Documentation of 'edu.rit.compbio.seq.Alignment' Java class
Alignment
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edu.rit.compbio.seq

Class Alignment

  • All Implemented Interfaces:
    java.io.Externalizable, java.io.Serializable, java.lang.Comparable<Alignment>

    public class Alignment
extends java.lang.Object
implements java.io.Externalizable, java.lang.Comparable<Alignment>
    Class Alignment encapsulates the result of a sequence alignment between a query sequence and a subject sequence. Alignment objects are returned by the align() method of class ProteinLocalAlignment.

    An alignment object does not record the actual query sequence and subject sequence that were aligned. The alignment object does record an ID associated with the query sequence and an ID associated with the subject sequence. For example, the ID could be the index of a sequence in a ProteinDatabase.

    Class Alignment implements interface Comparable and so has a natural ordering. The comparison order depends on the alignment scores and the subject sequence IDs. An alignment with a higher score comes before an alignment with a lower score. If the scores are equal, an alignment with a lower subject sequence ID comes before an alignment with a higher subject sequence ID.

    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field and Description
      static int QUERY_ALIGNED_WITH_GAP
      State of an alignment position: character in query sequence aligned with gap in subject sequence.
      static int QUERY_ALIGNED_WITH_SUBJECT
      State of an alignment position: character in query sequence aligned with character in subject sequence.
      static int SUBJECT_ALIGNED_WITH_GAP
      State of an alignment position: character in subject sequence aligned with gap in query sequence.

    • Constructor Summary

      Constructors 
      Constructor and Description
      Alignment()
      Construct a new, uninitialized alignment object.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method and Description
      int compareTo(Alignment alignment)
      Compare this alignment object to the given alignment object.
      int getAlignment(int i)
      Get the state of the given position in the alignment.
      int getAlignmentLength()
      Get the number of positions in the alignment.
      int getQueryFinish()
      Get the index of the last aligned character in the query sequence.
      long getQueryId()
      Get the ID associated with the query sequence.
      int getQueryLength()
      Get the length of the query sequence.
      int getQueryStart()
      Get the index of the first aligned character in the query sequence.
      int getSubjectFinish()
      Get the index of the last aligned character in the subject sequence.
      long getSubjectId()
      Get the ID associated with the subject sequence.
      int getSubjectLength()
      Get the length of the subject sequence.
      int getSubjectStart()
      Get the index of the first aligned character in the subject sequence.
      void readExternal(java.io.ObjectInput in)
      Read this alignment object from the given object input stream.
      java.lang.String toString()
      Returns a string version of this alignment object.
      void writeExternal(java.io.ObjectOutput out)
      Write this alignment object to the given object output stream.

      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Field Detail

      • QUERY_ALIGNED_WITH_SUBJECT

        public static final int QUERY_ALIGNED_WITH_SUBJECT
        State of an alignment position: character in query sequence aligned with character in subject sequence.
        See Also:
        Constant Field Values

      • QUERY_ALIGNED_WITH_GAP

        public static final int QUERY_ALIGNED_WITH_GAP
        State of an alignment position: character in query sequence aligned with gap in subject sequence.
        See Also:
        Constant Field Values

      • SUBJECT_ALIGNED_WITH_GAP

        public static final int SUBJECT_ALIGNED_WITH_GAP
        State of an alignment position: character in subject sequence aligned with gap in query sequence.
        See Also:
        Constant Field Values

    • Constructor Detail

      • Alignment

        public Alignment()
        Construct a new, uninitialized alignment object. This constructor is for use only by object deserialization.

    • Method Detail

      • getQueryId

        public long getQueryId()
        Get the ID associated with the query sequence. This is an arbitrary integer; for example, it could be the index of a sequence in a ProteinDatabase.
        Returns:
        Query sequence ID.

      • getSubjectId

        public long getSubjectId()
        Get the ID associated with the subject sequence. This is an arbitrary integer; for example, it could be the index of a sequence in a ProteinDatabase.
        Returns:
        Subject sequence ID.

      • getQueryLength

        public int getQueryLength()
        Get the length of the query sequence.
        Returns:
        Query sequence length.

      • getSubjectLength

        public int getSubjectLength()
        Get the length of the subject sequence.
        Returns:
        Subject sequence length.

      • getQueryStart

        public int getQueryStart()
        Get the index of the first aligned character in the query sequence. The index is in the range 1 .. M, where M is the length of the query sequence. If a local alignment was not found, 0 is returned.
        Returns:
        Query sequence start index.

      • getQueryFinish

        public int getQueryFinish()
        Get the index of the last aligned character in the query sequence. The index is in the range 1 .. M, where M is the length of the query sequence. If a local alignment was not found, 0 is returned.
        Returns:
        Query sequence finish index.

      • getSubjectStart

        public int getSubjectStart()
        Get the index of the first aligned character in the subject sequence. The index is in the range 1 .. N, where N is the length of the subject sequence. If a local alignment was not found, 0 is returned.
        Returns:
        Subject sequence start index.

      • getSubjectFinish

        public int getSubjectFinish()
        Get the index of the last aligned character in the subject sequence. The index is in the range 1 .. N, where N is the length of the subject sequence. If a local alignment was not found, 0 is returned.
        Returns:
        Subject sequence finish index.

      • getAlignmentLength

        public int getAlignmentLength()
        Get the number of positions in the alignment. If a local alignment was not found, 0 is returned.
        Returns:
        Alignment length.

      • getAlignment

        public int getAlignment(int i)
        Get the state of the given position in the alignment. The index i must be in the range 0 .. L−1, where L is the alignment length. The state of position i in the alignment is returned, one of the following:
        Parameters:
        i - Position in the alignment.
        Returns:
        State of position i in the alignment.

      • compareTo

        public int compareTo(Alignment alignment)
        Compare this alignment object to the given alignment object. The comparison order depends on the alignment scores and the subject sequence IDs. An alignment with a higher score comes before an alignment with a lower score. If the scores are equal, an alignment with a lower subject sequence ID comes before an alignment with a higher subject sequence ID.
        Specified by:
        compareTo in interface java.lang.Comparable<Alignment>
        Parameters:
        alignment - Alignment to compare to.
        Returns:
        An integer less than, equal to, or greater than 0 if this alignment comes before, is the same as, or comes after the given alignment, respectively.

      • toString

        public java.lang.String toString()
        Returns a string version of this alignment object.
        Overrides:
        toString in class java.lang.Object
        Returns:
        String version.

      • writeExternal

        public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException
        Write this alignment object to the given object output stream.
        Specified by:
        writeExternal in interface java.io.Externalizable
        Parameters:
        out - Object output stream.
        Throws:
        java.io.IOException - Thrown if an I/O error occurred.

      • readExternal

        public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException
        Read this alignment object from the given object input stream.
        Specified by:
        readExternal in interface java.io.Externalizable
        Parameters:
        in - Object input stream.
        Throws:
        java.io.IOException - Thrown if an I/O error occurred.
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