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support replacedBy and replacement for verilog2sbml

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This commit is contained in:
Tramy Nguyen 2019-01-15 16:43:30 -07:00
parent 5da84b3f73
commit 2111d56e9c
46 changed files with 5098 additions and 1871 deletions
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6
gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java
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@ -28,7 +28,6 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
import java.util.prefs.Preferences;
@ -69,11 +68,9 @@ import edu.utah.ece.async.ibiosim.gui.util.Utility;
import edu.utah.ece.async.ibiosim.synthesis.TechMapping;
import edu.utah.ece.async.ibiosim.synthesis.SBMLTechMapping.SynthesisGraph;
import edu.utah.ece.async.ibiosim.synthesis.SBMLTechMapping.Synthesizer;
import edu.utah.ece.async.ibiosim.synthesis.SBOLTechMapping.SBOLGraph;
import edu.utah.ece.async.ibiosim.synthesis.SBOLTechMapping.SBOLTechMap;
import edu.utah.ece.async.ibiosim.synthesis.SBOLTechMapping.SBOLTechMapException;
import edu.utah.ece.async.ibiosim.synthesis.SBOLTechMapping.Synthesis;
import edu.utah.ece.async.ibiosim.synthesis.SBOLTechMapping.SynthesisNode;
import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLEditorPreferences;
/**
@ -624,8 +621,7 @@ public class SynthesisView extends JTabbedPane implements ActionListener, Runnab
libDoc.createCopy(sbolDoc);
}
Synthesis syn = SBOLTechMap.runSBOLTechMap(specDoc, libDoc);
Map<SynthesisNode, SBOLGraph> solution = syn.getBestSolution();
SBOLDocument sbolTechMap_solution = syn.getSBOLfromTechMapping(solution, syn.getSpecification());
SBOLDocument sbolTechMap_solution = syn.getSBOLfromTechMapping();
// Note: Convert the solution back to SBML and load back to iBioSim workspace
String solution_dir = synthFilePath;
List<String> solutionFileIDs = new ArrayList<String>();