Package org.biojava.nbio.genome.parsers.gff

Class FeatureList

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.ArrayList<FeatureI>

org.biojava.nbio.genome.parsers.gff.FeatureList

All Implemented Interfaces:

Serializable, Cloneable, Iterable<FeatureI>, Collection<FeatureI>, List<FeatureI>, RandomAccess

public class FeatureList
extends ArrayList<FeatureI>

A list of FeatureI objects implemented using a Java ArrayList; corresponds to a GFF file. This class is implemented entirely using FeatureI objects, so everything here will work correctly if you choose to implement your own feature class -- there are no dependencies on JavaGene's native Feature class.

Author:

Hanno Hinsch, Carmelo Foti

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor	Description
FeatureList()	Construct an empty list.
FeatureList(Collection<FeatureI> features)	Construct a new list containing the same features as the specified list.

Method Summary

Modifier and Type	Method	Description
void	add(Collection<FeatureI> list)	Add all features in the specified list or collection to this list.
boolean	add(FeatureI feature)	Add specified feature to the end of the list.
void	addIndex(String index)	Add an attribute that will be used as index for queries
void	addIndexes(List<String> indexes)	Add a list of attributes that will be used as indexes for queries
Collection<String>	attributeValues(String key)	Create a collection of the unique values for the specified key.
Location	bounds()	The union of all locations of all features in this list, mapped to the positive strand.
Collection<String>	groupValues()	Create a collection of all unique group ids in the list, as defined by the group() method of the features.
boolean	hasAttribute(String key)	Check if any feature in list has the specified attribute key.
boolean	hasAttribute(String key, String value)	Check if any feature in list has the specified attribute key/value pair.
boolean	hasGaps(int gapLength)	Check size of gaps between successive features in list.
FeatureList	omitOverlapping(String seqname, Location location, boolean useBothStrands)	Create a list of all features that do not overlap the specified location on the specified sequence.
FeatureList	selectByAttribute(String key)	Create a list of all features that include the specified attribute key.
FeatureList	selectByAttribute(String key, String value)	Create a list of all features that include the specified attribute key/value pair.
FeatureList	selectByGroup(String groupid)	Create a list of all features that have the specified group id, as defined by the group() method of the features.
FeatureList	selectByType(String type)	Create a list of all features that are of the specified type, as defined by the type() method of the features.
FeatureList	selectByUserData(String key)	Create a list of all features that include the specified key in their userMap().
FeatureList	selectByUserData(String key, Object value)	Create a list of all features that include the specified key/value pair in their userMap().
FeatureList	selectOverlapping(String seqname, Location location, boolean useBothStrands)	Create a list of all features that overlap the specified location on the specified sequence.
FeatureList	sortByStart()	Create a new list that is ordered by the starting index of the features' locations.
String	splice(DNASequence sequence)	Concatenate successive portions of the specified sequence using the feature locations in the list.
String	toString()	Return a string representation of all features in this list.

Methods inherited from class java.util.ArrayList

add, addAll, addAll, clear, clone, contains, ensureCapacity, equals, forEach, get, hashCode, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeIf, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractCollection

containsAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection

parallelStream, stream, toArray

Methods inherited from interface java.util.List

containsAll

Constructor Detail

FeatureList

public FeatureList()

Construct an empty list.

FeatureList

public FeatureList(Collection<FeatureI> features)

Construct a new list containing the same features as the specified list.

Parameters:

features - An existing list or collection of FeatureI objects.

Method Detail

add

public boolean add(FeatureI feature)

Add specified feature to the end of the list. Updates the bounding location of the feature list, if needed.

Specified by:

add in interface Collection<FeatureI>

Specified by:

add in interface List<FeatureI>

Overrides:

add in class ArrayList<FeatureI>

Parameters:

feature - The FeatureI object to add.

Returns:

True if the feature was added.

add

public void add(Collection<FeatureI> list)

Add all features in the specified list or collection to this list.

Parameters:

list - The collection of FeatureI objects.

bounds

public Location bounds()

The union of all locations of all features in this list, mapped to the positive strand. If an added feature is on the negative strand, its positive strand image is added to the union. The bounding location is not updated when a feature is removed from the list, so it is not guaranteed to be the minimal bounding location.

Returns:

A location that is the union of all feature locations in the list.

hasGaps

public boolean hasGaps(int gapLength)

Check size of gaps between successive features in list. The features in the list are assumed to be appropriately ordered.

Parameters:

gapLength - The minimum gap length to consider. Use a gapLength of 0 to check if features are contiguous.

Returns:

True if list has any gaps equal to or greater than gapLength.

splice

public String splice(DNASequence sequence)

Concatenate successive portions of the specified sequence using the feature locations in the list. The list is assumed to be appropriately ordered.

Parameters:

sequence - The source sequence from which portions should be selected.

Returns:

The spliced data.

Throws:

IllegalStateException - Out of order or overlapping FeatureI locations detected.

groupValues

public Collection<String> groupValues()

Create a collection of all unique group ids in the list, as defined by the group() method of the features. For example, if the features are from a GFF1 file, then each group id identifies a particular gene, and this method returns a collection of all gene ids.

Returns:

A collection (suitable for iteration using Java's "for" loop) of all the group ids found in this list. The order of the values is undefined; it will not match the order of features in the list.

attributeValues

public Collection<String> attributeValues(String key)

Create a collection of the unique values for the specified key. Example: For GTF files, using the "gene_id" key will give the names of all the genes in this list.

Returns:

A collection (suitable for iteration using Java's "for" loop) of all the values found for this key. The order of the values is undefined; it will not match the order of features in the list.

selectByGroup

public FeatureList selectByGroup(String groupid)

Create a list of all features that have the specified group id, as defined by the group() method of the features.

Parameters:

groupid - The group to match.

Returns:

A list of features having the specified group id.

selectByType

public FeatureList selectByType(String type)

Create a list of all features that are of the specified type, as defined by the type() method of the features. This might be, for example, "exon" or "CDS".

Parameters:

type - The type to match.

Returns:

A list of features of the specified type.

selectByAttribute

public FeatureList selectByAttribute(String key,
                                     String value)

Create a list of all features that include the specified attribute key/value pair. This method now properly supports adding the index before or after adding the features. Adding features, then then index, then more features is still not supported.

Parameters:

key - The key to consider.

value - The value to consider.

Returns:

A list of features that include the key/value pair.

selectByAttribute

public FeatureList selectByAttribute(String key)

Create a list of all features that include the specified attribute key.

Parameters:

key - The key to consider.

Returns:

A list of features that include the key.

selectByUserData

public FeatureList selectByUserData(String key,
                                    Object value)

Create a list of all features that include the specified key/value pair in their userMap().

Parameters:

key - The key to consider.

value - The value to consider.

Returns:

A list of features that include the key/value pair.

selectByUserData

public FeatureList selectByUserData(String key)

Create a list of all features that include the specified key in their userMap().

Parameters:

key - The key to consider.

Returns:

A list of features that include the key.

selectOverlapping

public FeatureList selectOverlapping(String seqname,
                                     Location location,
                                     boolean useBothStrands)
                              throws Exception

Create a list of all features that overlap the specified location on the specified sequence.

Parameters:

seqname - The sequence name. Only features with this sequence name will be checked for overlap.

location - The location to check.

useBothStrands - If true, locations are mapped to their positive strand image before being checked for overlap. If false, only features whose locations are on the same strand as the specified location will be considered for inclusion.

Returns:

The new list of features that overlap the location.

Throws:

Exception

omitOverlapping

public FeatureList omitOverlapping(String seqname,
                                   Location location,
                                   boolean useBothStrands)

Create a list of all features that do not overlap the specified location on the specified sequence.

Parameters:

seqname - The sequence name. Only features with this sequence name will be checked for overlap.

location - The location to check.

useBothStrands - If true, locations are mapped to their positive strand image before being checked for overlap. If false, all features whose locations are on the opposite strand from the specified location will be considered non-overlapping.

Returns:

The new list of features that do not overlap the location.

hasAttribute

public boolean hasAttribute(String key)

Check if any feature in list has the specified attribute key.

Parameters:

key - The attribute key to consider.

Returns:

True if at least one feature has the attribute key.

hasAttribute

public boolean hasAttribute(String key,
                            String value)

Check if any feature in list has the specified attribute key/value pair.

Parameters:

key - The attribute key to consider.

value - The attribute value to consider.

Returns:

True if at least one feature has the key/value pair.

toString

public String toString()

Return a string representation of all features in this list.

Overrides:

toString in class AbstractCollection<FeatureI>

Returns:

A string.

sortByStart

public FeatureList sortByStart()

Create a new list that is ordered by the starting index of the features' locations. All locations must be on the same strand of the same sequence.

Returns:

An ordered list.

Throws:

IndexOutOfBoundsException - Cannot compare/sort features whose locations are on opposite strands, or whose seqnames differ.

addIndexes

public void addIndexes(List<String> indexes)

Add a list of attributes that will be used as indexes for queries

Parameters:

indexes - the List containing the attribute_id

addIndex

public void addIndex(String index)

Add an attribute that will be used as index for queries

Parameters:

index - an attribute_id