The Problem A common problem we have reported from users of SeqMonk is that when they try to launch the program on a Windows system they get an error message saying that java could not be found, even though they have installed this and they can show that it works fine in their browser. When…
- Home
- Posts tagged "java"
The true cost of object creation in java
I’ve been spending some time trying to optimise the data loading part of one of my java projects. The nature of the data we use means that we have to create hundreds of millions of objects, each of which internally stores only a single long value (it actually stores several fields packed into this value…
Getting the java heap size you asked for
In a recent post I discussed a method we’re using for automatically setting the java heap size appropriately at runtime. It now turns out that the issue of setting the heap size is complicated by the fact that the heap size you request on the command line isn’t necessarily what you get given. In some…
Dynamically setting the java heap size at runtime
One of the oddities about java programs is that they require you to set a maximum heap size when you start the program. What this means in effect is that you need to be able to predict the memory usage of your program before it starts, and whatever heap size you set needs to be…
Choosing the best format for raw sequence data
Introduction In the current Illumina pipeline raw sequence data is generated in qseq files, but can optionally be converted to the more standard FastQ format for use with other analysis programs. The FastQ files produced are uncompressed text files and take up a considerable amount of space in our storage system. We’ve therefore been thinking…
Sound Level Monitoring in Java
For a project I’ve been working on I needed what I thought should be fairly easy to make – a simple widget to monitor an input sound level. I’d never worked with the full javax.sound API before, but assumed that there would be ample documentation to do what I needed. Having started on the project…
Exporting SVG from Java
Several programs I’ve written in Java have had an image export componet to them. Up until now the export has always only been as a bitmap image. This is very easy to do using a BufferedImage and an ImageWriter. Given a Component (all AWT or Swing widgets) and a file you can create a PNG…
Swing Speedup!
I’d never really been one to subscribe to the popular perception that swing is so horrifically slow that it isn’t suitable for use in any serious application. Most of the problems I’ve seen with swing based programs have resulted from people not knowing how to make processing tasks run in a separate thread and therefore…