Example 1 with RelationshipObject
use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.
the class SpeciesPropertiesPanel method listLinkedPathwayObjects.
// wei's code
private String listLinkedPathwayObjects() {
if (getSpeciesContext() == null) {
return "no selected species";
}
if (bioModel == null || bioModel.getModel() == null) {
return "no biomodel";
}
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
String linkedPOlist = "";
for (RelationshipObject relObject : bioModel.getRelationshipModel().getRelationshipObjects(getSpeciesContext())) {
final BioPaxObject bpObject = relObject.getBioPaxObject();
if (bpObject instanceof Entity) {
JLabel label = new JLabel("<html><u>" + ((Entity) bpObject).getName().get(0) + "</u></html>");
label.setForeground(Color.blue);
label.addMouseListener(new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.PATHWAY_DIAGRAM_NODE, ActiveViewID.pathway_diagram), new Object[] { bpObject });
}
}
});
panel.add(label);
}
}
linkedPOScrollPane.setViewportView(panel);
return linkedPOlist;
}
Also used :
JPanel(javax.swing.JPanel)
Entity(org.vcell.pathway.Entity)
MouseEvent(java.awt.event.MouseEvent)
BioPaxObject(org.vcell.pathway.BioPaxObject)
BoxLayout(javax.swing.BoxLayout)
MouseAdapter(java.awt.event.MouseAdapter)
JLabel(javax.swing.JLabel)
RelationshipObject(org.vcell.relationship.RelationshipObject)
BioPaxObject(org.vcell.pathway.BioPaxObject)
ActiveView(cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Example 2 with RelationshipObject
use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.
the class MolecularTypeTableModel method getValueAt.
@Override
public Object getValueAt(int rowIndex, int columnIndex) {
Column col = Column.values()[columnIndex];
MolecularType molecularType = getValueAt(rowIndex);
if (molecularType == null) {
if (col == Column.name) {
return ADD_NEW_HERE_TEXT;
}
} else {
switch(col) {
case name:
return molecularType.getName();
case link:
HashSet<RelationshipObject> relObjsHash = bioModel.getRelationshipModel().getRelationshipObjects(molecularType);
if (relObjsHash != null && relObjsHash.size() > 0) {
return relObjsHash.iterator().next().getBioPaxObject();
}
return null;
case bngl_pattern:
return pattern(molecularType);
}
}
return null;
}
Also used :
MolecularType(org.vcell.model.rbm.MolecularType)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Example 3 with RelationshipObject
use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.
the class ReactionRuleKineticsPropertiesPanel method listLinkedPathwayObjects.
private String listLinkedPathwayObjects() {
if (reactionRule == null) {
return "no selected rule";
}
if (bioModel == null || bioModel.getModel() == null) {
return "no biomodel";
}
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel, BoxLayout.X_AXIS));
String linkedPOlist = "";
for (RelationshipObject relObject : bioModel.getRelationshipModel().getRelationshipObjects(reactionRule)) {
if (relObject == null) {
continue;
}
final BioPaxObject bpObject = relObject.getBioPaxObject();
if (bpObject == null) {
continue;
}
if (bpObject instanceof Entity) {
String name = new String();
if (((Entity) bpObject).getName().isEmpty()) {
name = ((Entity) bpObject).getID();
} else {
name = ((Entity) bpObject).getName().get(0);
}
if (name.contains("#")) {
name = name.substring(name.indexOf("#") + 1);
}
JLabel label = new JLabel("<html><u>" + name + "</u></html>");
label.setForeground(Color.blue);
label.addMouseListener(new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.PATHWAY_DIAGRAM_NODE, ActiveViewID.pathway_diagram), new Object[] { bpObject });
}
}
});
panel.add(label);
}
}
Dimension dim = new Dimension(200, 20);
panel.setMinimumSize(dim);
panel.setPreferredSize(dim);
linkedPOScrollPane.setViewportView(panel);
return linkedPOlist;
}
Also used :
JPanel(javax.swing.JPanel)
Entity(org.vcell.pathway.Entity)
MouseEvent(java.awt.event.MouseEvent)
BioPaxObject(org.vcell.pathway.BioPaxObject)
BoxLayout(javax.swing.BoxLayout)
MouseAdapter(java.awt.event.MouseAdapter)
JLabel(javax.swing.JLabel)
BioPaxObject(org.vcell.pathway.BioPaxObject)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Dimension(java.awt.Dimension)
ActiveView(cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Example 4 with RelationshipObject
use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.
the class BioModelEditorPathwayDiagramPanel method importIntoModel.
public void importIntoModel() {
if (bioModel == null) {
return;
}
String warningMessage = "";
String warningMessage2 = "";
int warningCount = 0;
int warningCount2 = 0;
String infoMessage = "";
ArrayList<BioPaxObject> importedBPObjects = new ArrayList<BioPaxObject>();
warningMessage = "The following pathway object(s) have been associated with object(s) in the physiology model:\n";
warningMessage2 = "The following transport reaction(s) will NOT be converted to the physiology model:\n";
warningCount = 0;
warningCount2 = 0;
infoMessage = "The following pathway object(s) have been coverted in the physiology model:\n\n";
boolean hasMembrane = false;
if (bioModel.getModel().getMembranes().size() > 0)
hasMembrane = true;
HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>();
// convert group Object to regular biopaxObjects
for (BioPaxObject bpo : getSelectedBioPaxObjects()) {
if (bpo instanceof GroupObject) {
selected.addAll(((GroupObject) bpo).computeGroupedBioPaxObjects());
} else {
selected.add(bpo);
}
}
for (BioPaxObject bpo : selected) {
if (bpo instanceof Conversion) {
if (bpo instanceof Transport && !hasMembrane) {
warningCount2++;
if (((Conversion) bpo).getName().size() > 0)
warningMessage2 += "\nTransport: \'" + ((Conversion) bpo).getName().get(0) + "\'\n";
else
warningMessage2 += "\nTransport: \'" + ((Conversion) bpo).getIDShort() + "\'\n";
} else if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
importedBPObjects.add(bpo);
} else {
warningCount++;
if (((Conversion) bpo).getName().size() > 0)
warningMessage += "\nReaction: \'" + ((Conversion) bpo).getName().get(0) + "\' =>\n";
else
warningMessage += "\nReaction: \'" + ((Conversion) bpo).getIDShort() + "\' =>\n";
for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
warningMessage += "\t=> \'" + r.getBioModelEntityObject().getName() + "\'\n";
}
}
} else if (bpo instanceof PhysicalEntity) {
if (bioModel.getRelationshipModel().getRelationshipObjects(bpo).size() == 0) {
importedBPObjects.add(bpo);
} else {
warningCount++;
if (((PhysicalEntity) bpo).getName().size() > 0)
warningMessage += "\nSpecies: \'" + ((PhysicalEntity) bpo).getName().get(0) + "\' =>\n";
else
warningMessage += "\nSpecies: \'" + ((PhysicalEntity) bpo).getIDShort() + "\' =>\n";
for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
warningMessage += "\t=> \'" + r.getBioModelEntityObject().getName() + "\'\n";
}
}
}
}
// create import panel
conversionPanel = new ConversionPanel();
conversionPanel.setBioModel(bioModel);
conversionPanel.setSelectionManager(getSelectionManager());
// show warning message
warningMessage2 += "\nNO membrane structures available in the physiology model.\n";
if (warningCount2 > 0) {
DialogUtils.showWarningDialog(conversionPanel, warningMessage2);
}
warningMessage += "\nThey will NOT be converted to the physiology model.\n";
if (warningCount > 0) {
DialogUtils.showWarningDialog(conversionPanel, warningMessage);
}
if (importedBPObjects.size() == 0) {
return;
}
// set the selected objects to be the validly imported biopaxObject set
conversionPanel.setBioPaxObjects(importedBPObjects);
int returnCode = DialogUtils.showComponentOKCancelDialog(this, conversionPanel, "Import into Physiology");
if (returnCode == JOptionPane.OK_OPTION) {
PathwayMapping pathwayMapping = new PathwayMapping();
try {
// function I:
// pass the table rows that contains user edited values to create Vcell object
pathwayMapping.createBioModelEntitiesFromBioPaxObjects(bioModel, conversionPanel.getTableRows(), conversionPanel.isAddSubunits());
for (BioPaxObject bpo : importedBPObjects) {
if (bpo instanceof Conversion) {
infoMessage += "Reaction: \t\'";
for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
infoMessage += r.getBioModelEntityObject().getName() + "\'\n";
}
infoMessage += "\n";
} else if (bpo instanceof PhysicalEntity) {
infoMessage += "Species: \t\'";
for (RelationshipObject r : bioModel.getRelationshipModel().getRelationshipObjects(bpo)) {
infoMessage += r.getBioModelEntityObject().getName() + "\'\n";
}
infoMessage += "\n";
}
}
DialogUtils.showInfoDialog(this, infoMessage);
// jump the view to reaction diagram panel
if (selectionManager != null) {
selectionManager.setActiveView(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram));
}
} catch (Exception e) {
e.printStackTrace(System.out);
DialogUtils.showErrorDialog(this, "Errors occur when converting pathway objects to VCell bioModel objects.\n" + e.getMessage());
}
}
}
Also used :
PathwayMapping(org.vcell.relationship.PathwayMapping)
BioPaxObject(org.vcell.pathway.BioPaxObject)
ArrayList(java.util.ArrayList)
GroupObject(org.vcell.pathway.GroupObject)
ActiveView(cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView)
Conversion(org.vcell.pathway.Conversion)
RelationshipObject(org.vcell.relationship.RelationshipObject)
ZoomRangeException(cbit.gui.graph.GraphResizeManager.ZoomRangeException)
UtilCancelException(org.vcell.util.UtilCancelException)
PhysicalEntity(org.vcell.pathway.PhysicalEntity)
Transport(org.vcell.pathway.Transport)
HashSet(java.util.HashSet)
Example 5 with RelationshipObject
use of org.vcell.relationship.RelationshipObject in project vcell by virtualcell.
the class BioModelEditorConversionTableModel method createTableRow.
private ConversionTableRow createTableRow(BioPaxObject bpObject, String interactionId, String interactionLabel, String participantType, double stoich, HashSet<RelationshipObject> relationshipObjects) {
String location = "";
ConversionTableRow conversionTableRow = new ConversionTableRow(bpObject);
conversionTableRow.setInteractionId(interactionId);
conversionTableRow.setInteractionLabel(interactionLabel);
conversionTableRow.setParticipantType(participantType);
// stoichiometry and location
if (participantType.equals("Reactant") || participantType.equals("Product")) {
// stoichiometry
if (stoich != 0)
conversionTableRow.setStoich(stoich);
else
conversionTableRow.setStoich(1.0);
// location
// if(((PhysicalEntity)bpObject).getCellularLocation() != null && ((PhysicalEntity)bpObject).getCellularLocation().getTerm().size()>0)
// location = ((PhysicalEntity)bpObject).getCellularLocation().getTerm().get(0);
// else
location = bioModel.getModel().getStructures()[0].getName();
conversionTableRow.setLocation(location);
} else {
conversionTableRow.setStoich(1.0);
// else
if (bpObject instanceof Transport) {
if (bioModel.getModel().getMembranes().size() > 0)
location = bioModel.getModel().getMembranes().get(0).getName();
else
location = bioModel.getModel().getStructures()[0].getName();
} else
location = bioModel.getModel().getStructures()[0].getName();
conversionTableRow.setLocation(location);
}
// id
if (relationshipObjects == null) {
if (bpObject instanceof Entity) {
String id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
if (isValid(id))
conversionTableRow.setId(id);
else
conversionTableRow.setId(changeID(id));
}
} else {
String id = null;
for (RelationshipObject relationshipObject : relationshipObjects) {
if (relationshipObject.getBioModelEntityObject() instanceof MolecularType) {
id = relationshipObject.getBioModelEntityObject().getName();
location = "";
} else if (relationshipObject.getBioModelEntityObject().getStructure().getName().equalsIgnoreCase(location)) {
id = relationshipObject.getBioModelEntityObject().getName();
}
}
if (id != null) {
// the linked bmObject with the same location will be used
conversionTableRow.setId(id);
} else {
// a new bmObject will be created if no linked bmObject in the same location
if (bpObject instanceof Entity) {
id = (BioPAXUtil.getName((Entity) bpObject) + "_" + location).trim();
if (isValid(id))
conversionTableRow.setId(id);
else
conversionTableRow.setId(changeID(id));
}
}
}
return conversionTableRow;
}
Also used :
MolecularType(org.vcell.model.rbm.MolecularType)
Entity(org.vcell.pathway.Entity)
PhysicalEntity(org.vcell.pathway.PhysicalEntity)
ConversionTableRow(org.vcell.relationship.ConversionTableRow)
Transport(org.vcell.pathway.Transport)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Aggregations
RelationshipObject (org.vcell.relationship.RelationshipObject)24
ArrayList (java.util.ArrayList)11
BioPaxObject (org.vcell.pathway.BioPaxObject)11
Entity (org.vcell.pathway.Entity)10
ActiveView (cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView)7
BioModelEntityObject (cbit.vcell.model.BioModelEntityObject)6
MolecularType (org.vcell.model.rbm.MolecularType)6
PhysicalEntity (org.vcell.pathway.PhysicalEntity)6
JLabel (javax.swing.JLabel)5
JPanel (javax.swing.JPanel)5
SpeciesContext (cbit.vcell.model.SpeciesContext)4
Dimension (java.awt.Dimension)4
MouseAdapter (java.awt.event.MouseAdapter)4
MouseEvent (java.awt.event.MouseEvent)4
BoxLayout (javax.swing.BoxLayout)4
Conversion (org.vcell.pathway.Conversion)4
ReactionStep (cbit.vcell.model.ReactionStep)3
ModelProcessEquation (cbit.gui.ModelProcessEquation)2
Shape (cbit.gui.graph.Shape)2
ModelProcess (cbit.vcell.model.ModelProcess)2
