charite.christo
Class ChAlignUtils

java.lang.Object
  charite.christo.ChAlignUtils

public class ChAlignUtils
extends Object

Constructor Summary

ChAlignUtils()

Method Summary

static float	findScore(byte[] txt, int from, int to, String pattern)
static byte[][]	gappedForPerfectMatch(byte[]... ungapped)
static byte[][]	getSequences123(byte[][] ss, String[] names)
static int	idxOfGappedInUngapped(byte[] gapped, byte[] ungapped)
static byte[][]	partialToGlobalAlignment(byte[] gR, byte[] gM, int[] iiR, int[] iiM)
static StringBuffer	toGappedMSF(byte[][] gapped, String headerPrefix, int offset, boolean fastaFormat) The gapped sequences may be 0-terminated!
static StringBuffer	toUngappedMultipleFasta(byte[][] sequences, String prefix, int offset)
static int[]	useGapsFromExternalAlignment(byte[] toBeAlignedAA, byte[] templateAA, int[] templateGap, int templateGapLen)

Methods inherited from class java.lang.Object

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

Constructor Detail

ChAlignUtils

public ChAlignUtils()

Method Detail

getSequences123

public static byte[][] getSequences123(byte[][] ss,
                                       String[] names)

toGappedMSF

public static StringBuffer toGappedMSF(byte[][] gapped,
                                       String headerPrefix,
                                       int offset,
                                       boolean fastaFormat)

The gapped sequences may be 0-terminated!

toUngappedMultipleFasta

public static StringBuffer toUngappedMultipleFasta(byte[][] sequences,
                                                   String prefix,
                                                   int offset)

findScore

public static float findScore(byte[] txt,
                              int from,
                              int to,
                              String pattern)

partialToGlobalAlignment

public static byte[][] partialToGlobalAlignment(byte[] gR,
                                                byte[] gM,
                                                int[] iiR,
                                                int[] iiM)

idxOfGappedInUngapped

public static int idxOfGappedInUngapped(byte[] gapped,
                                        byte[] ungapped)

useGapsFromExternalAlignment

public static int[] useGapsFromExternalAlignment(byte[] toBeAlignedAA,
                                                 byte[] templateAA,
                                                 int[] templateGap,
                                                 int templateGapLen)

gappedForPerfectMatch

public static byte[][] gappedForPerfectMatch(byte[]... ungapped)