Class SeqContentPattern

java.lang.Object
org.biojava.bio.search.SeqContentPattern
All Implemented Interfaces:
BioPattern

public class SeqContentPattern extends Object implements BioPattern
A pattern that can be used to find regions with given sequence content.

Regular expressions can be used to find sequence patterns. However, some things can't be easily expressed as a regular expression. For example, a region of length 10 that contains at least 8 Gs and up to two Ts and no other symbols. A SeqContentPattern can be built that does represent this.

 SeqContentPattern scp = new SeqContentPattern(DNATools.getDNA());
 scp.setLength(10);
 scp.setMinCounts(DNATools.g(), 8);
 scp.setMaxCounts(DNATools.t(), 2);
 scp.setMaxCounts(DNATools.c(), 0);
 scp.setMaxCounts(DNATools.a(), 0);
 

The minimum counts default to 0, and the maximum counts default to the length. If you have not manually set the maximum count for a symbol, it will continue to adjust while you change the length. Once you have set it, it will not vary, even if you do set the length. To re-set a maximum count to track the length, set it to -1.

All regions of the defined length for which all constraints are satisfied will potentialy be found. At the moment we have not defined what will happen for multiple regions that overlap all of which satisfy the constraints.

Since:
1.4
Author:
Matthew Pocock
  • Constructor Details

    • SeqContentPattern

      Create a new SeqContentPattern over an alphabet.
      Parameters:
      alpha - the FiniteAlphabet for this pattern
  • Method Details

    • getLength

      public int getLength()
      Get the current length.
      Returns:
      the length
    • setLength

      public void setLength(int length)
      Set the pattern length.
      Parameters:
      length - the new length
    • setMinCounts

      public void setMinCounts(AtomicSymbol as, int count) throws IllegalSymbolException
      Set the minimum counts required for a symbol.
      Parameters:
      as - the AtomicSymbol to check
      count - the minimum number of counts it must have
      Throws:
      IllegalSymbolException - if as is not known in this alphabet
    • getMinCounts

      Get the minimum counts required for a symbol.
      Parameters:
      as - the AtomicSymbol to check
      Returns:
      the minimum number of counts it must have
      Throws:
      IllegalSymbolException - if as is not known in this alphabet
    • setMaxCounts

      public void setMaxCounts(AtomicSymbol as, int count) throws IllegalSymbolException
      Set the maximum counts required for a symbol. Use -1 to reset it to track the length.
      Parameters:
      as - the AtomicSymbol to check
      count - the maximum number of counts it must have
      Throws:
      IllegalSymbolException - if as is not known in this alphabet
    • getMaxCounts

      Get the maximum counts required for a symbol.
      Parameters:
      as - the AtomicSymbol to check
      Returns:
      the maximum number of counts it must have
      Throws:
      IllegalSymbolException - if as is not known in this alphabet
    • matcher

      Description copied from interface: BioPattern
      Get a matcher that will use these parameters to search a SymbolList.

      The resulting BioMatcher is independant of this BioPattern. In particular, calling any mutator methods on this pattern will not affect the matcher.

      Specified by:
      matcher in interface BioPattern
      Parameters:
      symList - the SymbolList to match against
      Returns:
      a BioMatcher that will perform the search
      Throws:
      IllegalAlphabetException - if symList is not over the right alphabet