>> Linking with the CDK libraries almost doubles the size of the
>> JmolApplet:
>>
>>   JmolApplet.jar with SimpleModelAdapter   347,148 bytes
>>   JmolApplet.jar with CdkJmolModelAdapter  656,664 bytes
>
> The functionality is more than doubled... CDK has more IO formats
> supported.

True.
And that is important for some people.

>> So, I am still trying to come up with a scheme to split the applet
>> into two .jar files, where the second one is downloaded only if
>> needed. I still do not have this working properly.
>
> We could also have a solid build system where people can define which IO
>  formats the applet should support...

I think that most people who want to use the applet do *not* want to build
it.

And I certainly don't want to respond to all their email questions :-)


> That's an option... it might be better to see how the CDK classes can be
>  improved... they have not been optimized for memory or speeds or
> whatever so  far...

In my opinion this certainly needs to be done.

>
>> speed
>> -----
>> Larger data structures usually mean more CPU overhead. Using the
>> application, reading in hemoglobin is 8-10 times slower using CDK.
>
> This includes partly reading is I understood correctly... Or are these
> numbers  applicable to just the rendering speed when rotating...
This only applies to reading the file into memory.

Once Jmol has the data structures in memory, the rotation/execution speed
is not affected.

>> CDK compiles on 1.3... Patches to have classes compile on 1.2 are
> accepted... For classes for which that does not work with a simple patch
> (e.g.  Vector.addElement() instead of Vector.add()...), those are
> excluded from  compiling... This is what happens for 1.3, and can be
> used for 1.1 JVM's  too...
>
> (If only I had a JVM 1.1 installed on my machine...)

This goes back to an improved build system.

I do not like the patch mechanism because my productivity goes down the
toilet. Emacs (and presumably any IDE) doesn't work because the
filenames/line numbers are incorrect.

>> A harder example is the use of exceptions. As I recall, the last time
>> I tried to get CDK to run in the JmolApplet I was getting exceptions
>> on the NS JVM. Eliminating this type of problem will be slow, painful,
>> and frustrating.
>
> Note that has been always the case... also when Jmol was still Jmol, and
> had  nothing to do with CDK yet! Browser JVM's are a problem an sich...

I have put in a *lot* of energy to ensure that Jmol can run on a wider
variety of JVMs. I would hate to think that all that work was wasted.


>> I tried to make some of these changes about a month ago, but I ran
>> into difficulties, got frustrated, and postponed the work.
>
> Let's coordinate this... Tell me which changes you need, we'll discuss
> them on  the CDK mailling list, and get things done...

OK.

Let's talk about the patch-build mechanism on cdk-devel.


Miguel





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