On 14 Apr 2005, at 11:58, [EMAIL PROTECTED] wrote:
Hi!
I have added features to a sequence file using StrandedFeature.Template as a
template and RangeLocation class to define the locations. The sequence is saved
in Genbank format after the addition of all features. I want to output the
features later to a text file and this is how they look (type and location shown):
ER9_rc [15276,15296]
I would like to get rid of the [] brackets.
I modified the toString method of the RangeLocation class and removed these
brackets but after this I get an error message as the program tries to write the
features added to the genbank file using GenbankFormat class method
writeSequence. Does anyone have an explanation to this? Or a simple solution how
I can simplify my text file output to leave out the brackets?
Hi,
In general, it's not a good idea to rely on "toString" methods returning any particular format -- they're really for debugging purposes, rather than day to day uses. The best solution here is to use code like:
Feature f = ...;
System.out.println(
f.getType() + "\t" +
f.getLocation().getMin() + "," +
f.getLocation().getMax()
);This approach means you can have exactly the output format you want, and insulates you from any future changes to toString methods.
I am, however, worried about why GenbankFormat is giving you an error -- it shouldn't be relying on toString methods at all. Could you send me a copy of the error stack trace?
Thanks,
Thomas.
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