Package org.forester.util

Class SequenceAccessionTools

java.lang.Object

org.forester.util.SequenceAccessionTools

public final class SequenceAccessionTools
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static java.util.regex.Pattern	ENSEMBL_PATTERN
static java.util.regex.Pattern	GENBANK_NUC_PATTERN_1
static java.util.regex.Pattern	GENBANK_NUC_PATTERN_2
static java.util.regex.Pattern	GENBANK_PROT_PATTERN
static java.util.regex.Pattern	GI_PATTERN
static java.lang.String	UNIPROT_KB_BASE_PATTERN_STR
static java.util.regex.Pattern	UNIPROT_KB_PATTERN_0
static java.util.regex.Pattern	UNIPROT_KB_PATTERN_1
static java.util.regex.Pattern	UNIPROT_KB_PATTERN_2

Method Summary

Modifier and Type	Method	Description
static boolean	isProteinDbQuery(java.lang.String query)
static Accession	obtainAccessorFromDataFields(PhylogenyNode n)
static Accession	obtainFromSeqAccession(PhylogenyNode n)
static java.lang.String	obtainGenbankAccessorFromDataFields(PhylogenyNode n)
static java.lang.String	obtainGiNumberFromDataFields(PhylogenyNode n)
static java.lang.String	obtainRefSeqAccessorFromDataFields(PhylogenyNode n)
static java.lang.String	obtainUniProtAccessorFromDataFields(PhylogenyNode n)
static Accession	parseAccessorFromString(java.lang.String s)
static java.lang.String	parseEnsemlAccessorFromString(java.lang.String s)
static java.lang.String	parseGenbankAccessorFromString(java.lang.String s)
static java.lang.String	parseGenbankProteinAccessorFromString(java.lang.String s)
static java.lang.String	parseGInumberFromString(java.lang.String s)
static java.lang.String	parseRefSeqAccessorFromString(java.lang.String s)
static java.lang.String	parseUniProtAccessorFromString(java.lang.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 java.util.regex.Pattern GENBANK_NUC_PATTERN_1

GENBANK_NUC_PATTERN_2

public static final java.util.regex.Pattern GENBANK_NUC_PATTERN_2

GENBANK_PROT_PATTERN

public static final java.util.regex.Pattern GENBANK_PROT_PATTERN

GI_PATTERN

public static final java.util.regex.Pattern GI_PATTERN

UNIPROT_KB_BASE_PATTERN_STR

public static final java.lang.String UNIPROT_KB_BASE_PATTERN_STR

See Also:

Constant Field Values

UNIPROT_KB_PATTERN_0

public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_0

UNIPROT_KB_PATTERN_1

public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_1

UNIPROT_KB_PATTERN_2

public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_2

ENSEMBL_PATTERN

public static final java.util.regex.Pattern ENSEMBL_PATTERN

Method Detail

isProteinDbQuery

public static final boolean isProteinDbQuery(java.lang.String query)

obtainAccessorFromDataFields

public static final Accession obtainAccessorFromDataFields(PhylogenyNode n)

obtainFromSeqAccession

public static final Accession obtainFromSeqAccession(PhylogenyNode n)

obtainGenbankAccessorFromDataFields

public static final java.lang.String obtainGenbankAccessorFromDataFields(PhylogenyNode n)

obtainGiNumberFromDataFields

public static final java.lang.String obtainGiNumberFromDataFields(PhylogenyNode n)

obtainRefSeqAccessorFromDataFields

public static final java.lang.String obtainRefSeqAccessorFromDataFields(PhylogenyNode n)

obtainUniProtAccessorFromDataFields

public static final java.lang.String obtainUniProtAccessorFromDataFields(PhylogenyNode n)

parseAccessorFromString

public static final Accession parseAccessorFromString(java.lang.String s)

parseGenbankAccessorFromString

public static final java.lang.String parseGenbankAccessorFromString(java.lang.String s)

parseGenbankProteinAccessorFromString

public static final java.lang.String parseGenbankProteinAccessorFromString(java.lang.String s)

parseGInumberFromString

public static final java.lang.String parseGInumberFromString(java.lang.String s)

parseEnsemlAccessorFromString

public static final java.lang.String parseEnsemlAccessorFromString(java.lang.String s)

parseRefSeqAccessorFromString

public static final java.lang.String parseRefSeqAccessorFromString(java.lang.String s)

parseUniProtAccessorFromString

public static final java.lang.String parseUniProtAccessorFromString(java.lang.String s)