Package org.biojava.bio.symbol

Interface SymbolList

    • Field Detail

      • EDIT

        static final ChangeType EDIT
        Signals that the SymbolList is being edited. The getChange field of the event should contain the SymbolList.Edit object describing the change.

      • EMPTY_LIST

        static final SymbolList EMPTY_LIST
        A useful object that represents an empty symbol list, to avoid returning null.

    • Method Detail

      • getAlphabet

        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.

        Returns:
        the alphabet

      • length

        int length()
        The number of symbols in this SymbolList.
        Returns:
        the length

      • toList

        List<Symbol> toList()
        Returns a List of symbols.

        This is an immutable list of symbols. Do not edit it.

        Returns:
        a List of Symbols

      • iterator

        Iterator<Symbol> 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.

        Returns:
        an iterator

      • subList

        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.

        Parameters:
        start - the first symbol of the new SymbolList
        end - the last symbol (inclusive) of the new SymbolList
        Throws:
        IndexOutOfBoundsException

      • seqString

        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.

        Returns:
        a string representation of the symbol list

      • subStr

        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.

        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

        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());
        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