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Archive for November, 2009

Java Classpaths are Evil

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While working with Phylogenetic Analysis Library (PAL) for an alignment problem, I ran into the problem of having to specify classpaths to a jar file… it should have be straight forward enough…

Java classpaths are a pain.

Here are a few observations I’ve made about how to specify them in the command line.

  • an Item can either be a directory that contains .class and .java files OR
  • an Item can be a .jar file.
  • to specify more than one Item.jar in Unix, use:
javac -classpath .:Item1.jar:Item2.jar
  • note that you cannot put a space between the colons
  • note that you must include an extra Item ‘.’ to specify the current working directory
  • note that in Windows, you must use ‘;’ instead of ‘:’
  • note that after compiling with javac, the same -classpath and its arguments must then be applied with java

Nuisance? Yes! Necessary Evil? No!

In the compiled Java class, there certainly could have been some metadata implemented that is a copy of the last known classpath string… why is there a disparity between the symbols used in Unix and Windows? … Why aren’t spaces allowed? Why does one have to specify the current working directory?


A side effect of not being able to put spaces in between the colons of several paths is that one can’t just put a backslash in to negate a newline– you would need to have the next path start at the very beginning of the next line which is just ugly.

Eddie Ma

November 23rd, 2009 at 12:28 pm

Posted in Pure Programming

Tagged with ,

Back from Conference!

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Brief: The BIBM09 conference was the very first conference I have ever attended. I learned a lot from the various speakers and poster sessions–

I thought it was really interesting how the trend is to now study and manipulate large interaction pathways in silico– a theme of which is the utilization of many different data sources integrating chemical, drug and free text as well as the connection of physical protein interaction pathways and gene expression pathways. There was even a project which dealt with the alignment of pathway graphs (topology).

Dealing with pathways especially by hand and in the form of a picture is probably the bane of many biologists’ existence– I think that the solutions we’ll see in the next few years will turn this task into simple data-in-data-out software components, much like the kind we have to deal with sequence alignments.

And now, back to the real world!

Addendum: My talk went very well 🙂

And here are my slides with a preview below.

Eddie Ma

November 6th, 2009 at 10:36 am