Problem starting and running Gmaj (MAF file viewer and manipulator)

I am trying to run Gmaj.

The usage guide is as follows:

[path1]java -jar [path2]gmaj.jar

My input command is as follows (I am in the same directory as the gmaj.jar file):

java -jar gmaj.jar

The output is as follows:

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)

The software is written in Java, and depends upon the Java Runtime Environment. As I have very little familiarity with Java, I am not sure about the next step forward. Any help would be appreciated

NB: To learn more about Gmaj and the information it takes as input, see:

Blanchette, M., et al. (2004). "Aligning multiple genomic sequences with the threaded blockset aligner." Genome Research 14(4): 708-715.

gmaj jre java maf ucsc

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updated 7.9 years ago by Ram

• written 10.5 years ago by Thomas

it looks like a programming error. You should ask the authors of the paper.

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written 10.5 years ago by Pierre Lindenbaum

I have exactly the same problem:

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)

• 0 views • link

written 9.1 years ago by biomagician

Hi,

Did this ever get resolved? I have the same problem and am trying to figure out how else to view the .MAF files I have from Mugsy.

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written 6.4 years ago by cssulliv •

Hi cssuliv,

I am afraid I never managed to resolve this issue. I emailed the first author of the paper but never received a reply.

Best wishes, Thomas

• 0 views • link

written 6.2 years ago by Thomas

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