com.hfg.bio.seq.format

Class EMBL<T extends BioSequence>

java.lang.Object

com.hfg.bio.seq.format.ReadableSeqFormatBase<T>

com.hfg.bio.seq.format.EMBL<T>

All Implemented Interfaces:

ReadableSeqFormat<T>

public class EMBL<T extends BioSequence>
extends ReadableSeqFormatBase<T>

EMBL sequence format.

See ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt

See http://web.expasy.org/docs/userman.html for info on the Uniprot format variant.

Field Summary

Fields

Modifier and Type	Field and Description
static String	AC_LINE_CODE
static String	AH_LINE_CODE
static String	AS_LINE_CODE
static String	CC_LINE_CODE
static String	CLONE_ATTR
static String	CO_LINE_CODE
static String	DE_LINE_CODE
static String	DR_LINE_CODE
static String	DT_LINE_CODE
static String	EMBL_DATA_CLASS_ATTR
static String	FH_LINE_CODE
static String	FT_LINE_CODE
static String	GN_LINE_CODE
static String	ID_LINE_CODE
static String	KW_LINE_CODE
static String	OC_LINE_CODE
static String	OG_LINE_CODE
static String	OH_LINE_CODE
static String	ORGANISM_CLASSIFICATION_ATTR
static String	ORGANISM_NCBI_TAXON_ID_ATTR
static String	OS_LINE_CODE
static String	OX_LINE_CODE
static String	PE_LINE_CODE
static String	PR_LINE_CODE
static String	RA_LINE_CODE
static String	RC_LINE_CODE
static String	RG_LINE_CODE
static String	RL_LINE_CODE
static String	RN_LINE_CODE
static String	RP_LINE_CODE
static String	RT_LINE_CODE
static String	RX_LINE_CODE
static String	SPECIES_SCIENTIFIC_NAME_ATTR
static String	SQ_LINE_CODE
static String	XX_LINE_CODE

Constructor Summary

Constructors

Constructor and Description
EMBL(BioSequenceFactory<T> inSeqFactory)

Method Summary

Modifier and Type	Method and Description
static Logger	getLogger()
boolean	hasJanusDelimiter() A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record.
boolean	isEndOfRecord(String inLine)
T	readRecord(BufferedReader inReader)

Methods inherited from class com.hfg.bio.seq.format.ReadableSeqFormatBase

getBioSequenceFactory, read, read, readRecord

Methods inherited from class java.lang.Object

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

Field Detail

AC_LINE_CODE

public static final String AC_LINE_CODE

See Also:

Constant Field Values

AH_LINE_CODE

public static final String AH_LINE_CODE

See Also:

Constant Field Values

AS_LINE_CODE

public static final String AS_LINE_CODE

See Also:

Constant Field Values

CC_LINE_CODE

public static final String CC_LINE_CODE

See Also:

Constant Field Values

CO_LINE_CODE

public static final String CO_LINE_CODE

See Also:

Constant Field Values

DE_LINE_CODE

public static final String DE_LINE_CODE

See Also:

Constant Field Values

DR_LINE_CODE

public static final String DR_LINE_CODE

See Also:

Constant Field Values

DT_LINE_CODE

public static final String DT_LINE_CODE

See Also:

Constant Field Values

FH_LINE_CODE

public static final String FH_LINE_CODE

See Also:

Constant Field Values

FT_LINE_CODE

public static final String FT_LINE_CODE

See Also:

Constant Field Values

ID_LINE_CODE

public static final String ID_LINE_CODE

See Also:

Constant Field Values

KW_LINE_CODE

public static final String KW_LINE_CODE

See Also:

Constant Field Values

OC_LINE_CODE

public static final String OC_LINE_CODE

See Also:

Constant Field Values

OG_LINE_CODE

public static final String OG_LINE_CODE

See Also:

Constant Field Values

OS_LINE_CODE

public static final String OS_LINE_CODE

See Also:

Constant Field Values

PR_LINE_CODE

public static final String PR_LINE_CODE

See Also:

Constant Field Values

RA_LINE_CODE

public static final String RA_LINE_CODE

See Also:

Constant Field Values

RC_LINE_CODE

public static final String RC_LINE_CODE

See Also:

Constant Field Values

RG_LINE_CODE

public static final String RG_LINE_CODE

See Also:

Constant Field Values

RL_LINE_CODE

public static final String RL_LINE_CODE

See Also:

Constant Field Values

RN_LINE_CODE

public static final String RN_LINE_CODE

See Also:

Constant Field Values

RP_LINE_CODE

public static final String RP_LINE_CODE

See Also:

Constant Field Values

RT_LINE_CODE

public static final String RT_LINE_CODE

See Also:

Constant Field Values

RX_LINE_CODE

public static final String RX_LINE_CODE

See Also:

Constant Field Values

SQ_LINE_CODE

public static final String SQ_LINE_CODE

See Also:

Constant Field Values

XX_LINE_CODE

public static final String XX_LINE_CODE

See Also:

Constant Field Values

GN_LINE_CODE

public static final String GN_LINE_CODE

See Also:

Constant Field Values

OH_LINE_CODE

public static final String OH_LINE_CODE

See Also:

Constant Field Values

OX_LINE_CODE

public static final String OX_LINE_CODE

See Also:

Constant Field Values

PE_LINE_CODE

public static final String PE_LINE_CODE

See Also:

Constant Field Values

CLONE_ATTR

public static final String CLONE_ATTR

See Also:

Constant Field Values

EMBL_DATA_CLASS_ATTR

public static final String EMBL_DATA_CLASS_ATTR

See Also:

Constant Field Values

SPECIES_SCIENTIFIC_NAME_ATTR

public static final String SPECIES_SCIENTIFIC_NAME_ATTR

See Also:

Constant Field Values

ORGANISM_CLASSIFICATION_ATTR

public static final String ORGANISM_CLASSIFICATION_ATTR

See Also:

Constant Field Values

ORGANISM_NCBI_TAXON_ID_ATTR

public static final String ORGANISM_NCBI_TAXON_ID_ATTR

See Also:

Constant Field Values

Constructor Detail

EMBL

public EMBL(BioSequenceFactory<T> inSeqFactory)

Method Detail

getLogger

public static Logger getLogger()

isEndOfRecord

public boolean isEndOfRecord(String inLine)

hasJanusDelimiter

public boolean hasJanusDelimiter()

Description copied from interface: ReadableSeqFormat

A format has a Janus delimiter if the line that indicates that the previous record is over is also part of the next record. Will return true for formats like FASTA.

Returns:

whether or not this format's record delimiter is also part of the next record

readRecord

public T readRecord(BufferedReader inReader)
             throws SeqIOException

Throws:

SeqIOException