org.forester.util

Class SequenceAccessionTools

java.lang.Object

org.forester.util.SequenceAccessionTools

public final class SequenceAccessionTools
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static Pattern	ENSEMBL_PATTERN
static Pattern	GENBANK_NUC_PATTERN_1
static Pattern	GENBANK_NUC_PATTERN_2
static Pattern	GENBANK_PROT_PATTERN
static Pattern	GI_PATTERN
static String	UNIPROT_KB_BASE_PATTERN_STR
static Pattern	UNIPROT_KB_PATTERN_0
static Pattern	UNIPROT_KB_PATTERN_1
static Pattern	UNIPROT_KB_PATTERN_2

Method Summary

Modifier and Type	Method and Description
static boolean	isProteinDbQuery(String query)
static Accession	obtainAccessorFromDataFields(PhylogenyNode n)
static Accession	obtainFromSeqAccession(PhylogenyNode n)
static String	obtainGenbankAccessorFromDataFields(PhylogenyNode n)
static String	obtainGiNumberFromDataFields(PhylogenyNode n)
static String	obtainRefSeqAccessorFromDataFields(PhylogenyNode n)
static String	obtainUniProtAccessorFromDataFields(PhylogenyNode n)
static Accession	parseAccessorFromString(String s)
static String	parseEnsemlAccessorFromString(String s)
static String	parseGenbankAccessorFromString(String s)
static String	parseGenbankProteinAccessorFromString(String s)
static String	parseGInumberFromString(String s)
static String	parseRefSeqAccessorFromString(String s)
static String	parseUniProtAccessorFromString(String s)

Methods inherited from class java.lang.Object

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

Field Detail

GENBANK_NUC_PATTERN_1

public static final Pattern GENBANK_NUC_PATTERN_1

GENBANK_NUC_PATTERN_2

public static final Pattern GENBANK_NUC_PATTERN_2

GENBANK_PROT_PATTERN

public static final Pattern GENBANK_PROT_PATTERN

GI_PATTERN

public static final Pattern GI_PATTERN

UNIPROT_KB_BASE_PATTERN_STR

public static final String UNIPROT_KB_BASE_PATTERN_STR

See Also:

Constant Field Values

UNIPROT_KB_PATTERN_0

public static final Pattern UNIPROT_KB_PATTERN_0

UNIPROT_KB_PATTERN_1

public static final Pattern UNIPROT_KB_PATTERN_1

UNIPROT_KB_PATTERN_2

public static final Pattern UNIPROT_KB_PATTERN_2

ENSEMBL_PATTERN

public static final Pattern ENSEMBL_PATTERN

Method Detail

isProteinDbQuery

public static final boolean isProteinDbQuery(String query)

obtainAccessorFromDataFields

public static final Accession obtainAccessorFromDataFields(PhylogenyNode n)

obtainFromSeqAccession

public static final Accession obtainFromSeqAccession(PhylogenyNode n)

obtainGenbankAccessorFromDataFields

public static final String obtainGenbankAccessorFromDataFields(PhylogenyNode n)

obtainGiNumberFromDataFields

public static final String obtainGiNumberFromDataFields(PhylogenyNode n)

obtainRefSeqAccessorFromDataFields

public static final String obtainRefSeqAccessorFromDataFields(PhylogenyNode n)

obtainUniProtAccessorFromDataFields

public static final String obtainUniProtAccessorFromDataFields(PhylogenyNode n)

parseAccessorFromString

public static final Accession parseAccessorFromString(String s)

parseGenbankAccessorFromString

public static final String parseGenbankAccessorFromString(String s)

parseGenbankProteinAccessorFromString

public static final String parseGenbankProteinAccessorFromString(String s)

parseGInumberFromString

public static final String parseGInumberFromString(String s)

parseEnsemlAccessorFromString

public static final String parseEnsemlAccessorFromString(String s)

parseRefSeqAccessorFromString

public static final String parseRefSeqAccessorFromString(String s)

parseUniProtAccessorFromString

public static final String parseUniProtAccessorFromString(String s)