Property Detail

• static final java.lang.String HALOPLEX_DEFAULT_ENZYMES

  Enzymes possibly used by HaloPlex, extracted from the UCSC cutters database

• RestrictionEnzyme complement

• java.lang.String forwardPrefix

• java.util.regex.Pattern forwardPrefixPattern

• java.lang.String forwardSuffix

• java.util.regex.Pattern forwardSuffixPattern

• java.lang.String motif

• int motifSize

• java.lang.String name

• java.lang.String reversePrefix

• java.util.regex.Pattern reversePrefixPattern

• java.lang.String reverseSuffix

• java.util.regex.Pattern reverseSuffixPattern

Constructor Detail

• RestrictionEnzyme(java.lang.String name, java.lang.String motif, int forwardCutPoint, int overHang, boolean withComplement)

  Create a restriction enzyme object with given name, motif cut point and overhang.

Method Detail

• boolean cutsSequenceBefore(java.lang.String sequence, int position)

  Returns true if this restriction enzyme would cut the given sequence in between the given position and the previous position.

  Parameters:

  sequence

  position - zero-based position. ie: 0 means the cut would be prior to the first base in the sequence

  Returns:

  true iff the enzyme would cut the specified position

• static java.util.List load(java.lang.String fileName)

• static java.util.List load(java.io.InputStream inStream)

  Convenience method to load enzymes from UCSC's cutter table format

  Parameters:

  inStream - Input stream to load from

  Returns:

  list of enzymes loaded

• java.lang.String toRegex(java.lang.String motif)

  Convert N's to wildcards and select IUPAC codes to appropriate character sets

• java.lang.String toString()