Package org.forester.util

Class SequenceAccessionTools

java.lang.Object
org.forester.util.SequenceAccessionTools
public final class SequenceAccessionTools extends Object

  • Field Details

    • 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:

    • 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 Details

    • 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)