Package pal.alignment

Class AbstractAlignment

java.lang.Object
pal.alignment.AbstractAlignment
All Implemented Interfaces:
Serializable, Alignment, IdGroup, Report
Direct Known Subclasses:
BootstrappedAlignment, ConcatenatedAlignment, ConcatenatedAnnotatedAlignment, GapBalancedAlignment, IndelAlignment, JumbledAlignment, ReadAlignment, ReadAlignmentOld, SimpleAlignment, SimulatedAlignment, SitePattern, StrippedAlignment
public abstract class AbstractAlignment extends Object implements Alignment, Serializable, IdGroup, Report
abstract base class for any alignment data.
Version:
$Id: AbstractAlignment.java,v 1.7 2003/03/23 00:12:57 matt Exp $
Author:
Alexei Drummond, Korbinian Strimmer
See Also:

  • Field Details

    • numSeqs

      protected int numSeqs
      number of sequences

    • numSites

      protected int numSites
      length of each sequence

    • idGroup

      protected IdGroup idGroup
      sequence identifiers

  • Constructor Details

    • AbstractAlignment

      public AbstractAlignment()

  • Method Details

    • getData

      public abstract char getData(int seq, int site)
      sequence alignment at (sequence, site)
      Specified by:
      getData in interface Alignment

    • isGap

      public boolean isGap(int seq, int site)
      returns true if there is a gap in the give position.

    • guessDataType

      public void guessDataType()
      Guess data type

    • getChar

      protected final char getChar(int state)
      Same as getDataType().getChar(state)

    • getState

      protected final int getState(char c)
      Same as getDataType().getState(char)

    • isUnknownState

      protected final boolean isUnknownState(int state)
      Same as getDataType().isUnknownState(state)

    • getDataType

      public final DataType getDataType()
      Returns the datatype of this alignment
      Specified by:
      getDataType in interface Alignment

    • setDataType

      public final void setDataType(DataType d)
      Sets the datatype of this alignment

    • toString

      public String toString()
      returns representation of this alignment as a string
      Overrides:
      toString in class Object

    • report

      public void report(PrintWriter out)
      Description copied from interface: Report
      print human readable report (e.g., on parameters and associated model)
      Specified by:
      report in interface Report
      Parameters:
      out - output stream

    • getStates

      public int[][] getStates()
      Fills a [numsequences][length] matrix with indices. Each index represents the sequence state, -1 means a gap.

    • getLength

      public final int getLength()
      Return number of sites in this alignment

    • getSequenceCount

      public final int getSequenceCount()
      Return number of sequences in this alignment
      Specified by:
      getSequenceCount in interface Alignment

    • getSiteCount

      public final int getSiteCount()
      Return number of sites for each sequence in this alignment
      Specified by:
      getSiteCount in interface Alignment
      Returns:
      number of sites for each sequence in this alignment

    • getAlignedSequenceString

      public String getAlignedSequenceString(int seq)
      Returns a string representing a single sequence (including gaps) from this alignment.
      Specified by:
      getAlignedSequenceString in interface Alignment

    • getIdentifier

      public Identifier getIdentifier(int i)
      Description copied from interface: IdGroup
      Returns the ith identifier.
      Specified by:
      getIdentifier in interface IdGroup

    • setIdentifier

      public void setIdentifier(int i, Identifier ident)
      Description copied from interface: IdGroup
      Sets the ith identifier.
      Specified by:
      setIdentifier in interface IdGroup

    • getIdCount

      public int getIdCount()
      Description copied from interface: IdGroup
      Returns the number of identifiers in this group
      Specified by:
      getIdCount in interface IdGroup

    • whichIdNumber

      public int whichIdNumber(String name)
      Description copied from interface: IdGroup
      returns the index of the identifier with the given name.
      Specified by:
      whichIdNumber in interface IdGroup