Package org.biojava.nbio.core.alignment

Class SimpleProfile<S extends Sequence<C>,C extends Compound>

java.lang.Object
org.biojava.nbio.core.alignment.SimpleProfile<S,C>
Type Parameters:
S - each element of the alignment Profile is of type S
C - each element of an AlignedSequence is a Compound of type C
All Implemented Interfaces:
Serializable, Iterable<AlignedSequence<S,C>>, Profile<S,C>
Direct Known Subclasses:
SimpleProfilePair, SimpleSequencePair
public class SimpleProfile<S extends Sequence<C>,C extends Compound> extends Object implements Serializable, Profile<S,C>
Implements a data structure for the results of sequence alignment. Every List returned is unmodifiable.
Author:
Mark Chapman, Paolo Pavan
See Also:

  • Field Details

  • Constructor Details

    • SimpleProfile

      protected SimpleProfile(AlignedSequence<S,C> query, AlignedSequence<S,C> target)
      Creates a pair profile for the given already aligned sequences.
      Parameters:
      query - the first sequence of the pair
      target - the second sequence of the pair
      Throws:
      IllegalArgumentException - if sequences differ in size

    • SimpleProfile

      public SimpleProfile(S sequence)
      Creates a profile from a single sequence.
      Parameters:
      sequence - sequence to seed profile

    • SimpleProfile

      protected SimpleProfile(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya)
      Creates a pair profile for the given sequences.
      Parameters:
      query - the first sequence of the pair
      target - the second sequence of the pair
      sx - lists whether the query sequence aligns a Compound or gap at each index of the alignment
      xb - number of Compounds skipped in the query sequence before the aligned region
      xa - number of Compounds skipped in the query sequence after the aligned region
      sy - lists whether the target sequence aligns a Compound or gap at each index of the alignment
      yb - number of Compounds skipped in the target sequence before the aligned region
      ya - number of Compounds skipped in the target sequence after the aligned region
      Throws:
      IllegalArgumentException - if alignments differ in size or given sequences do not fit in alignments

    • SimpleProfile

      protected SimpleProfile(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)
      Creates a pair profile for the given profiles.
      Parameters:
      query - the first profile of the pair
      target - the second profile of the pair
      sx - lists whether the query profile aligns a Compound or gap at each index of the alignment
      sy - lists whether the target profile aligns a Compound or gap at each index of the alignment
      Throws:
      IllegalArgumentException - if alignments differ in size or given profiles do not fit in alignments

    • SimpleProfile

      public SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences)
      Creates a profile for the already aligned sequences.
      Parameters:
      alignedSequences - the already aligned sequences
      Throws:
      IllegalArgument - if aligned sequences differ in length or collection is empty.

  • Method Details

    • getAlignedSequence

      public AlignedSequence<S,C> getAlignedSequence(int listIndex)
      Description copied from interface: Profile
      Returns AlignedSequence at given index.
      Specified by:
      getAlignedSequence in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      listIndex - index of sequence in profile
      Returns:
      desired sequence

    • getAlignedSequence

      public AlignedSequence<S,C> getAlignedSequence(S sequence)
      Description copied from interface: Profile
      Searches for the given Sequence within this alignment profile. Returns the corresponding AlignedSequence.
      Specified by:
      getAlignedSequence in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      sequence - an original Sequence
      Returns:
      the corresponding AlignedSequence

    • getAlignedSequences

      public List<AlignedSequence<S,C>> getAlignedSequences()
      Description copied from interface: Profile
      Returns a List containing the individual AlignedSequences of this alignment.
      Specified by:
      getAlignedSequences in interface Profile<S extends Sequence<C>,C extends Compound>
      Returns:
      list of aligned sequences

    • getAlignedSequences

      public List<AlignedSequence<S,C>> getAlignedSequences(int... listIndices)
      Description copied from interface: Profile
      Returns a List containing some of the individual AlignedSequences of this alignment.
      Specified by:
      getAlignedSequences in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      listIndices - indices of sequences in profile
      Returns:
      list of aligned sequences

    • getAlignedSequences

      public List<AlignedSequence<S,C>> getAlignedSequences(S... sequences)
      Description copied from interface: Profile
      Returns a List containing some of the individual AlignedSequences of this alignment.
      Specified by:
      getAlignedSequences in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      sequences - original Sequences
      Returns:
      list of aligned sequences

    • getCompoundAt

      public C getCompoundAt(int listIndex, int alignmentIndex)
      Description copied from interface: Profile
      Returns the Compound at row of given sequence and column of alignment index. If the given sequence has overlap, this will return the Compound from the top row of the sequence.
      Specified by:
      getCompoundAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      listIndex - index of sequence in profile
      alignmentIndex - column index within an alignment
      Returns:
      the sequence element

    • getCompoundAt

      public C getCompoundAt(S sequence, int alignmentIndex)
      Description copied from interface: Profile
      Returns the Compound at row of given sequence and column of alignment index. If the given sequence has overlap, this will return the Compound from the top row of the sequence.
      Specified by:
      getCompoundAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      sequence - either an AlignedSequence or an original Sequence
      alignmentIndex - column index within an alignment
      Returns:
      the sequence element

    • getCompoundCountsAt

      public int[] getCompoundCountsAt(int alignmentIndex)
      Description copied from interface: Profile
      Returns the number of each Compound in the given column for all compounds in CompoundSet.
      Specified by:
      getCompoundCountsAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      alignmentIndex - column index within an alignment
      Returns:
      list of counts

    • getCompoundCountsAt

      public int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds)
      Description copied from interface: Profile
      Returns the number of each Compound in the given column only for compounds in the given list.
      Specified by:
      getCompoundCountsAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      alignmentIndex - column index within an alignment
      compounds - list of compounds to count
      Returns:
      corresponding list of counts

    • getCompoundsAt

      public List<C> getCompoundsAt(int alignmentIndex)
      Description copied from interface: Profile
      Returns the Compound elements of the original Sequences at the given column.
      Specified by:
      getCompoundsAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      alignmentIndex - column index within an alignment
      Returns:
      the sequence elements

    • getCompoundSet

      public CompoundSet<C> getCompoundSet()
      Description copied from interface: Profile
      Returns CompoundSet of all AlignedSequences
      Specified by:
      getCompoundSet in interface Profile<S extends Sequence<C>,C extends Compound>
      Returns:
      set of Compounds in contained sequences

    • getCompoundWeightsAt

      public float[] getCompoundWeightsAt(int alignmentIndex)
      Description copied from interface: Profile
      Returns the fraction of each Compound in the given column for all compounds in CompoundSet.
      Specified by:
      getCompoundWeightsAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      alignmentIndex - column index within an alignment
      Returns:
      list of fractional weights

    • getCompoundWeightsAt

      public float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds)
      Description copied from interface: Profile
      Returns the fraction of each Compound in the given column only for compounds in the given list.
      Specified by:
      getCompoundWeightsAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      alignmentIndex - column index within an alignment
      compounds - list of compounds to count
      Returns:
      corresponding list of fractional weights

    • getIndexOf

      public int getIndexOf(C compound)
      Description copied from interface: Profile
      Searches for the given Compound within this alignment profile. Returns column index nearest to the start of the alignment profile, or -1 if not found.
      Specified by:
      getIndexOf in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      compound - search element
      Returns:
      index of column containing search element nearest to the start of the alignment profile

    • getIndicesAt

      public int[] getIndicesAt(int alignmentIndex)
      Description copied from interface: Profile
      Returns the indices in the original Sequences corresponding to the given column. All indices are 1-indexed and inclusive.
      Specified by:
      getIndicesAt in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      alignmentIndex - column index within an alignment
      Returns:
      the sequence indices

    • getLastIndexOf

      public int getLastIndexOf(C compound)
      Description copied from interface: Profile
      Searches for the given Compound within this alignment profile. Returns column index nearest to the end of the alignment profile, or -1 if not found.
      Specified by:
      getLastIndexOf in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      compound - search element
      Returns:
      index of column containing search element nearest to the end of the alignment profile

    • getLength

      public int getLength()
      Description copied from interface: Profile
      Returns the number of columns in the alignment profile.
      Specified by:
      getLength in interface Profile<S extends Sequence<C>,C extends Compound>
      Returns:
      the number of columns

    • getOriginalSequences

      public List<S> getOriginalSequences()
      Description copied from interface: Profile
      Returns a List containing the original Sequences used for alignment.
      Specified by:
      getOriginalSequences in interface Profile<S extends Sequence<C>,C extends Compound>
      Returns:
      list of original sequences

    • getSize

      public int getSize()
      Description copied from interface: Profile
      Returns the number of rows in this profile. If any AlignedSequences are circular and overlap within the alignment, the returned size will be greater than the number of sequences, otherwise the numbers will be equal.
      Specified by:
      getSize in interface Profile<S extends Sequence<C>,C extends Compound>
      Returns:
      number of rows

    • getSubProfile

      public ProfileView<S,C> getSubProfile(Location location)
      Description copied from interface: Profile
      Returns a ProfileView windowed to contain only the given Location. This only includes the AlignedSequences which overlap the location.
      Specified by:
      getSubProfile in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      location - portion of profile to view
      Returns:
      a windowed view of the profile

    • hasGap

      public boolean hasGap(int alignmentIndex)
      Description copied from interface: Profile
      Returns true if any AlignedSequence has a gap at the given index.
      Specified by:
      hasGap in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      alignmentIndex - column index within an alignment
      Returns:
      true if any AlignedSequence has a gap at the given index

    • isCircular

      public boolean isCircular()
      Description copied from interface: Profile
      Returns true if any AlignedSequence is circular. If so, sequences may simply wrap around from the end to the start of the alignment or they may contribute multiple overlapping lines to the profile.
      Specified by:
      isCircular in interface Profile<S extends Sequence<C>,C extends Compound>
      Returns:
      true if any AlignedSequence is circular

    • toString

      public String toString(int width)
      Description copied from interface: Profile
      Returns a formatted view of the alignment profile. This shows the start and end indices of the profile and each sequence for each group of lines of the given width. Each line may also be labeled.
      Specified by:
      toString in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      width - limit on the line length
      Returns:
      a formatted view of the alignment profile

    • toString

      public String toString(Profile.StringFormat format)
      Description copied from interface: Profile
      Returns a formatted view of the alignment profile. Details depend on the format given.
      Specified by:
      toString in interface Profile<S extends Sequence<C>,C extends Compound>
      Parameters:
      format - output format
      Returns:
      a formatted view of the alignment profile

    • toString

      public String toString()
      Description copied from interface: Profile
      Returns a simple view of the alignment profile. This shows each sequence on a separate line (or multiple lines, if circular) and nothing more. This should result in Profile.getSize() lines with Profile.getLength() Compounds per line.
      Specified by:
      toString in interface Profile<S extends Sequence<C>,C extends Compound>
      Overrides:
      toString in class Object
      Returns:
      a simple view of the alignment profile

    • iterator

      public Iterator<AlignedSequence<S,C>> iterator()
      Specified by:
      iterator in interface Iterable<S extends Sequence<C>>