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Gui option for Cello Modeling

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Added neccesary changes to make cello modeling an option for the user through the Gui interface
This commit is contained in:
Pedro Fontanarrosa 2019-11-01 20:17:16 -03:00
parent 299bf44d17
commit e301b76604
5 changed files with 71 additions and 32 deletions
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17
gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java
View file

@ -4586,7 +4586,8 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
// // TODO Auto-generated catch block
// e.printStackTrace();
// }
generateSBMLFromSBOL(selection, root);
//TODO PEDRO revisit what boolean value to input here
generateSBMLFromSBOL(selection, root, false);
// TODO: update to attachment class
String sedmlFile = null;
for (Attachment attachment : selection.getAttachments()) {
@ -4719,7 +4720,8 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
String filePath = filename.trim();
org.sbolstandard.core2.SBOLDocument inputSBOLDoc = SBOLReader.read(new FileInputStream(filePath));
inputSBOLDoc.setDefaultURIprefix(SBOLEditorPreferences.INSTANCE.getUserInfo().getURI().toString());
int numGeneratedSBML = generateSBMLFromSBOL(inputSBOLDoc, filePath);
//TODO PEDRO revisit what boolean value to input here
int numGeneratedSBML = generateSBMLFromSBOL(inputSBOLDoc, filePath, false);
getSBOLDocument().createCopy(inputSBOLDoc);
writeSBOLDocument();
JOptionPane.showMessageDialog(frame, "Successfully Imported SBOL file containing: \n"
@ -5944,10 +5946,11 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
chosenDesign = s.getSelection();
}
boolean celloModel = s.isCelloModel();
if(s.isVPRGenerator())
{
runVPRGenerator(filePath, fileName, chosenDesign);
runVPRGenerator(filePath, fileName, chosenDesign, celloModel);
}
else if(s.isSBOLDesigner())
{
@ -5962,7 +5965,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
* @param fileName - The name of the SBOL file that the given SBOLDocument was created from.
* @param chosenDesign - The chosen design that the user would like to perform VPR Model Generation from.
*/
private void runVPRGenerator(String filePath, String fileName, SBOLDocument chosenDesign)
private void runVPRGenerator(String filePath, String fileName, SBOLDocument chosenDesign, boolean CelloModel)
{
try
{
@ -5993,7 +5996,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
VPRModelGenerator.generateModel(selectedRepo, chosenDesign, circuitID);
//update SBOL library file with newly generated components that vpr model generator created.
generateSBMLFromSBOL(chosenDesign, filePath);
generateSBMLFromSBOL(chosenDesign, filePath, CelloModel);
// TODO: should be using libSBOLj for this
SBOLUtility.copyAllTopLevels(chosenDesign, sbolDocument);
writeSBOLDocument();
@ -6173,14 +6176,14 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
* @param filePath - The file location where the SBOL document is located.
* @return The number of SBML models that was converted from SBOL.
*/
public int generateSBMLFromSBOL(SBOLDocument inputSBOLDoc, String filePath) {
public int generateSBMLFromSBOL(SBOLDocument inputSBOLDoc, String filePath, boolean CelloModel) {
int numGeneratedSBML = 0;
try {
for (ModuleDefinition moduleDef : inputSBOLDoc.getRootModuleDefinitions()) {
if (moduleDef.getModels().size()==0) {
HashMap<String,BioModel> models;
try {
models = SBOL2SBML.generateModel(root, moduleDef, inputSBOLDoc);
models = SBOL2SBML.generateModel(root, moduleDef, inputSBOLDoc, CelloModel);
for (BioModel model : models.values()) {
if (overwrite(root + File.separator + model.getSBMLDocument().getModel().getId() + ".xml",
model.getSBMLDocument().getModel().getId() + ".xml")) {

33
gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/sbol/SBOLInputDialog.java
View file

@ -106,13 +106,15 @@ public class SBOLInputDialog extends InputDialog<SBOLDocument> {
private static final Part ALL_PARTS = new Part("All parts", "All");
private JCheckBox showRootDefs;
private JCheckBox celloModel;
private JRadioButton showModDefs, showCompDefs;
private JButton openSBOLDesigner, openVPRGenerator, optionsButton; //, cancelButton;
private SBOLDocument sbolDesigns;
private boolean sbolDesigner, vprGenerator;
private boolean sbolDesigner, vprGenerator, CelloModel;
/**
* An instance of the SBOL Design/Part selection dialog that will allow the user to open their selected design
@ -213,6 +215,23 @@ public class SBOLInputDialog extends InputDialog<SBOLDocument> {
filteredDesignPanel.add(showRootDefs);
builder.add("", filteredDesignPanel);
celloModel = new JCheckBox("Cello Modeling");
celloModel.setSelected(false);
celloModel.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent event) {
if (celloModel.isSelected()) {
CelloModel = true;
}
else if (!celloModel.isSelected()) {
CelloModel = false;
}
}
});
filteredDesignPanel.add(celloModel);
builder.add("", filteredDesignPanel);
typeSelection = new JComboBox<Types>(Types.values());
typeSelection.setSelectedItem(Types.DNA);
typeSelection.addActionListener(new ActionListener() {
@ -406,6 +425,18 @@ public class SBOLInputDialog extends InputDialog<SBOLDocument> {
return outputDoc;
}
/**
* Check if Cello Modeling is to be performed
*/
public boolean isCelloModel() {
if (CelloModel == true) {
return true;
}
else {
return false;
}
}
private void updateRoleRefinement()
{

3
gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java
View file

@ -586,7 +586,8 @@ public class SynthesisView extends JTabbedPane implements ActionListener, Runnab
List<String> solutionFileIDs = new ArrayList<String>();
for (ModuleDefinition moduleDef : solution.getRootModuleDefinitions())
{
HashMap<String,BioModel> models = SBOL2SBML.generateModel(solution_dir, moduleDef, solution);
//TODO PEDRO revisit what boolean value to input here
HashMap<String,BioModel> models = SBOL2SBML.generateModel(solution_dir, moduleDef, solution, false);
solutionFileIDs.addAll(SBMLutilities.exportMultSBMLFile(models, solution_dir));
}
return solutionFileIDs;