[cedance]

I had a speed increase of about 100x converting some Perl code to Java (mostly because of really fast string manipulation), so it had some use there. But usually the speed increase is less, and converting doesn't really make sense if the code already finishes in a reasonable time.

Unfortunately, the time taken to write Java code is much longer, and it's easier to introduce unexpected bugs into Java code than into R or Perl (I use warnings/strict mode). So I usually write my code in Perl or R, only switching to Java when I need the speed.

This is really interesting! Could you tell me what was the string manipulation problem you felt was slower in perl? I code a lot in perl and would like to test it.

@rskr, if you are *really* wanting to have a discussion on the advantages of *java* as a software, then

http://stackoverflow.com/

is a nice place to start.

[Jim Robinson]

Don't know why I'm wasting time over an obvious troll, but... I'm the developer of IGV, Java was used because it gave me the ability to immediately deploy to Linux, Mac, and Windows, the major platforms. I would love to do it as a native Mac application, I do iOS programming as well and know what I'm talking about. I've also built plenty of native window apps, and a fair number of X-window applications. The native route generally always results in a superior look for that platform, and can be faster as well, but running on another platform is a rewrite. (I'm speaking of GUI apps here). Java / Swing apps are slightly ugly, but the ability for a single person like myself to deploy to the 3 major platforms with no coding changes is invaluable. If I had a team of people to support multiple platforms it might be different, but probably not, there would be more important things to do.

[damiankao]

Don't know why I'm wasting time over an obvious troll, but... I'm the developer of IGV, Java was used because it gave me the ability to immediately deploy to Linux, Mac, and Windows, the major platforms. I would love to do it as a native Mac application, I do iOS programming as well and know what I'm talking about. I've also built plenty of native window apps, and a fair number of X-window applications. The native route generally always results in a superior look for that platform, and can be faster as well, but running on another platform is a rewrite. (I'm speaking of GUI apps here). Java / Swing apps are slightly ugly, but the ability for a single person like myself to deploy to the 3 major platforms with no coding changes is invaluable. If I had a team of people to support multiple platforms it might be different, but probably not, there would be more important things to do.

I agree. I am sure we all understand the drawbacks of using java. If we had a team of developers, then we can worry about what language to use and optimize the **** out of our software. We would also be software developers at that point. I don't think he understands that the point of all of this is to do science. We develop something enough so we can investigate the biology. We can't spend all our time making tools.

By the way, IGV is awesome. I actually copied IGV's interface and wrote a standalone javascript version to run within a web browser for my lab.

[rskr]

Don't know why I'm wasting time over an obvious troll, but... I'm the developer of IGV, Java was used because it gave me the ability to immediately deploy to Linux, Mac, and Windows, the major platforms. I would love to do it as a native Mac application, I do iOS programming as well and know what I'm talking about. I've also built plenty of native window apps, and a fair number of X-window applications. The native route generally always results in a superior look for that platform, and can be faster as well, but running on another platform is a rewrite. (I'm speaking of GUI apps here). Java / Swing apps are slightly ugly, but the ability for a single person like myself to deploy to the 3 major platforms with no coding changes is invaluable. If I had a team of people to support multiple platforms it might be different, but probably not, there would be more important things to do.

Sure, you may relish your choice of Java now, but if you ever encounter a problem you'll be wishing it had some compile directives.

[Jim Robinson]

Ahh yes, boy I sure do miss those!

[rskr]

Ahh yes, boy I sure do miss those!

Ah I see you just use run time checks, now there's some maintainable code.

[rskr]

Hmm IGV seems to have problems in OSX

http://code.google.com/p/igv/issues/detail?id=25&can=1&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Summary%20Reporter

[ECO]

rskr...please ease up on the trolling.

Jim has created a great (free!) resource that is appreciated by the community, nothing's perfect.

[Jim Robinson]

Its not perfect, but that's an old bug long fixed. OsX is actually my platform.

Hmm IGV seems to have problems in OSX

http://code.google.com/p/igv/issues/...ary%20Reporter

[rskr]

Its not perfect, but that's an old bug long fixed. OsX is actually my platform.

Yes, yes, but you had to fix it to make it port. There is another one here.

http://code.google.com/p/igv/issues/detail?id=1&can=1&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Summary%20Reporter

I just think if the Java community quit lying to themselves about cross-platform, then maybe they could actually port their code and make it run cross-platform.

[Jim Robinson]

That doesn't make any sense, of course there are platform tweaks but its orders of magnitude less work than rewrites in different languages with different libaries on the different platforms. If we all had Mac's I would do everything in objective-C / IOS. I don't care for the language syntax but the finished product is slick. You can't write a "cross-platform" app in IOS however, you write it for the Mac. Its been 20 years since I did an X-windows app but the same applies there.

[nilshomer]

I am closing this thread as this discussion is not progressing. The user rskr has been warned several times about insulting behavior. Keep it clean!