousSymbolList

        public InfinitelyAmbiguousSymbolList​(FiniteAlphabet fa)
        Creates a new instance of InfinitelyAmbiguousSymbolList
        Parameters:
        fa - the finite alphabet to return ambiguous symbols from.

    • Method Detail

      • edit

        public void edit​(Edit edit)
          throws IndexOutOfBoundsException,
                 IllegalAlphabetException,
                 ChangeVetoException
        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

        public Alphabet 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

      • 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

      • 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