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:

  • Constructor Details

    • 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 Details

    • 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.

    • main

      @Deprecated public static void main(String[] args)
      Deprecated.

    • 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