Example 11 with Entity
use of org.vcell.pathway.Entity in project vcell by virtualcell.
the class BioPaxObjectPropertiesPanel method initialize.
private void initialize() {
try {
table = new ScrollTable();
tableModel = new BioPaxObjectPropertiesTableModel(table);
table.setModel(tableModel);
details = new JTextPane();
details.setContentType("text/html");
details.setEditable(false);
JScrollPane scrl = new JScrollPane(details);
table.getSelectionModel().addListSelectionListener(new ListSelectionListener() {
@Override
public void valueChanged(ListSelectionEvent e) {
if (!e.getValueIsAdjusting()) {
BioPaxObjectProperty property = tableModel.getValueAt(table.getSelectedRow());
if (property != null) {
final String htmlStart = "<html><font face = \"Arial\"><font size =\"-2\">";
final String htmlEnd = "</font></font></html>";
if (!property.getDetails().isEmpty()) {
details.setText(htmlStart + property.getDetails() + htmlEnd);
} else if ((property.value != null) && !property.value.isEmpty()) {
String text = FormatDetails(property);
details.setText(htmlStart + text + htmlEnd);
} else {
details.setText(htmlStart + "row: " + table.getSelectedRow() + ", col: " + table.getSelectedColumn() + htmlEnd);
}
}
}
}
});
splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, table.getEnclosingScrollPane(), scrl);
splitPane.setOneTouchExpandable(true);
splitPane.setDividerLocation(150);
// provide minimum sizes for the two components in the split pane
Dimension minimumSize = new Dimension(100, 50);
table.getEnclosingScrollPane().setMinimumSize(minimumSize);
scrl.setMinimumSize(minimumSize);
setLayout(new BorderLayout());
// add(table.getEnclosingScrollPane(), BorderLayout.CENTER);
// add(details, BorderLayout.CENTER);
add(splitPane, BorderLayout.CENTER);
setBackground(Color.white);
table.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
// launch the browser when double click on hyperlinks
Point pt = e.getPoint();
int crow = table.rowAtPoint(pt);
int ccol = table.columnAtPoint(pt);
if (table.convertColumnIndexToModel(ccol) == BioPaxObjectPropertiesTableModel.Column_Value) {
BioPaxObjectProperty property = tableModel.getValueAt(crow);
BioPaxObject bioPaxObject = property.bioPaxObject;
if (bioPaxObject == null) {
BioModelEntityObject bioModelEntityObject = property.bioModelEntityObject;
if (bioModelEntityObject != null) {
if (bioModelEntityObject instanceof SpeciesContext) {
selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTION_DIAGRAM_NODE, ActiveViewID.reaction_diagram), new Object[] { bioModelEntityObject });
} else if (bioModelEntityObject instanceof MolecularType) {
selectionManager.followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE, ActiveViewID.species_definitions), new Object[] { bioModelEntityObject });
}
} else if (((Entity) BioPaxObjectPropertiesPanel.this.bioPaxObject).getFormalNames() == null || ((Entity) BioPaxObjectPropertiesPanel.this.bioPaxObject).getFormalNames().size() == 0) {
lookupFormalName(crow);
}
} else if (bioPaxObject instanceof Xref) {
// if xRef, get url
String url = ((Xref) bioPaxObject).getURL();
DialogUtils.browserLauncher(BioPaxObjectPropertiesPanel.this, url, "Wrong URL.");
} else if (bioPaxObject instanceof SBEntity) {
// TODO: kineticLaw
SBEntity sbE = (SBEntity) bioPaxObject;
if (sbE.getID().contains("kineticLaw")) {
// String url = "http://sabio.h-its.org/sabioRestWebServices/kineticLaws/" + sbE.getID().substring(sbE.getID().indexOf("kineticLaw") + 10);
String url = "http://sabiork.h-its.org/kindatadirectiframe.jsp?kinlawid=" + sbE.getID().substring(sbE.getID().indexOf("kineticLaw") + 10);
DialogUtils.browserLauncher(BioPaxObjectPropertiesPanel.this, url, "Wrong URL.");
}
}
}
}
}
});
// --- end of addMouseListener()
table.getColumnModel().getColumn(BioPaxObjectPropertiesTableModel.Column_Value).setCellRenderer(new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (column == BioPaxObjectPropertiesTableModel.Column_Value) {
BioPaxObjectProperty property = tableModel.getValueAt(row);
BioPaxObject bpObject = property.bioPaxObject;
String text = property.value;
// colorize BLUE and add surround text with <html></html> tags
if (bpObject == null) {
BioModelEntityObject bioModelEntityObject = property.bioModelEntityObject;
if (bioModelEntityObject != null) {
if (!isSelected) {
setForeground(Color.blue);
}
setText("<html><u>" + text + "</u></html>");
}
} else {
if (bpObject instanceof Xref) {
String url = ((Xref) bpObject).getURL();
if (url != null) {
setToolTipText(url);
if (!isSelected) {
setForeground(Color.blue);
}
setText("<html><u>" + text + "</u></html>");
}
} else if (bpObject instanceof SBEntity) {
String url = ((SBEntity) bpObject).getID();
if (url.contains("kineticLaw")) {
setToolTipText(url);
if (!isSelected) {
setForeground(Color.blue);
}
if (url.contains("http")) {
setText("<html><u>" + text + "</u></html>");
}
}
}
}
}
BioPaxObjectProperty property = tableModel.getValueAt(row);
if (!property.tooltip.isEmpty()) {
setToolTipText(property.tooltip);
}
return this;
}
});
// --- end of setCellRenderer()
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
Also used :
SBEntity(org.vcell.pathway.sbpax.SBEntity)
PhysicalEntity(org.vcell.pathway.PhysicalEntity)
Entity(org.vcell.pathway.Entity)
ScrollTable(org.vcell.util.gui.ScrollTable)
BioPaxObject(org.vcell.pathway.BioPaxObject)
ListSelectionEvent(javax.swing.event.ListSelectionEvent)
SpeciesContext(cbit.vcell.model.SpeciesContext)
ActiveView(cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView)
SBEntity(org.vcell.pathway.sbpax.SBEntity)
JTextPane(javax.swing.JTextPane)
Xref(org.vcell.pathway.Xref)
UnificationXref(org.vcell.pathway.UnificationXref)
RelationshipXref(org.vcell.pathway.RelationshipXref)
PublicationXref(org.vcell.pathway.PublicationXref)
BorderLayout(java.awt.BorderLayout)
Component(java.awt.Component)
JScrollPane(javax.swing.JScrollPane)
MouseEvent(java.awt.event.MouseEvent)
MouseAdapter(java.awt.event.MouseAdapter)
Dimension(java.awt.Dimension)
Point(java.awt.Point)
BioModelEntityObject(cbit.vcell.model.BioModelEntityObject)
Point(java.awt.Point)
ListSelectionListener(javax.swing.event.ListSelectionListener)
MolecularType(org.vcell.model.rbm.MolecularType)
JTable(javax.swing.JTable)
GroupObject(org.vcell.pathway.GroupObject)
BioPaxObject(org.vcell.pathway.BioPaxObject)
RelationshipObject(org.vcell.relationship.RelationshipObject)
BioModelEntityObject(cbit.vcell.model.BioModelEntityObject)
DefaultScrollTableCellRenderer(org.vcell.util.gui.DefaultScrollTableCellRenderer)
JSplitPane(javax.swing.JSplitPane)
Example 12 with Entity
use of org.vcell.pathway.Entity in project vcell by virtualcell.
the class BioModelEditorConversionTableModel method createTableRowForTransportParticipant.
private ConversionTableRow createTableRowForTransportParticipant(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
Model model = bioModel.getModel();
StructureTopology structTopology = model.getStructureTopology();
if (participantType.equals("Reactant")) {
// stoichiometry
if (stoich != 0)
conversionTableRow.setStoich(stoich);
else
conversionTableRow.setStoich(1.0);
// else{
if (model.getMembranes().size() > 0)
location = structTopology.getOutsideFeature(model.getMembranes().get(0)).getName();
else
location = model.getStructures()[0].getName();
// }
conversionTableRow.setLocation(location);
} else if (participantType.equals("Product")) {
// stoichiometry
if (stoich != 0)
conversionTableRow.setStoich(stoich);
else
conversionTableRow.setStoich(1.0);
// else{
if (model.getMembranes().size() > 0)
location = structTopology.getInsideFeature(model.getMembranes().get(0)).getName();
else
location = model.getStructures()[0].getName();
// }
conversionTableRow.setLocation(location);
} else {
conversionTableRow.setStoich(1.0);
// else
if (bpObject instanceof Transport) {
if (model.getMembranes().size() > 0)
location = model.getMembranes().get(0).getName();
else
location = model.getStructures()[0].getName();
} else
location = model.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().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 :
Entity(org.vcell.pathway.Entity)
PhysicalEntity(org.vcell.pathway.PhysicalEntity)
StructureTopology(cbit.vcell.model.Model.StructureTopology)
ConversionTableRow(org.vcell.relationship.ConversionTableRow)
DefaultComboBoxModel(javax.swing.DefaultComboBoxModel)
BioModel(cbit.vcell.biomodel.BioModel)
AutoCompleteTableModel(org.vcell.util.gui.AutoCompleteTableModel)
Model(cbit.vcell.model.Model)
Transport(org.vcell.pathway.Transport)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Example 13 with Entity
use of org.vcell.pathway.Entity in project vcell by virtualcell.
the class ReactionPropertiesPanel method listLinkedPathwayObjects.
private String listLinkedPathwayObjects() {
// Kinetics kinetics = reactionStep.getKinetics();
if (reactionStep == null) {
return "no selected reaction";
}
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(reactionStep)) {
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 14 with Entity
use of org.vcell.pathway.Entity in project vcell by virtualcell.
the class MolecularTypePropertiesPanel method listLinkedPathwayObjects.
private String listLinkedPathwayObjects() {
if (molecularType == null) {
return "no selected molecule";
}
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(molecularType)) {
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);
}
}
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)
RelationshipObject(org.vcell.relationship.RelationshipObject)
BioPaxObject(org.vcell.pathway.BioPaxObject)
Dimension(java.awt.Dimension)
ActiveView(cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Example 15 with Entity
use of org.vcell.pathway.Entity in project vcell by virtualcell.
the class MolecularTypeTableModel method computeData.
@Override
protected List<MolecularType> computeData() {
if (getModel() == null) {
return new ArrayList<MolecularType>();
}
List<MolecularType> mtList;
if (searchText == null || searchText.length() == 0) {
mtList = new ArrayList<MolecularType>(getModel().getRbmModelContainer().getMolecularTypeList());
} else {
mtList = new ArrayList<MolecularType>();
String lowerCaseSearchText = searchText.toLowerCase();
for (MolecularType mt : getModel().getRbmModelContainer().getMolecularTypeList()) {
boolean bMatchRelationshipObj = false;
HashSet<RelationshipObject> relObjsHash = bioModel.getRelationshipModel().getRelationshipObjects(mt);
for (RelationshipObject relObj : relObjsHash) {
if (relObj.getBioPaxObject() instanceof Entity) {
if (((Entity) relObj.getBioPaxObject()).getName().get(0).toLowerCase().contains(lowerCaseSearchText)) {
bMatchRelationshipObj = true;
break;
}
}
}
String expression = pattern(mt);
if (expression != null && expression.toLowerCase().contains(lowerCaseSearchText)) {
mtList.add(mt);
}
}
}
return mtList;
}
Also used :
MolecularType(org.vcell.model.rbm.MolecularType)
Entity(org.vcell.pathway.Entity)
ArrayList(java.util.ArrayList)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Aggregations
Entity (org.vcell.pathway.Entity)15
RelationshipObject (org.vcell.relationship.RelationshipObject)12
BioPaxObject (org.vcell.pathway.BioPaxObject)8
PhysicalEntity (org.vcell.pathway.PhysicalEntity)7
ArrayList (java.util.ArrayList)6
ActiveView (cbit.vcell.client.desktop.biomodel.SelectionManager.ActiveView)5
MouseAdapter (java.awt.event.MouseAdapter)5
MouseEvent (java.awt.event.MouseEvent)5
Dimension (java.awt.Dimension)4
BoxLayout (javax.swing.BoxLayout)4
JLabel (javax.swing.JLabel)4
JPanel (javax.swing.JPanel)4
GroupObject (org.vcell.pathway.GroupObject)4
PublicationXref (org.vcell.pathway.PublicationXref)4
RelationshipXref (org.vcell.pathway.RelationshipXref)4
Xref (org.vcell.pathway.Xref)4
SBEntity (org.vcell.pathway.sbpax.SBEntity)4
BioModelEntityObject (cbit.vcell.model.BioModelEntityObject)3
MolecularType (org.vcell.model.rbm.MolecularType)3
UnificationXref (org.vcell.pathway.UnificationXref)3
