Class SequenceAccessionTools


  • public final class SequenceAccessionTools
    extends java.lang.Object
    • 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)
      • 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)