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I have installed GMAJ using:

wget http://globin.bx.psu.edu/dist/gmaj/gmaj.zip  -O output/software/gmaj.zip
unzip -u output/software/gmaj.zip -d output/software/gmaj/
rm output/software/gmaj.zip

I ran lastz on two chromosomes from two different assemblies of C. elegans:

lastz c_elegans.PRJNA13758.WS263.genomicI.fa I.fa --format=maf > MAF.maf

and got a MAF file.

Then, I tried to visualise the file using:

java -jar output/software/gmaj/gmaj.jar MAF.maf

but I got the following error:

Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
    at edu.psu.bx.gmaj.MajGui.setDefaults(MajGui.java:272)
    at edu.psu.bx.gmaj.Maj.<init>(Maj.java:53)
    at edu.psu.bx.gmaj.MajMain.main(MajMain.java:86)

Can someone help me resolve this error or suggest an alternative way to visualise my alignment?

I work on Mac OS X.

Cheers.

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It's a programming error that should look like this:

StringBuffer sb = (...)
(...)
String s = (String)sb;

while it should be

StringBuffer sb = (...)
(...)
String s = sb.toString();

( see also https://www.biostars.org/p/177992/ ) . You cannot do anything about it but asking the authors of the software.

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  • $\begingroup$ Sent an email to Cathy Riemer asking for help. $\endgroup$ Jul 11 '18 at 11:15

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