package statalign.model.ext.plugins;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import statalign.base.Tree;
import statalign.model.ext.ModelExtension;
import statalign.postprocess.PostprocessManager;
import statalign.postprocess.utils.RNAalifold;
public class PPFold extends ModelExtension {
private final String pluginID = "ppfold";
@Override
public String getPluginID() {
return pluginID;
}
@Override
public double logLikeFactor(Tree tree) {
// TODO Auto-generated method stub
return 0;
}
@Override
public void setActive(boolean active) {
super.setActive(active);
PostprocessManager.pluginParameters.setParameter("ppfold", "");
PostprocessManager.rnaMode = true;
System.out.println("PPFold plugin is now "+(active?"enabled":"disabled"));
}
@Override
public void setParam(String paramName, boolean paramValue) {
if (paramName.equals("experimental")) {
PostprocessManager.pluginParameters.setParameter("experimental", "");
}
}
@Override
public String getUsageInfo() {
StringBuilder usage = new StringBuilder();
usage.append("____________________\n\n");
usage.append(" PPFold plugin \n\n");
usage.append("^^^^^^^^^^^^^^^^^^^^\n\n");
usage.append("java -jar statalign.jar -plugin:ppfold[[OPTION1,OPTION2,...]]\n");
usage.append("OPTIONS: \n");
usage.append("\texperimental\t\t(Activates experimental features. See online tutorial for details.)\n");
usage.append("\nNote that the above syntax is designed to work in bash shells. " +
"Other shells such as csh may require square brackets to be preceded by a backslash.");
return usage.toString();
}
}