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Added the option to run c++ genenet.

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This commit is contained in:
leandrohw 2018-01-03 16:22:38 -07:00
parent 99633f1e9b
commit a603f01f89
2 changed files with 86 additions and 22 deletions
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14
gui/src/main/java/edu/utah/ece/async/ibiosim/gui/learnView/LearnView.java
View file

@ -1527,19 +1527,7 @@ public class LearnView extends JPanel implements ActionListener, Runnable
private void runGeneNet()
{
String geneNet = "";
if (System.getProperty("os.name").contentEquals("Linux"))
{
geneNet = "GeneNet.linux64";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os"))
{
geneNet = "GeneNet.mac64";
}
else
{
geneNet = "GeneNet.exe";
}
String geneNet = "GeneNet";
geneNet += " --debug " + debug.getSelectedItem();
try
{

94
learn/src/main/java/edu/utah/ece/async/ibiosim/learn/Learn.java
View file

@ -25,7 +25,9 @@ import org.sbml.jsbml.Parameter;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLReader;
import edu.utah.ece.async.ibiosim.dataModels.util.Message;
import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObserver;
import edu.utah.ece.async.ibiosim.learn.genenet.Experiments;
import edu.utah.ece.async.ibiosim.learn.genenet.Run;
import edu.utah.ece.async.ibiosim.learn.genenet.SpeciesCollection;
@ -67,7 +69,7 @@ import edu.utah.ece.async.ibiosim.learn.parameterestimator.ParameterEstimator;
* <li>--output_donotTossChangedInfluenceSingleParents: Determines if parents that change influence should not be tossed</li>
* <li>-binNumbers: Equal spacing per bin</li>
* <li>-noSUCC: to not use successors in calculating probabilities</li>
* <li>-PRED: use preicessors in calculating probabilities</li>
* <li>-PRED: use predecessors in calculating probabilities</li>
* <li>-basicFBP: to use the basic FindBaseProb function</li>
* </ul>
*
@ -77,9 +79,8 @@ import edu.utah.ece.async.ibiosim.learn.parameterestimator.ParameterEstimator;
* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim Contributors </a>
* @version %I%
*/
public class Learn {
public class Learn implements BioObserver
{
private double ta, tr, ti, tm, tn, tj, tt;
private int d, wr, ws, nb;
private boolean runParameterEstimation, lvl, readLevels, cpp, cpp_harshenBoundsOnTie, cpp_cmp_output_donotInvertSortOrder,
@ -88,7 +89,7 @@ public class Learn {
private String directory;
private String filename;
private List<String> listOfParameters;
private Learn()
{
ta = 1.15;
@ -103,7 +104,7 @@ public class Learn {
ws = 1;
nb = 4;
}
private static void usage() {
System.err.println("Description:");
System.err.println("\tExecutes bayesian methods for structural learning of regulatory networks using GeneNet or parameter estimation using SRES.");
@ -115,7 +116,30 @@ public class Learn {
System.err.println("Options:");
System.err.println("\t-e to execute parameter estimation.");
System.err.println("\t-l to specify the list of parameters to estimate. If not specified, all parameters are estimated. To use it, specify the parameters separated by commas (e.g. p1,p2,p3).");
System.err.println("\t-ta [num]: Sets the activation threshold. Default 1.15");
System.err.println("\t-tr [num]: Sets the repression threshold. Default 0.75");
System.err.println("\t-ti [num]: Sets how high a score must be to be considered a parent. Default 0.5");
System.err.println("\t-tm [num]: Sets how close IVs must be in score to be considered for combination. Default 0.01");
System.err.println("\t-tn [num]: Sets minimum number of parents to allow through in SelectInitialParents. Default 2");
System.err.println("\t-tj [num]: Sets the max parents of merged influence vectors, Default 2");
System.err.println("\t-tt [num]: Sets how fast the bound is relaxed for ta and tr, Default 0.025");
System.err.println("\t-d [num]: Sets the debug or output level. Default 0");
System.err.println("\t-wr [num]: Sets how much larger a number must be to be considered as a rise. Default 1");
System.err.println("\t-ws [num]: Sets how far the TSD points are when compared. Default 1");
System.err.println("\t-nb [num]: Sets how many bins are used in the evaluation. Default 4");
System.err.println("\t--lvl: Writes out the suggested levels for every species.");
System.err.println("\t--readLevels: Reads the levels from level.lvl file for every species.");
System.err.println("\t--cpp: runs the C++ GeneNet. Default is the Java version.");
System.err.println("\t--cpp_harshenBoundsOnTie: Determines if harsher bounds are used when parents tie in CPP.");
System.err.println("\t--cpp_cmp_output_donotInvertSortOrder: Sets the inverted sort order in the 3 places back to normal");
System.err.println("\t--cpp_seedParents Determines if parents should be ranked by score, not tsd order in CPP.");
System.err.println("\t--cmp_score_mustNotWinMajority: Determines if score should be used when following conditions are not met a &gt; r+n || r &gt; a + n");
System.err.println("\t--score_donotTossSingleRatioParents: Determines if single ratio parents should be kept");
System.err.println("\t--output_donotTossChangedInfluenceSingleParents: Determines if parents that change influence should not be tossed");
System.err.println("\t-binNumbers: Equal spacing per bin");
System.err.println("\t-noSUCC: to not use successors in calculating probabilities");
System.err.println("\t-PRED: use preicessors in calculating probabilities");
System.err.println("\t-basicFBP: to use the basic FindBaseProb function");
System.exit(1);
}
@ -373,15 +397,67 @@ public class Learn {
}
}
private void runGeneNet() throws BioSimException
private void runGeneNet() throws BioSimException, IOException
{
if(cpp)
{
File work = new File(directory);
Runtime exec = Runtime.getRuntime();
exec.exec(getProcessArguments(), null, work);
}
else
{
Run.run(filename, directory);
}
}
private String[] getProcessArguments()
{
ArrayList<String> args = new ArrayList<String>();
args.add("GeneNet");
args.add("-ta");
args.add(String.valueOf(ta));
args.add("-tr");
args.add(String.valueOf(tr));
args.add("-ti");
args.add(String.valueOf(ti));
args.add("-tm");
args.add(String.valueOf(tm));
args.add("-tn");
args.add(String.valueOf(tn));
args.add("-tj");
args.add(String.valueOf(tj));
args.add("-tt");
args.add(String.valueOf(tt));
args.add("-d");
args.add(String.valueOf(d));
args.add("-wr");
args.add(String.valueOf(wr));
args.add("-ws");
args.add(String.valueOf(ws));
args.add("-nb");
args.add(String.valueOf(nb));
if(lvl) args.add("--lvl");
if(readLevels) args.add("--readLevels");
if(cpp_harshenBoundsOnTie) args.add("--cpp_harshenBoundsOnTie");
if(cpp_cmp_output_donotInvertSortOrder) args.add("--cpp_cmp_output_donotInvertSortOrder");
if(cpp_seedParents) args.add("--cpp_seedParents");
if(cmp_score_mustNotWinMajority) args.add("--cmp_score_mustNotWinMajority");
if(score_donotTossSingleRatioParents) args.add("--score_donotTossSingleRatioParents");
if(output_donotTossChangedInfluenceSingleParents) args.add("--output_donotTossChangedInfluenceSingleParents");
if(binNumbers) args.add("-binNumbers");
if(noSUCC) args.add("-noSUCC");
if(PRED) args.add("-PRED");
if(basicFBP) args.add("-basicFBP");
return args.toArray(new String[args.size()]);
}
@Override
public void update(Message message)
{
System.out.println(message);
}
}