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.