statalign.postprocess.plugins.benchmarks
Class AlignmentSample

java.lang.Object
  statalign.postprocess.plugins.benchmarks.AlignmentSample

All Implemented Interfaces:

java.io.Serializable

public class AlignmentSample
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Field Summary

statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment	mpd
java.util.ArrayList<java.lang.Double>	posteriors
statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment	reference
java.util.ArrayList<statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment>	samples

Constructor Summary

AlignmentSample()

Method Summary

static AlignmentSample	loadAlignments(java.io.File file) Loads an alignment sample object from a file.
static void	parseAlignmentString(java.lang.String alignmentString, java.util.ArrayList<java.lang.String> sequences, java.util.ArrayList<java.lang.String> sequenceNames) Fills a vector of sequences and vector of sequence names from a specified fasta alignment string.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

reference

public statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment reference

mpd

public statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment mpd

posteriors

public java.util.ArrayList<java.lang.Double> posteriors

samples

public java.util.ArrayList<statalign.postprocess.plugins.benchmarks.AlignmentSample.Alignment> samples

Constructor Detail

AlignmentSample

public AlignmentSample()

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

loadAlignments

public static AlignmentSample loadAlignments(java.io.File file)

Loads an alignment sample object from a file.

Parameters:

file -

Returns:

parseAlignmentString

public static void parseAlignmentString(java.lang.String alignmentString,
                                        java.util.ArrayList<java.lang.String> sequences,
                                        java.util.ArrayList<java.lang.String> sequenceNames)

Fills a vector of sequences and vector of sequence names from a specified fasta alignment string.

Parameters:

alignmentString -

sequences -

sequenceNames -