public final class SequenceAccessionTools
extends java.lang.Object
Modifier and Type | Field and 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 |
Modifier and Type | Method and 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) |
public static final java.util.regex.Pattern GENBANK_NUC_PATTERN_1
public static final java.util.regex.Pattern GENBANK_NUC_PATTERN_2
public static final java.util.regex.Pattern GENBANK_PROT_PATTERN
public static final java.util.regex.Pattern GI_PATTERN
public static final java.lang.String UNIPROT_KB_BASE_PATTERN_STR
public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_0
public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_1
public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_2
public static final java.util.regex.Pattern ENSEMBL_PATTERN
public static final boolean isProteinDbQuery(java.lang.String query)
public static final Accession obtainAccessorFromDataFields(PhylogenyNode n)
public static final Accession obtainFromSeqAccession(PhylogenyNode n)
public static final java.lang.String obtainGenbankAccessorFromDataFields(PhylogenyNode n)
public static final java.lang.String obtainGiNumberFromDataFields(PhylogenyNode n)
public static final java.lang.String obtainRefSeqAccessorFromDataFields(PhylogenyNode n)
public static final java.lang.String obtainUniProtAccessorFromDataFields(PhylogenyNode n)
public static final Accession parseAccessorFromString(java.lang.String s)
public static final java.lang.String parseGenbankAccessorFromString(java.lang.String s)
public static final java.lang.String parseGenbankProteinAccessorFromString(java.lang.String s)
public static final java.lang.String parseGInumberFromString(java.lang.String s)
public static final java.lang.String parseEnsemlAccessorFromString(java.lang.String s)
public static final java.lang.String parseRefSeqAccessorFromString(java.lang.String s)
public static final java.lang.String parseUniProtAccessorFromString(java.lang.String s)