Package org.biojava.bio.seq.impl

Class SubSequence

  • All Implemented Interfaces:
    Serializable, Annotatable, FeatureHolder, Sequence, SymbolList, Changeable
    public class SubSequence
extends Object
implements Sequence, Serializable
    View a sub-section of a given sequence object, including all the features intersecting that region.

    All features entirely contained within the region are projected by just translating their locations. The features that overlap the region are replaced by RemoteFeature instances with fuzzy locations that are trunchated to fit inside the sub-section. All features not contained by the region are not projected.

    Since:
    1.2
    Author:
    Thomas Down, Matthew Pocock
    See Also:
    Serialized Form

    • Constructor Detail

      • SubSequence

        public SubSequence​(Sequence seq,
                   int start,
                   int end,
                   String name)
        Construct a new SubSequence of the specified sequence. Generally you would use the SequenceTools.subSequence() methods to get an instance of this class.
        Parameters:
        seq - A sequence to view
        start - The start of the range to view
        end - The end of the range to view
        name - Name for the subsequence
        Throws:
        IndexOutOfBoundsException - is the start or end position is illegal.

      • SubSequence

        public SubSequence​(Sequence seq,
                   int start,
                   int end)
        Construct a new SubSequence of the specified sequence. Generally you would use the SequenceTools.subSequence() methods to get an instance of this class.
        Parameters:
        seq - A sequence to view
        start - The start of the range to view
        end - The end of the range to view
        Throws:
        IndexOutOfBoundsException - if the start or end position is illegal.

    • Method Detail

      • 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

      • 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

      • 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

      • 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)
        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

      • 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

      • 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

      • 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

      • edit

        public void edit​(Edit edit)
          throws 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:
        ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

      • countFeatures

        public int countFeatures()
        Description copied from interface: FeatureHolder
        Count how many features are contained.
        Specified by:
        countFeatures in interface FeatureHolder
        Returns:
        a positive integer or zero, equal to the number of features contained

      • filter

        public FeatureHolder filter​(FeatureFilter ff,
                            boolean recurse)
        Description copied from interface: FeatureHolder
        Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.
        Specified by:
        filter in interface FeatureHolder
        Parameters:
        ff - the FeatureFilter to apply
        recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

      • filter

        public FeatureHolder filter​(FeatureFilter ff)
        Description copied from interface: FeatureHolder
        Query this set of features using a supplied FeatureFilter.
        Specified by:
        filter in interface FeatureHolder
        Parameters:
        ff - the FeatureFilter to apply.
        Returns:
        all features in this container which match filter.

      • getSchema

        public FeatureFilter getSchema()
        Description copied from interface: FeatureHolder
        Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

        For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

        Specified by:
        getSchema in interface FeatureHolder
        Returns:
        the schema filter

      • getName

        public String getName()
        Description copied from interface: Sequence
        The name of this sequence.

        The name may contain spaces or odd characters.

        Specified by:
        getName in interface Sequence
        Returns:
        the name as a String

      • getURN

        public String getURN()
        Description copied from interface: Sequence
        A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g. 
         urn:sequence/embl:AL121903
        It may also be a URL identifying a specific resource, either locally or over the network 
         file:///home/thomas/myseq.fa|seq22
 http://www.mysequences.net/chr22.seq
        Specified by:
        getURN in interface Sequence
        Returns:
        the URI as a String

      • getSequence

        public Sequence getSequence()
        Return the parent sequence of which this is a partial view
        Since:
        1.3

      • getEnd

        public int getEnd()

      • isUnchanging

        public boolean isUnchanging​(ChangeType ct)
        Description copied from interface: Changeable

        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.

        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