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simulfold's Issues

Seems to fail on example input.

I downloaded the git repository and compiled it with javac -O *.java
(I'm using Oracle Java 1.8.0_144)

I then ran the following command:
java SimulFold tRNA_low.in tRNA_low.dnd -S
(where the files are directly from the manuscript data in simulfold.tar.bz2 from your website)

When I run the command, the output is as shown below. (I get the same output for any other input I've tried).

temperature: 1.0
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
... (continues like this until I kill it)

Am I running the command incorrectly? Is there an argument I should be passing to set the temperature? Is my java version (Java 8) not supported? I got the same results on Windows (Win10) and Linux (Ubuntu 16.04).

Compilation fails

I cannot compile the release or a clone of the current version in github.

javac -O *.java Note: MCMC.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details.

Source Code is Missing

Source code for the following classes is missing:

  • Alignment.class
  • AlignmentColumn.class
  • AlignmentProposal.class
  • SingleStranded.class
  • Tree.class
  • TreeNode.class

Are these classes supposed to be provided by the standard Java installation? Or are they from a third-party who has the code? Was this an oversight or is this a closed-source project?

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