charite.christo.protein
Class ChAlignUtils

java.lang.Object
  charite.christo.protein.ChAlignUtils

public class ChAlignUtils
extends java.lang.Object

Field Summary

static long	PRINT_ALI_IDENT_LETTER
static long	PRINT_ALI_TRUNCATE

Constructor Summary

ChAlignUtils()

Method Summary

static void	aliWithMidline(long options, byte[] gg1, int start1, java.lang.String header1, byte[] gg2, int start2, java.lang.String header2, int width, BA ba)
static void	appendName(java.lang.String prefix, int i, BA sb) The gapped sequences may be 0-terminated!
static byte[][]	applyAlignPositions(int[][] resNum, byte[][] sequences)
static boolean	atLeastNumLettersInColumn(int num, int col, byte[][] ali)
static int[]	column2letterIdx(byte[] text)
static int	column2letterIdx(byte[] seq, int from)
static java.lang.String	defaultAligner2Class()
static byte[][]	gappedForPerfectMatch(byte[]... ungapped)
static int[]	gaps2Columns(int[] gg, int toIndex)
static byte[][]	insertWhereNoCoordinates(int startIdxR, byte[] gapped3dR, int startIdxM, byte[] gapped3dM, byte[] seqR, byte[] seqM)
static int[]	letterIdx2column(byte[] text)
static void	msfHeader(char type, byte[][] gapped, BA sb)
static SequenceAligner	newDefaultAligner2()
static void	setDefaultAligner2(java.lang.String className)
static BA	toGappedFasta(byte[][] gapped)
static BA	toGappedFasta(byte[][] gapped, java.lang.String headerPrefix, int offset, BA sb)
static BA	toGappedMSF(byte[][] gapped)
static BA	toGappedMSF(byte[][] gapped, java.lang.String headerPrefix, int offset, BA sb)
static BA	toUngappedMultipleFasta(byte[][] sequences, java.lang.String prefix, int offset)
static byte[][]	trimAlignment(int numLetters, byte[][] ali)
static int[]	useGapsFromExternalAlignment(byte[] tGapped, byte[] mGapped, byte[] tResidues, byte[] mResidues, int[] tGaps, int[] mGaps)

Methods inherited from class java.lang.Object

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

Field Detail

PRINT_ALI_IDENT_LETTER

public static final long PRINT_ALI_IDENT_LETTER

See Also:

Constant Field Values

PRINT_ALI_TRUNCATE

public static final long PRINT_ALI_TRUNCATE

See Also:

Constant Field Values

Constructor Detail

ChAlignUtils

public ChAlignUtils()

Method Detail

appendName

public static void appendName(java.lang.String prefix,
                              int i,
                              BA sb)

The gapped sequences may be 0-terminated!

toGappedFasta

public static BA toGappedFasta(byte[][] gapped,
                               java.lang.String headerPrefix,
                               int offset,
                               BA sb)

toGappedMSF

public static BA toGappedMSF(byte[][] gapped,
                             java.lang.String headerPrefix,
                             int offset,
                             BA sb)

toGappedFasta

public static BA toGappedFasta(byte[][] gapped)

toGappedMSF

public static BA toGappedMSF(byte[][] gapped)

msfHeader

public static void msfHeader(char type,
                             byte[][] gapped,
                             BA sb)

toUngappedMultipleFasta

public static BA toUngappedMultipleFasta(byte[][] sequences,
                                         java.lang.String prefix,
                                         int offset)

insertWhereNoCoordinates

public static byte[][] insertWhereNoCoordinates(int startIdxR,
                                                byte[] gapped3dR,
                                                int startIdxM,
                                                byte[] gapped3dM,
                                                byte[] seqR,
                                                byte[] seqM)

gaps2Columns

public static int[] gaps2Columns(int[] gg,
                                 int toIndex)

letterIdx2column

public static int[] letterIdx2column(byte[] text)

column2letterIdx

public static int[] column2letterIdx(byte[] text)

column2letterIdx

public static int column2letterIdx(byte[] seq,
                                   int from)

useGapsFromExternalAlignment

public static int[] useGapsFromExternalAlignment(byte[] tGapped,
                                                 byte[] mGapped,
                                                 byte[] tResidues,
                                                 byte[] mResidues,
                                                 int[] tGaps,
                                                 int[] mGaps)

gappedForPerfectMatch

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

atLeastNumLettersInColumn

public static boolean atLeastNumLettersInColumn(int num,
                                                int col,
                                                byte[][] ali)

trimAlignment

public static byte[][] trimAlignment(int numLetters,
                                     byte[][] ali)

aliWithMidline

public static void aliWithMidline(long options,
                                  byte[] gg1,
                                  int start1,
                                  java.lang.String header1,
                                  byte[] gg2,
                                  int start2,
                                  java.lang.String header2,
                                  int width,
                                  BA ba)

applyAlignPositions

public static byte[][] applyAlignPositions(int[][] resNum,
                                           byte[][] sequences)

setDefaultAligner2

public static void setDefaultAligner2(java.lang.String className)

defaultAligner2Class

public static java.lang.String defaultAligner2Class()

newDefaultAligner2

public static SequenceAligner newDefaultAligner2()