Package org.biojavax.bio.seq

Class CompoundRichLocation

    • Constructor Detail

      • CompoundRichLocation

        public CompoundRichLocation​(Collection members)
        Constructs a CompoundRichLocation from the given set of members, with the default term of "join". Note that you really shouldn't use this if you are unsure if your members set contains overlapping members. Use RichLocation.Tools.construct() instead. The members collection must only contain Location instances. Any that are not RichLocations will be converted using RichLocation.Tools.enrich(). All members must come from the same strand of the same sequence with the same circular length.
        Parameters:
        members - the members to put into the compound location.
        See Also:
        RichLocation.Tools

      • CompoundRichLocation

        public CompoundRichLocation​(ComparableTerm term,
                            Collection members)
        Constructs a CompoundRichLocation from the given set of members. Note that you really shouldn't use this if you are unsure if your members set contains overlapping members. Use RichLocation.Tools.construct(members) instead. The members collection must only contain Location instances. Any that are not RichLocations will be converted using RichLocation.Tools.enrich().
        Parameters:
        term - the term to use when describing the group of members.
        members - the members to put into the compound location.
        See Also:
        RichLocation.Tools

    • Method Detail

      • sort

        public void sort()
        Sorts the member locations of a compound location. Does nothing for non-compound locations. Sorting depends on the compareTo() method of the member locations - usually they will be sorted by their start position. This might be useful when used with the location returned by a union or intersection, or when setting the term of a compound location to ORDER_TERM.
        Specified by:
        sort in interface RichLocation
        Overrides:
        sort in class SimpleRichLocation

      • getNoteSet

        public Set getNoteSet()
        Returns the set of notes associated with this object. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable. ALWAYS RETURNS THE EMPTY ANNOTATION NOTE SET
        Specified by:
        getNoteSet in interface RichAnnotatable
        Overrides:
        getNoteSet in class SimpleRichLocation
        Returns:
        set a set of Note objects.
        See Also:
        Note

      • setNoteSet

        public void setNoteSet​(Set notes)
                throws ChangeVetoException
        Clears the notes associated with this object and replaces them with the contents of this set. Would normally delegate call to internal RichAnnotation instance. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable. NOT IMPLEMENTED
        Specified by:
        setNoteSet in interface RichAnnotatable
        Overrides:
        setNoteSet in class SimpleRichLocation
        Parameters:
        notes - the set of Note objects to replace the existing ones with.
        Throws:
        ChangeVetoException - ALWAYS
        See Also:
        Note

      • setCircularLength

        public void setCircularLength​(int sourceSeqLength)
                       throws ChangeVetoException
        Sets the circular length of this location. If it is 0, the location is not circular. If it is not zero, then the number refers to the wrapping length of the location. eg. 100 would signify that a position of 112 would actually be a position of 112-100 = 12. RECURSIVELY APPLIES CALL TO ALL MEMBERS
        Specified by:
        setCircularLength in interface RichLocation
        Overrides:
        setCircularLength in class SimpleRichLocation
        Parameters:
        sourceSeqLength - the circular length of this location
        Throws:
        ChangeVetoException - if it doesn't want to change.

      • blockIterator

        public Iterator blockIterator()
        Return an Iterator over the set of maximal contiguous sub-locations.

        Given any location, it can be considered to contain zero or more maximal contiguous blocks of width 1 or greater. The empty location is composed from nothing. A contiguous location is composed from itself. A non-contiguous location is composed from contiguous blocks seperated by gaps.

        This method should return an Iterator over these maximally contiguous blocks starting with the left-most block, and finishing at the right-most block.

        Specified by:
        blockIterator in interface Location
        Overrides:
        blockIterator in class SimpleRichLocation
        Returns:
        an Iterator over Location objects that are the maximally contiguous set of locations contained within this location

      • contains

        public boolean contains​(int p)
        Checks if this location contains a point. Recursively applies this call to all members.
        Specified by:
        contains in interface Location
        Overrides:
        contains in class SimpleRichLocation
        Parameters:
        p - the point to check
        Returns:
        true if this contains p, otherwise false

      • getDecorator

        public Location getDecorator​(Class decoratorClass)
        Checks the decorator chain for an instance of decoratorClass and return it if found.

        The default behavior is to return null. If the current object is a decorator and is an instance of decoratorClass it should return itself. Otherwise, the decorator should chain this method onto the instance it wraps. ALWAYS RETURNS NULL

        Specified by:
        getDecorator in interface Location
        Overrides:
        getDecorator in class SimpleRichLocation
        Parameters:
        decoratorClass - the Class to check
        Returns:
        a Location if an instance of this class is present in the decorator chain and null otherwise.

      • newInstance

        public Location newInstance​(Location loc)
        Create a new instance of Location with all of the same decorators as this instance but with the data stored in loc.

        The default behavior is to return loc unchanged. If the class is a location decorator then it should instantiate an instance of the same type that decorates loc. ALWAYS RETURNS SELF

        Specified by:
        newInstance in interface Location
        Overrides:
        newInstance in class SimpleRichLocation
        Parameters:
        loc - the Location to use as template
        Returns:
        a Location instance based on loc with the same decorators as the current instance

      • translate

        public Location translate​(int dist)
        Create a location that is a translation of this location. Recursively translates all members of this location.
        Specified by:
        translate in interface Location
        Overrides:
        translate in class SimpleRichLocation
        Parameters:
        dist - the distance to translate (to the right)

      • contains

        public boolean contains​(Location l)
        Checks if this location contains the other.

        Abstractly, a location contains another if every point in the other location is contained within this one. A location contains another location if it overlaps it, and the coordinates enclose those of the other location at both ends, and they fall on the same strand. Recursively applies this call to all members. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich().

        Specified by:
        contains in interface Location
        Overrides:
        contains in class SimpleRichLocation
        Parameters:
        l - the Location to check
        Returns:
        true if an only if one of the members of this Location wholey contains l.
        See Also:
        RichLocation.Tools

      • overlaps

        public boolean overlaps​(Location l)
        Checks if these two locations overlap, using this location's concept of overlapping.

        Abstractly, two locations overlap if they both contain any point. A location overlaps another location if it is on the same sequence, and the coordinates overlap, and both are of the same circularity. Recursively applies this call to all members.

        Specified by:
        overlaps in interface Location
        Overrides:
        overlaps in class SimpleRichLocation
        Parameters:
        l - the Location to check
        Returns:
        true if and only if at least on of the members overlaps l

      • union

        public Location union​(Location l)
        Return a Location containing all points in either ranges. A merged SimpleRichLocation is returned if the two locations overlap and are on the same strand. Otherwise, a CompoundRichLocation is returned containing the two locations as members. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich(). The resulting location may or may not be a compound location. If it is a compound location, its contents will be a set of simple locations. Regions that overlap will be merged into a single location.
        Specified by:
        union in interface Location
        Overrides:
        union in class SimpleRichLocation
        Parameters:
        l - the Location to union with
        Returns:
        a CompoundLocation if the components of the union cannot be merged else a SimpleRichLocation
        See Also:
        RichLocation.Tools

      • intersection

        public Location intersection​(Location l)
        Returns a Location that contains all points common to both ranges. If the locations overlap and are on the same strand, the intersection is returned. If they overlap but are on different strands, a CompoundRichLocation of the overlapping portions is returned. If they do not overlap, the empty sequence is returned. If passed a Location which is not a RichLocation, it converts it first using RichLocation.Tools.enrich(). The resulting location may or may not be a compound location. If it is a compound location, its contents will be a set of simple locations.
        Specified by:
        intersection in interface Location
        Overrides:
        intersection in class SimpleRichLocation
        Parameters:
        l - the Location to intersect with
        Returns:
        a CompoundLocation if there is more than one region of intersection that cannot be merged. Else a SimpleRichLocation.

      • symbols

        public SymbolList symbols​(SymbolList seq)
        Return the symbols in a sequence that fall within this range. If the location is circular but the sequence is not, or they are both circular but of different circular lengths, an exception is thrown. The symbol list passed in is the sequence used to obtain symbols if the cross reference for this location has not been set. If the cross reference has been set, then the symbol list passed in is only used if it has the same accession, namespace and version as the cross reference on this location. Otherwise, the cross referenced symbol list is looked up and used instead. This function concatenates the symbols of all its child locations.

        The most obvious application of this method to a CompoundRichLocation is the contatenation of the components of a gene with multiple exons.

        Specified by:
        symbols in interface Location
        Overrides:
        symbols in class SimpleRichLocation
        Parameters:
        seq - the SymbolList to process
        Returns:
        the SymbolList containing the symbols in seq in this range

      • equals

        public boolean equals​(Object o)
        Checks if this location is equivalent to the other.

        Abstractly, a location is equal to another if for every point in one it is also in the other. This is equivalent to a.contains(b) && b.contains(a). You should call LocationTools.areEqual after casting l to Location. Locations are equal if their term, min, max, strand, and crossref are the same, and if their rank is the same too. Compound locations are only equal to other Locations if all their components are equal.

        Specified by:
        equals in interface Location
        Overrides:
        equals in class SimpleRichLocation
        Parameters:
        o - the Object to check
        Returns:
        true if this equals l, otherwise false