Build instructions:

javac -cp args4j-2.0.12.jar:src/main/java -d bin src/main/java/de/tum/in/lrr/hmm/cli/*.java

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Testing:

javac -cp args4j-2.0.12.jar:test/junit_3.8.2.v20080602-1318.jar:src/main/java:src/test/java -d test src/test/java/de/tum/in/lrr/hmm/AllTests.java 
java -cp args4j-2.0.12.jar:test/junit_3.8.2.v20080602-1318.jar:test junit.textui.TestRunner de.tum.in.lrr.hmm.AllTests

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Runnning: 

java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceTrainer

Print usage.

java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceTrainer <options> <HMM output file> <sequence file(s)...>

Creates a new model from the sequence files and writes it to the HMM output file.

Sequence files can be either in EMBL or FASTA format.

Example sequences files are example/hpv_e1.fasta, example/hpv_e1_test_full.embl, or example/hpv_e1_training.embl. 


java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceFinder

Print usage.

java -cp args4j-2.0.12.jar:bin de.tum.in.lrr.hmm.cli.SequenceFinder <options> <HMM file> <sequence file>

Reads a model from the HMM file and looks for matching sequences in the sequence file.

Useful Java VM options:
	-server	start server VM (longer startup time, more optimizations)
	-ea	enable assertions
	-Xmx1024m	increase maximum Java heap size to 1GB (adjust as neccessary)
	-Xss2m	increase Java stack size to 2MB