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//
// BCToolMassCalculator.m
// BioCocoa
//
// Created by Koen van der Drift on Wed Aug 25 2004.
// Copyright (c) 2003-2009 The BioCocoa Project.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// 3. The name of the author may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
// IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
// NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
// THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#import "BCToolMassCalculator.h"
#import "BCToolSymbolCounter.h"
#import "BCSequence.h"
#import "BCSymbol.h"
#import "BCFoundationDefines.h"
@implementation BCToolMassCalculator
-(id) initWithSequence:(BCSequence *)list
{
if ( (self = [super initWithSequence:list]) )
{
[self setMassType: BCMonoisotopic];
}
return self;
}
+ (BCToolMassCalculator *) massCalculatorWithSequence: (BCSequence *)list
{
BCToolMassCalculator *massCalculator = [[BCToolMassCalculator alloc] initWithSequence: list];
return [massCalculator autorelease];
}
- (void)setMassType:(BCMassType)type
{
massType = type;
}
-(NSArray *)calculateMass{
return [self calculateMassForRange: NSMakeRange(0, [[self sequence] length])];
}
-(NSArray *)calculateMassForRange: (NSRange)aRange
{
float totalMin, totalMax;
BCSymbol *aSymbol;
totalMin = totalMax = 0.0;
#if 1
unsigned symbolCount;
BCToolSymbolCounter *symbolCounter = [BCToolSymbolCounter symbolCounterWithSequence: [self sequence]];
NSCountedSet *sequenceSet = [symbolCounter countSymbolsForRange: aRange];
NSEnumerator *objectEnumerator = [sequenceSet objectEnumerator];
while ( (aSymbol = [objectEnumerator nextObject]) )
{
symbolCount = [sequenceSet countForObject: aSymbol];
totalMin += ((float)symbolCount * [aSymbol minMassUsingType: massType]);
totalMax += ((float)symbolCount * [aSymbol maxMassUsingType: massType]);
}
#else
CFIndex i;
NSArray *array = [sequence symbolArray];
for ( i = 0; i < [array count]; i++ )
{
aSymbol = (BCSymbol *)CFArrayGetValueAtIndex( (CFArrayRef) array, i); // use NSData instead ?
totalMin += [aSymbol minMassUsingType: massType];
totalMax += [aSymbol maxMassUsingType: massType];
}
#endif
if ( totalMin )
{
totalMin += [self addWater];
totalMax += [self addWater];
}
return [NSArray arrayWithObjects:
[NSNumber numberWithFloat:totalMin], [NSNumber numberWithFloat: totalMax], nil];
}
-(float) addWater
{
// add water - cheers!
if ( massType == BCMonoisotopic )
return 2 * hydrogenMonoisotopicMass + oxygenMonoisotopicMass;
else if ( massType == BCAverage )
return 2 * hydrogenAverageMass + oxygenAverageMass;
else
return 0;
}
@end
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