[Jalview-discuss] Using JalView source code

Andy Lai andycw.lai at utoronto.ca
Wed Jun 22 23:43:22 BST 2011

Hi all,

I would like to write an interface that shows some tabularized data for a
set of genes. The nature of this table is such that it pops up a window that
shows a MSA using JalView (along with its cool features) upon selection of a
gene. What I need is to somehow pipe info from my interface directly to
JalView without having to open a separate JalView process each time. Is
there some easy way I can do this or do I have to actually call the JalView
source code?

Also, I appear to be having trouble compiling the JalView source code.  It
appears there are some non-standard characters being used in some of the
classes. I've tried a few common encoding schemes like UTF-8, UTF-16, and
ASCII, but these characters are still unreadable (I am using NetBeans IDE
but I doubt that makes much of a difference). Based on what I gathered from
the code-level descriptions, these are delimiter characters. Do you happen
to know what encoding scheme I should be using?

Finally, it appears the JMol jar file is missing the
org.jmol.applet.AppleConsole class. I nabbed that class from the JMol
website, so it's okay, but I am wondering if I am the only one having that


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