[Biococoa-dev] mass calculator bug

Alexander Griekspoor mek at mekentosj.com
Sun Aug 29 16:21:14 EDT 2004

>> So we start with the first interface line in the BCSequence header:
>> @interface BCSequence : NSObject {
>> should become:
>> @interface BCSequence : NSObject <NSCopying, NSCoding> {
> Hmm, I have never used such a construction before and have done 
> similar things (passing an object to another class).

It's not passing an object to another class:

With the line:
@interface BCSequence: NSObject <protocol1, protocol2> {
you simply declare that the BCSequence object adheres to protocol1 and 
Protocols are lists of methods that you promise this class has 
implemented. An example protocol from EnzymeX:

@protocol EXMapSequenceViewDelegate <NSObject>

- (NSString *) sequenceForMapView:(EXMapSequenceView *)mview;

- (void) setVisibleSequence: (NSRange) aRange;
- (NSRange) visibleSequence;
- (NSRange) selectedSequence;

- (void)generateMap;


This has a number of big advantages, first the compiler will help to 
check if classes conform to required protocols. Second, it allows you 
to check if an object at runtime supports certain methods using 
NSObject's conformsToProtocol: classmethod. Finally, you can promise 
the compiler that a class you are calling supports the protocol:   [< 
EXMapSequenceViewDelegate>theObject doThis]; , even if you don't know 
exactly what type of class theObject will be at runtime (as long as it 
adheres to the protocol it's fine).

A number of protocols are predefined in the cocoa frameworks and for 
instance <NSDraggingInfo> <NSCopying> <NSCoding>. In order to make your 
class NSCoding compatible, you have to let this know by adding that 
particular part to your @interface line, plus you have to implement the 
methods declared in the protocol (initWithCoder and encodeWithCoder in 
this case). These are described in the docs.

>> In BCMassCalculator, InitWithSequence, change:
>>> 	sequence = [seq copy];		<--------- error
>> to sequence = [seq copyWithZone: [self zone]];  // I believe this is 
>> more efficient memory wise
> Even if I use an accessor:
> [self setSequence: seq];
> and then:
> - (void)setSequence:(BCSequence *)s
> {
> 	[s retain];
> 	[sequence release];
> 	sequence = s;
> }
> I get the same copywithZone error.  But maybe this is different 
> because BCSequence passes a copy of itself?

That's probably because you still did not implement the copyWithZone 
method and thus did not implement the NSCopying protocol.
Did you implement the methods that I wrote in my email, and change the 
interface line?

                      ** Alexander Griekspoor **
                The Netherlands Cancer Institute
                Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                  AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

    The requirements said: Windows 2000 or better.
    So I got a Macintosh.


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