palCon-class {cosmo} | R Documentation

## Class "palCon" ~~~

### Description

This class defines a global constraint when palindromic patterns are known to be found in the motif.

### Objects from the Class

Objects can be created by calls of the form `new('palCon',`
`int1 = ...., # Object of class numeric`
`int2 = ...., # Object of class numeric`
`errBnd = ...., # Object of class numeric`
`)` or by: `makePalCon(`
`int1 = ...., # Object of class numeric`
`int2 = ...., # Object of class numeric`
`errBnd = ...., # Object of class numeric`
`)`

### Slots

`int1`:
  Object of class `"numeric"` first palindromic interval
`int2`:
  Object of class `"numeric"` second palindromic interval
`errBnd`:
  Object of class `"numeric"` error tolerated in mismatches

### Methods

No methods defined with class "palCon" in the signature.

### Note

~~further notes~~

### Author(s)

Fabian Gallusser, fgallusser@berkeley.edu

### References

### See Also

`shapeCon`, `subMotifCon`, `posFreqCon`, `boundCon`, `shapeDiffCon` `makeConSet`

### Examples

    set=makeConSet(3,c("B","V","B"),c(4,NA,4))
    palcon=makePalCon(1,3,0.5)
    set=addCon(set,list(palcon),NA)

[Package cosmo version 1.2.0 Index]