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The main deficiency Java applications seem to have is that they do not look and feel like native applications. The reasons behind this are obvious: 100% Pure Java must support the lowest common denominator, but there are many platform-specific features and quirks that the users of specific platforms expect, and your application will seem to be lacking without them.
In today's competitive application arena, these features may be critically necessary to your application's marketplace success. A competitor's native application can use these features to beat your Java application every time, producing a product that's faster, looks and feels right, and works with the operating system and other native applications as expected.
The solution, of course, is to use Java Native Interface (JNI) extensions. But what will this mean for Java's cross-platform capabilities? If your application is only 60% Pure Java, it won't run on other platforms -- so why use Java at all? Admittedly, Java has other benefits: the language is easy to learn and use, the code is simple to maintain and debug, and by using it you leave open the possibility of migrating to other platforms in the future -- if you design your application with such migration in mind.
So, is JNI a compromise? It doesn't have to be. You can have a 100% Pure Java application in which JNI features are added benefits that appear only on specific platforms. There will be no loss for those who use the platforms not supported by your JNI features, and you will compete with native applications on equal terms where needed. The trick is to design an application that can take advantage of JNI features, but is still fully operational without them.
(Although Microsoft's virtual machine does not support JNI, it has many Windows-specific packages of features that give the same result: powerful native support. Unlike JNI extensions, however, you cannot replace these features with an alternate JNI library for an additional platform. If you use these Windows-specific features, you're committed to Windows and Microsoft's VM.)
Start out with a 100% Pure Java application design. Think of the application as being contained entirely within the virtual machine, which is otherwise platform neutral. All your features must be based on whatever the Java platform has to offer. When you're finished, congratulate yourself! Your design will work on any Java Virtual Machine (JVM) running on any platform.
Next, look at your Java application from a user's point of view. It's probably not the only application running in his or her environment. What features is your application lacking that its native neighbors have? Run a few native applications together with yours, and ask yourself some questions about the differences: