Peptide/Peak Conditions

Overview
Example I
Example II

Overview

This object is a wrapper over ConditionInterpreter and Condition on a PeptideType. It interpretes string expression over peptide type conditions. Each peptide type condition is defined as specific internal names (a, b, c, x, y, z, i or p). Here is the grammar below:

  EXPR := COND | UOP EXPR | COND BOP EXPR
  COND := MPT_COND{1,2} | SPT_COND
  UOP := "!"
  BOP := "&" | "|"
  MPT_COND := "a" | "b" | "c" | "x" | "y" | "z"
  SPT_COND := "p" | "i"

with the following term definitions:

BOP: Binary Operator
UOP: Unary Operator
MPT_COND: Multiple Peptide Type Condition
SPT_COND: Single Peptide Type Condition

Example I

Condition<PeptideType> condition =
	new PeptideTypeCondition.Builder<PeptideType>("b & !y").build();
  
PeptideType pepType =
	PeptideType.getInstance(TerminusTypeImpl.TypeN.FRAG_Y,
        TerminusTypeImpl.TypeC.FRAG_B);
  
Assert.assertTrue(condition.isFalse(pepType));

Warning

Any object can be tested in the condition whenever an instance of PeptideType is reachable from that object through a Transformer given a stub method of the condition builder:

Example II

import import org.apache.commons.collections15.Transformer;

// the peptide to test type on
Peptide peptide = new Peptide.Builder("ARHBRH")
	.nterm(TerminusTypeImpl.TypeN.FRAG_X).cterm(TerminusTypeImpl.TypeC.FRAG_B).build()
    
// lead to peptide's type
Transformer<Peptide, PeptideType> toPepType =
	new Transformer<Peptide, PeptideType>() {

		public PeptideType transform(Peptide peptide) {
			return peptide.getPeptideType();
  		}
	};
  
// create the condition
Condition<Peptide> cond = 
  	new PeptideTypeCondition.Builder<Peptide>("b|y")
  	        .accessor(toPepType).build();
  
// testing conditions on peptides
Assert.assertTrue(cond.isTrue(peptide));

[See also ConditionInterpreter]