Package org.forester.util
Class SequenceAccessionTools
- java.lang.Object
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- org.forester.util.SequenceAccessionTools
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public final class SequenceAccessionTools extends java.lang.Object
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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
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Method Summary
All Methods Static Methods Concrete Methods 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)
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Field Detail
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GENBANK_NUC_PATTERN_1
public static final java.util.regex.Pattern GENBANK_NUC_PATTERN_1
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GENBANK_NUC_PATTERN_2
public static final java.util.regex.Pattern GENBANK_NUC_PATTERN_2
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GENBANK_PROT_PATTERN
public static final java.util.regex.Pattern GENBANK_PROT_PATTERN
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GI_PATTERN
public static final java.util.regex.Pattern GI_PATTERN
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UNIPROT_KB_BASE_PATTERN_STR
public static final java.lang.String UNIPROT_KB_BASE_PATTERN_STR
- See Also:
- Constant Field Values
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UNIPROT_KB_PATTERN_0
public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_0
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UNIPROT_KB_PATTERN_1
public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_1
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UNIPROT_KB_PATTERN_2
public static final java.util.regex.Pattern UNIPROT_KB_PATTERN_2
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ENSEMBL_PATTERN
public static final java.util.regex.Pattern ENSEMBL_PATTERN
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Method Detail
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isProteinDbQuery
public static final boolean isProteinDbQuery(java.lang.String query)
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obtainAccessorFromDataFields
public static final Accession obtainAccessorFromDataFields(PhylogenyNode n)
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obtainFromSeqAccession
public static final Accession obtainFromSeqAccession(PhylogenyNode n)
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obtainGenbankAccessorFromDataFields
public static final java.lang.String obtainGenbankAccessorFromDataFields(PhylogenyNode n)
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obtainGiNumberFromDataFields
public static final java.lang.String obtainGiNumberFromDataFields(PhylogenyNode n)
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obtainRefSeqAccessorFromDataFields
public static final java.lang.String obtainRefSeqAccessorFromDataFields(PhylogenyNode n)
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obtainUniProtAccessorFromDataFields
public static final java.lang.String obtainUniProtAccessorFromDataFields(PhylogenyNode n)
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parseAccessorFromString
public static final Accession parseAccessorFromString(java.lang.String s)
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parseGenbankAccessorFromString
public static final java.lang.String parseGenbankAccessorFromString(java.lang.String s)
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parseGenbankProteinAccessorFromString
public static final java.lang.String parseGenbankProteinAccessorFromString(java.lang.String s)
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parseGInumberFromString
public static final java.lang.String parseGInumberFromString(java.lang.String s)
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parseEnsemlAccessorFromString
public static final java.lang.String parseEnsemlAccessorFromString(java.lang.String s)
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parseRefSeqAccessorFromString
public static final java.lang.String parseRefSeqAccessorFromString(java.lang.String s)
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parseUniProtAccessorFromString
public static final java.lang.String parseUniProtAccessorFromString(java.lang.String s)
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