Package jgromacs.data

Class Alignment

java.lang.Object
jgromacs.data.Alignment
All Implemented Interfaces:
Cloneable

public class Alignment extends Object implements Cloneable
Objects of this class represent a sequence alignment
  • Constructor Details

    • Alignment

      public Alignment()
      Constructs a new Alignment object
  • Method Details

    • getSequence

      public Sequence getSequence(int i)
      Returns sequence #i of the alignment
      Returns:
      sequence #i
    • getSequencesAsArrayList

      public ArrayList<Sequence> getSequencesAsArrayList()
      Returns sequences of the alignment as an ArrayList object
      Returns:
      list of sequences as an ArrayList
    • getNumberOfSequences

      public int getNumberOfSequences()
      Returns the number of sequences in the alignment
      Returns:
      number of sequences
    • getMaxSequenceLength

      public int getMaxSequenceLength()
      Returns the length of the longest sequence in the alignment
      Returns:
      length of longest sequence
    • getMinSequenceLength

      public int getMinSequenceLength()
      Returns the length of the shortest sequence in the alignment
      Returns:
      length of shortest sequence
    • addSequence

      public void addSequence(Sequence seq)
      Adds a new sequence to the alignment
      Parameters:
      seq - new sequence
    • setSequence

      public void setSequence(int i, Sequence seq)
      Replaces sequence #i of the alignment with a new sequence
      Parameters:
      seq - new sequence
    • removeSequence

      public void removeSequence(int i)
      Removes sequence #i from the alignment
    • removeSequence

      public void removeSequence(Sequence seq)
      Removes the given sequence from the alignment
      Parameters:
      seq - the sequence to be removed
    • removeColumn

      public void removeColumn(int i)
      Removes column #i from the alignment
    • isMatchColumn

      public boolean isMatchColumn(int i)
      Returns true if column #i is a match column (i.e. there is no gap in column #i of the alignment)
    • getCollapsedAlignment

      public Alignment getCollapsedAlignment()
      Returns the collapsed alignment in which only the match columns are included (i.e. the columns without gaps)
      Returns:
      collapsed alignment
    • getMatchPositionIndices

      public IndexSet getMatchPositionIndices(int i)
      Returns the set of position indices in sequence #i that are included in the match columns of alignment
      Returns:
      index set of match positions
    • getMatchPositionIndexSets

      public IndexSetList getMatchPositionIndexSets()
      Returns the list of match position index sets (i.e. match position index group of each sequence in the alignment)
      Returns:
      list of match positions index set
    • getMatchPositionIndicesAsArrayList

      public ArrayList<Integer> getMatchPositionIndicesAsArrayList(int i)
      Returns the list of match position indices in sequence #i as an ArrayList object
      Returns:
      ArrayList of match positions
    • getMostFrequentResidueType

      public ResidueType getMostFrequentResidueType(int i)
      Returns the most frequent residue type in column #i of the alignment
      Returns:
      most frequent residue type
    • getConsensusSequence

      public Sequence getConsensusSequence()
      Returns the (majority) consensus sequence of the alignment
      Returns:
      consensus sequence
    • toString

      public String toString()
      Returns the String representation of alignment
      Overrides:
      toString in class Object
      Returns:
      String representation
    • toStringInfo

      public String toStringInfo()
      Returns summary information about the alignment
      Returns:
      summary information
    • clone

      public Object clone()
      Returns an identical Alignment object
      Overrides:
      clone in class Object
      Returns:
      clone of the alignment
    • equals

      public boolean equals(Object other)
      Returns true if the two alignments are identical
      Overrides:
      equals in class Object
      Parameters:
      other - the other alignment
    • hashCode

      public int hashCode()
      Returns hash code
      Overrides:
      hashCode in class Object