charite.christo.protein
Class MultipleSequenceParser

java.lang.Object
  charite.christo.protein.MultipleSequenceParser

public class MultipleSequenceParser
extends java.lang.Object

Reads multiple sequences formats: clustalW, MSF, WIKI:Fasta see

• http://www.molecularevolution.org/mbl/resources/fileformats/
• http://bioinformatics.abc.hu/tothg/biocomp/other/Stockholm.html WIKI:Stockholm_format
• http://www.ebi.ac.uk/help/formats_frame.html
• http://www.bioinformatics.nl/tools/crab_pir.html

Field Summary

static int	CLUSTALW
static int	FASTA
static int	HSSP
static int	MSF
static int	NEXUS
static int	PIR
static int	PRODOM
static int	SIMPLE
static int	STOCKHOLM

Constructor Summary

MultipleSequenceParser()


Method Summary

static int	countFasta(BA ba, int format)
java.lang.String[]	getAccessionIDs()
byte[][]	getFastaHeader()
int[]	getFirstResidueIndex()
byte[][]	getGappedSequences()
byte[][]	getGappedSequences0123(char pfx)
int[]	getLastResidueIndex()
byte[][]	getSecondaryStructures()
java.lang.String[]	getSequenceNames()
java.lang.String[][]	getSequenceRefs()
java.lang.String[]	getSharedDatabaseRefs()
static int	isFormat(int whatFormat, BA ba, Range returnLineRange, int[] returnProteinCount)
MultipleSequenceParser	setGap(char g)
MultipleSequenceParser	setNamesStartWith(char start)
MultipleSequenceParser	setText(BA ba)
MultipleSequenceParser	setText(int format, BA ba, Range fromToLine)

Methods inherited from class java.lang.Object

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

Field Detail

MSF

public static final int MSF

See Also:

Constant Field Values

STOCKHOLM

public static final int STOCKHOLM

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Constant Field Values

PRODOM

public static final int PRODOM

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Constant Field Values

HSSP

public static final int HSSP

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Constant Field Values

FASTA

public static final int FASTA

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Constant Field Values

NEXUS

public static final int NEXUS

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Constant Field Values

CLUSTALW

public static final int CLUSTALW

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Constant Field Values

PIR

public static final int PIR

See Also:

Constant Field Values

SIMPLE

public static final int SIMPLE

See Also:

Constant Field Values

Constructor Detail

MultipleSequenceParser

public MultipleSequenceParser()

Method Detail

getSequenceNames

public java.lang.String[] getSequenceNames()

getFastaHeader

public byte[][] getFastaHeader()

getGappedSequences

public byte[][] getGappedSequences()

getSecondaryStructures

public byte[][] getSecondaryStructures()

getAccessionIDs

public java.lang.String[] getAccessionIDs()

getSequenceRefs

public java.lang.String[][] getSequenceRefs()

getSharedDatabaseRefs

public java.lang.String[] getSharedDatabaseRefs()

getFirstResidueIndex

public int[] getFirstResidueIndex()

getLastResidueIndex

public int[] getLastResidueIndex()

setGap

public MultipleSequenceParser setGap(char g)

setNamesStartWith

public MultipleSequenceParser setNamesStartWith(char start)

isFormat

public static int isFormat(int whatFormat,
                           BA ba,
                           Range returnLineRange,
                           int[] returnProteinCount)

countFasta

public static int countFasta(BA ba,
                             int format)

setText

public MultipleSequenceParser setText(BA ba)

setText

public MultipleSequenceParser setText(int format,
                                      BA ba,
                                      Range fromToLine)

getGappedSequences0123

public byte[][] getGappedSequences0123(char pfx)