Package org.biojava.bio.symbol

Class RelabeledAlignment

    • Method Detail

      • getLabels

        public List<String> 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

      • symbolAt

        public Symbol symbolAt​(String label,
                       int column)
                throws 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
        column - 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'

      • subAlignment

        public Alignment subAlignment​(Set<String> 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

      • 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 min,
                     int max)
        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:
        min - the first symbol to include
        max - the last symbol to include
        Returns:
        the string representation

      • 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

      • iterator

        public Iterator 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

      • 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

      • toList

        public List 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

      • subList

        public SymbolList subList​(int min,
                          int max)
        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:
        min - the first symbol of the new SymbolList
        max - the last symbol (inclusive) of the new SymbolList

      • symbolAt

        public Symbol symbolAt​(int pos)
        Description copied from interface: SymbolList
        Return the symbol at index, counting from 1.
        Specified by:
        symbolAt in interface SymbolList
        Parameters:
        pos - the offset into this SymbolList
        Returns:
        the Symbol at that index

      • edit

        public void edit​(Edit edit)
          throws IllegalAlphabetException,
                 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:

        • 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
        ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

      • symbolListIterator

        public Iterator 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