Question: Problem starting and running Gmaj (MAF file viewer and manipulator)
0
gravatar for Thomas
4.3 years ago by
Thomas90
Cambridge, UK
Thomas90 wrote:

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.

ucsc jre gmaj java maf • 1.5k views
ADD COMMENTlink modified 20 months ago by RamRS27k • written 4.3 years ago by Thomas90
1

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.

ADD REPLYlink written 9 weeks ago by cssulliv20

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

ADD REPLYlink written 20 days ago by Thomas90

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

ADD REPLYlink written 4.3 years ago by Pierre Lindenbaum128k

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)
ADD REPLYlink written 2.9 years ago by cristian240
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