pal.alignment
Class GapBalancedAlignment

java.lang.Object
  |
  +--pal.alignment.AbstractAlignment
        |
        +--pal.alignment.GapBalancedAlignment
All Implemented Interfaces:
Alignment, IdGroup, Report, java.io.Serializable

public class GapBalancedAlignment
extends AbstractAlignment
implements java.io.Serializable

Creates a "Gap-Balanced" alignment.

See Also:
Serialized Form

Fields inherited from class pal.alignment.AbstractAlignment
dataType, frequency, idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP
 
Constructor Summary
GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap)
          The standard GapBalanced constructor
GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength)
          GapBalanced power user constructor
GapBalancedAlignment(Alignment base, int startingCodonPosition, int codonLength)
          GapBalanced power user constructor
 
Method Summary
 char getData(int seq, int site)
          sequence alignment at (sequence, site)
 
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

GapBalancedAlignment

public GapBalancedAlignment(Alignment base,
                            int startingCodonPosition,
                            boolean alignGap)
The standard GapBalanced constructor
Parameters:
Alignment - on which to based this gap balanced alignment
the - estimated startingCodonPosition of the alignment

GapBalancedAlignment

public GapBalancedAlignment(Alignment base,
                            int startingCodonPosition,
                            int codonLength)
GapBalanced power user constructor
Parameters:
Alignment - on which to based this gap balanced alignment
startingCodonPosition - the starting codon position of the alignment
codonLength - the length of a codon (to make things general, - the author is a Computer Scientist)

GapBalancedAlignment

public GapBalancedAlignment(Alignment base,
                            int startingCodonPosition,
                            boolean alignGap,
                            int codonLength)
GapBalanced power user constructor
Parameters:
Alignment - on which to based this gap balanced alignment
startingCodonPosition - the starting codon position of the alignment
alignGap - sometimes a large cap may occur in the middle of a sequence's codon. If this is true than no columns can match up in this area (it's hard to explain - for safety choose true!)
codonLength - the length of a codon (to make things general, - the author is a Computer Scientist)
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)
Overrides:
getData in class AbstractAlignment