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Finished the standalone for learn.

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This commit is contained in:
leandrohw 2018-01-08 09:52:02 -07:00
parent c415c09993
commit c999456ed2
2 changed files with 1697 additions and 1756 deletions
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33
learn/src/main/java/edu/utah/ece/async/ibiosim/learn/Learn.java
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@ -420,16 +420,16 @@ public class Learn implements BioObserver
List<String> speciesList = Learn.writeBackgroundFile(filename, directory);
Learn.writeLevelsFile(directory, speciesList, nb);
String[] command = getProcessArguments();
System.out.println(SBMLutilities.commandString(command));
System.out.println("Executing:");
System.out.println("\t" + SBMLutilities.commandString(command));
Process process = exec.exec(command, null, work);
process.waitFor();
System.out.println("Terminated");
}
else
{
System.out.println("Running GeneNet (Java)");
Run.run(filename, directory);
System.out.println("Terminated");
}
}
@ -472,10 +472,16 @@ public class Learn implements BioObserver
if(noSUCC) args.add("-noSUCC");
if(PRED) args.add("-PRED");
if(basicFBP) args.add("-basicFBP");
args.add(directory);
return args.toArray(new String[args.size()]);
}
/**
* Writes the learn properties file associated that can be used in iBioSim.
*
* @param learn - the object that contains the parameters for the learn procedure.
* @throws IOException - if a problem occurs with the reading/write of learn files.
*/
public static void writeLearnFile(Learn learn) throws IOException
{
if(learn == null)
@ -559,6 +565,14 @@ public class Learn implements BioObserver
}
/**
* Writes a default levels file.
*
* @param directory - the directory of the project
* @param species - the interesting species of the regulatory network
* @param bins - number of bins
* @throws IOException - if something wrong happens when writing the levels file.
*/
public static void writeLevelsFile(String directory, List<String> species, int bins) throws IOException
{
FileWriter write = new FileWriter(new File(directory + File.separator + "levels.lvl"));
@ -579,6 +593,17 @@ public class Learn implements BioObserver
write.close();
}
/**
* Write background file that informs GeneNet of known prior information about
* the regulatory networks.
*
* @param learnFile - the sbml file that the background file is generated from.
* @param directory - the directory the background file is saved to
* @return a list of interesting species.
*
* @throws XMLStreamException - when reading bad formatted sbml file
* @throws IOException - when something wrong happens when saving the background file.
*/
public static List<String> writeBackgroundFile(String learnFile, String directory) throws XMLStreamException, IOException
{
ArrayList<String> speciesList = new ArrayList<String>();