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Eclipse Rich Client Application Performance

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I have some code which I run as a Java Application. Performance was great. However, when I ported this code to run as a plugin in Eclipse, it was about 5 times slower. This is also consistently slow with codes running in an application server. Is it because of running codes using classloaders? How to I achieve the same level of performance as a Java Application?

My application code has a lot of loops and accesses native com objects.

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