calhoun.analysis.crf.io
Class SequenceConverter

java.lang.Object
  calhoun.analysis.crf.io.SequenceConverter

public class SequenceConverter
extends java.lang.Object

used for converting between different encodings of gene structure in a hidden sequence. Mostly for legacy use

Constructor Summary

SequenceConverter()

Method Summary

static void	convertSeqFrom13To39(TrainingSequence<java.lang.Character> seq)
static void	convertSeqFrom39To13(int[] seq)
static void	convertSeqFrom39To13(TrainingSequence<java.lang.Character> seq)
static int[]	convertSeqFromInterval13ToInterval29(int[] states)
static java.lang.String	convertSeqFromInterval13ToTricycle13(java.lang.String seq2)
static void	convertSeqFromInterval13ToTricycle13(TrainingSequence<java.lang.Character> seq)
static int[]	convertSeqFromInterval29ToInterval13(int[] seq)
static int[]	convertSeqFromInterval29ToInterval13Wrong(int[] states)
static java.lang.String	convertSeqFromTricycle13ToInterval13(java.lang.String seq2)
static void	convertSeqFromTricycle13ToInterval13(TrainingSequence<java.lang.Character> seq)
static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>	stateVector2StateLengths(java.util.List<? extends TrainingSequence<?>> data, int nStates)
void	writeHiddenSequence39GFF(TrainingSequence<java.lang.Character> refStates, java.lang.String filename)
static void	writeHiddenSequenceGFF(TrainingSequence<java.lang.Character> refStates, java.lang.String filename)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceConverter

public SequenceConverter()

Method Detail

stateVector2StateLengths

public static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> stateVector2StateLengths(java.util.List<? extends TrainingSequence<?>> data,
                                                                                                   int nStates)

convertSeqFromInterval13ToInterval29

public static int[] convertSeqFromInterval13ToInterval29(int[] states)

convertSeqFromInterval29ToInterval13

public static int[] convertSeqFromInterval29ToInterval13(int[] seq)

convertSeqFromInterval29ToInterval13Wrong

public static int[] convertSeqFromInterval29ToInterval13Wrong(int[] states)

convertSeqFromTricycle13ToInterval13

public static void convertSeqFromTricycle13ToInterval13(TrainingSequence<java.lang.Character> seq)

convertSeqFromTricycle13ToInterval13

public static java.lang.String convertSeqFromTricycle13ToInterval13(java.lang.String seq2)

convertSeqFromInterval13ToTricycle13

public static void convertSeqFromInterval13ToTricycle13(TrainingSequence<java.lang.Character> seq)

convertSeqFromInterval13ToTricycle13

public static java.lang.String convertSeqFromInterval13ToTricycle13(java.lang.String seq2)

convertSeqFrom13To39

public static void convertSeqFrom13To39(TrainingSequence<java.lang.Character> seq)

convertSeqFrom39To13

public static void convertSeqFrom39To13(TrainingSequence<java.lang.Character> seq)

convertSeqFrom39To13

public static void convertSeqFrom39To13(int[] seq)

writeHiddenSequenceGFF

public static void writeHiddenSequenceGFF(TrainingSequence<java.lang.Character> refStates,
                                          java.lang.String filename)
                                   throws java.io.IOException

Throws:

java.io.IOException

writeHiddenSequence39GFF

public void writeHiddenSequence39GFF(TrainingSequence<java.lang.Character> refStates,
                                     java.lang.String filename)
                              throws java.io.IOException

Throws:

java.io.IOException