use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.
the class XmlReader method getRbmReactantPatternsList.
private void getRbmReactantPatternsList(Element e, ReactionRule r, Model newModel) {
if (e != null) {
List<Element> rpChildren = e.getChildren(XMLTags.RbmReactantPatternTag, vcNamespace);
for (Element rpElement : rpChildren) {
Structure structure = null;
String structureName = rpElement.getAttributeValue(XMLTags.StructureAttrTag);
if (structureName == null || structureName.isEmpty()) {
// the tag is missing
throw new RuntimeException("XMLReader: structure missing for reaction rule pattern.");
} else {
structure = newModel.getStructure(structureName);
}
Element spe = rpElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace);
SpeciesPattern s = getSpeciesPattern(spe, newModel);
if (s != null) {
r.addReactant(new ReactantPattern(s, structure), false);
}
}
// older models have the species pattern saved directly and using the structure or the rule
List<Element> spChildren = e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace);
for (Element element : spChildren) {
SpeciesPattern s = getSpeciesPattern(element, newModel);
if (s != null) {
r.addReactant(new ReactantPattern(s, r.getStructure()), false);
}
}
}
}
use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.
the class BioModelEditorSpeciesTableModel method isCellEditable.
public boolean isCellEditable(int row, int column) {
switch(column) {
case COLUMN_NAME:
return true;
case COLUMN_DEFINITION:
SpeciesContext sc = getValueAt(row);
if (sc == null) {
return false;
}
SpeciesPattern sp = sc.getSpeciesPattern();
if (sp == null) {
// we can edit a species pattern if none is present
return true;
}
final List<MolecularTypePattern> mtpList = sp.getMolecularTypePatterns();
for (MolecularTypePattern mtp : mtpList) {
MolecularType mt = mtp.getMolecularType();
if (mt.getComponentList().size() != 0) {
return false;
}
}
return true;
default:
return false;
}
}
use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.
the class BioModelEditorSpeciesTableModel method checkInputValue.
public String checkInputValue(String inputValue, int row, int column) {
SpeciesContext speciesContext = getValueAt(row);
String errMsg = null;
switch(column) {
case COLUMN_NAME:
if (speciesContext == null || !speciesContext.getName().equals(inputValue)) {
if (getModel().getSpeciesContext(inputValue) != null) {
errMsg = "Species '" + inputValue + "' already exists!";
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
}
break;
case COLUMN_STRUCTURE:
if (getModel().getStructure(inputValue) == null) {
errMsg = "Structure '" + inputValue + "' does not exist!";
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
break;
case COLUMN_DEFINITION:
try {
inputValue = inputValue.trim();
if (inputValue.length() > 0) {
// parsing will throw appropriate exception if molecular type or component don't exist
// our change
SpeciesPattern spThis = RbmUtils.parseSpeciesPattern(inputValue, bioModel.getModel());
// here we can restrict what the user can do
for (MolecularTypePattern mtpThis : spThis.getMolecularTypePatterns()) {
MolecularType mtThis = mtpThis.getMolecularType();
for (MolecularComponent mcThis : mtThis.getComponentList()) {
// we check that each component is present in the molecular type pattern (as component pattern)
if (mtpThis.getMolecularComponentPattern(mcThis) == null) {
// not found
errMsg = "All " + MolecularComponent.typeName + "s in the " + mtThis.getDisplayType() + " definition must be present. Missing: " + mcThis.getName();
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
} else if (mtpThis.getMolecularComponentPattern(mcThis).isImplied()) {
errMsg = "All " + MolecularComponent.typeName + "s in the " + mtThis.getDisplayType() + " definition must be present. Missing: " + mcThis.getName();
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
} else {
// now need to also check the states
if (mcThis.getComponentStateDefinitions().size() == 0) {
// nothing to do if the molecular component has no component state definition
continue;
// note that we raise exception in parseSpeciesPattern() if we attempt to use an undefined state
// so no need to check that here
}
boolean found = false;
for (ComponentStateDefinition csThis : mcThis.getComponentStateDefinitions()) {
MolecularComponentPattern mcpThis = mtpThis.getMolecularComponentPattern(mcThis);
if ((mcpThis.getComponentStatePattern() == null) || mcpThis.getComponentStatePattern().isAny()) {
// no component state pattern means no state, there's no point to check for this component again
break;
// we get out of the for and complain that we found no matching state
}
if (csThis.getName().equals(mcpThis.getComponentStatePattern().getComponentStateDefinition().getName())) {
found = true;
}
}
if (found == false) {
// we should have found a matching state for the molecular component pattern
errMsg = MolecularComponent.typeName + " " + mcThis.getDisplayName() + " of " + mtThis.getDisplayType() + " " + mtThis.getDisplayName() + " must be in one of the following states: ";
for (int i = 0; i < mcThis.getComponentStateDefinitions().size(); i++) {
ComponentStateDefinition csThis = mcThis.getComponentStateDefinitions().get(i);
errMsg += csThis.getName();
if (i < mcThis.getComponentStateDefinitions().size() - 1) {
errMsg += ", ";
}
}
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
}
}
}
}
} catch (Exception ex) {
errMsg = ex.getMessage();
errMsg += VCellErrorMessages.PressEscToUndo;
errMsg = "<html>" + errMsg + "</html>";
return errMsg;
}
break;
}
return null;
}
use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.
the class OutputSpeciesResultsPanel method initialize.
private void initialize() {
try {
setName("ViewGeneratedSpeciesPanel");
setLayout(new GridBagLayout());
shapePanel = new LargeShapePanel() {
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (spls != null) {
spls.paintSelf(g);
}
}
@Override
public DisplayMode getDisplayMode() {
return DisplayMode.other;
}
@Override
public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleParticipantSignature getSignature() {
return null;
}
@Override
public GroupingCriteria getCriteria() {
return null;
}
@Override
public boolean isViewSingleRow() {
return true;
}
};
Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
shapePanel.setLayout(new GridBagLayout());
shapePanel.setBackground(Color.white);
// not really editable but we don't want the brown contours here
shapePanel.setEditable(true);
shapePanel.setShowMoleculeColor(true);
shapePanel.setShowNonTrivialOnly(true);
JScrollPane scrollPane = new JScrollPane(shapePanel);
scrollPane.setBorder(loweredBevelBorder);
scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
JPanel optionsPanel = new JPanel();
optionsPanel.setLayout(new GridBagLayout());
getZoomSmallerButton().setEnabled(true);
getZoomLargerButton().setEnabled(false);
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.insets = new Insets(0, 0, 0, 10);
gbc.anchor = GridBagConstraints.WEST;
optionsPanel.add(getZoomLargerButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 1;
gbc.insets = new Insets(2, 0, 4, 10);
gbc.anchor = GridBagConstraints.WEST;
optionsPanel.add(getZoomSmallerButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 2;
gbc.weightx = 1;
// fake cell used for filling all the vertical empty space
gbc.weighty = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new Insets(4, 4, 4, 10);
optionsPanel.add(new JLabel(""), gbc);
JPanel containerOfScrollPanel = new JPanel();
containerOfScrollPanel.setLayout(new BorderLayout());
containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
Dimension dim = new Dimension(500, 135);
// dimension of shape panel
containerOfScrollPanel.setPreferredSize(dim);
containerOfScrollPanel.setMinimumSize(dim);
containerOfScrollPanel.setMaximumSize(dim);
// ------------------------------------------------------------------------
table = new EditorScrollTable();
tableModel = new OutputSpeciesResultsTableModel();
table.setModel(tableModel);
table.getSelectionModel().addListSelectionListener(eventHandler);
table.getModel().addTableModelListener(eventHandler);
DefaultTableCellRenderer rightRenderer = new DefaultTableCellRenderer();
rightRenderer.setHorizontalAlignment(JLabel.RIGHT);
int gridy = 0;
gbc = new java.awt.GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.weightx = 1.0;
gbc.weighty = 1.0;
gbc.gridwidth = 8;
gbc.fill = GridBagConstraints.BOTH;
gbc.insets = new Insets(4, 4, 4, 4);
table.setPreferredScrollableViewportSize(new Dimension(400, 200));
add(table.getEnclosingScrollPane(), gbc);
// add toolTipText for each table cell
table.addMouseMotionListener(new MouseMotionAdapter() {
public void mouseMoved(MouseEvent e) {
Point p = e.getPoint();
int row = table.rowAtPoint(p);
int column = table.columnAtPoint(p);
table.setToolTipText(String.valueOf(table.getValueAt(row, column)));
}
});
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.anchor = GridBagConstraints.LINE_END;
gbc.insets = new Insets(4, 4, 4, 4);
add(new JLabel("Search "), gbc);
textFieldSearch = new JTextField(70);
textFieldSearch.addActionListener(eventHandler);
textFieldSearch.getDocument().addDocumentListener(eventHandler);
textFieldSearch.putClientProperty("JTextField.variant", "search");
gbc = new java.awt.GridBagConstraints();
gbc.weightx = 1.0;
gbc.gridx = 1;
gbc.gridy = gridy;
gbc.gridwidth = 3;
gbc.anchor = GridBagConstraints.LINE_START;
gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 0, 4, 4);
add(textFieldSearch, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 4;
gbc.gridy = gridy;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 10);
add(totalSpeciesLabel, gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
// gbc.weightx = 1.0;
gbc.gridwidth = 8;
gbc.anchor = GridBagConstraints.LINE_END;
gbc.fill = java.awt.GridBagConstraints.BOTH;
gbc.insets = new Insets(4, 4, 4, 4);
add(containerOfScrollPanel, gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.weightx = 1.0;
gbc.gridwidth = 2;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
add(getSpeciesFileLocationPanel(), gbc);
// // button to copy to clipboard the content of the JTextField.
// // TODO: do not delete! this is how it's done
// JButton buttonCopy = new JButton("Copy");
// buttonCopy.setToolTipText("Copy to clipboard the species file path");
// buttonCopy.addActionListener(new ActionListener() {
// public void actionPerformed(ActionEvent le) {
// if(speciesFileLocationTextField.getSelectionStart() == speciesFileLocationTextField.getSelectionEnd()) {
// speciesFileLocationTextField.setSelectionStart(0);
// speciesFileLocationTextField.setSelectionEnd(speciesFileLocationTextField.getText().length());
// }
// speciesFileLocationTextField.copy();
// speciesFileLocationTextField.setSelectionStart(0);
// speciesFileLocationTextField.setSelectionEnd(0);
// }
// });
// gbc = new GridBagConstraints();
// gbc.gridx = 4;
// gbc.gridy = gridy;
// gbc.fill = java.awt.GridBagConstraints.HORIZONTAL;
// gbc.insets = new Insets(4,4,4,4);
// add(buttonCopy, gbc);
// rendering the small shapes of the flattened species in the Depiction column of this viewer table)
DefaultScrollTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
SpeciesPatternSmallShape spss = null;
@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 (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == tableModel) {
selectedObject = tableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof GeneratedSpeciesTableRow) {
SpeciesContext sc = ((GeneratedSpeciesTableRow) selectedObject).species;
if (sc == null || sc.getSpeciesPattern() == null) {
spss = null;
} else {
SpeciesPattern sp = sc.getSpeciesPattern();
Graphics panelContext = table.getGraphics();
spss = new SpeciesPatternSmallShape(4, 2, sp, panelContext, sc, isSelected, issueManager);
}
}
} else {
spss = null;
}
}
setText("");
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (spss != null) {
spss.paintSelf(g);
}
}
};
table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setPreferredWidth(400);
table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDepiction).setMinWidth(400);
table.getColumnModel().getColumn(OutputSpeciesResultsTableModel.iColDefinition).setPreferredWidth(30);
table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.
the class IssueTableModel method getSourceObjectPathDescription.
private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
VCAssert.assertValid(issue);
Object source = issue.getSource();
{
IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
if (io != null) {
return io.getDescription();
}
}
if (vcDocument instanceof BioModel) {
BioModel bioModel = (BioModel) vcDocument;
String description = "";
if (source instanceof SymbolTableEntry) {
if (source instanceof SpeciesContext) {
description = "Model / Species";
} else if (source instanceof RbmObservable) {
description = "Model / Observables";
} else {
description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
}
} else if (source instanceof MolecularType) {
description = "Model / Molecules";
} else if (source instanceof ReactionStep) {
ReactionStep reactionStep = (ReactionStep) source;
description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
} else if (source instanceof ReactionRule) {
ReactionRule reactionRule = (ReactionRule) source;
description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
} else if (source instanceof SpeciesPattern) {
// if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
// description = "Model / Species";
// }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
// ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
// description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
// }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
// description = "Model / Observables";
// } else {
System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
description = ((SpeciesPattern) source).toString();
// }
} else if (source instanceof Structure) {
Structure structure = (Structure) source;
description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
} else if (source instanceof StructureMapping) {
StructureMapping structureMapping = (StructureMapping) source;
description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
} else if (source instanceof OutputFunctionIssueSource) {
SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
} else if (source instanceof Simulation) {
Simulation simulation = (Simulation) source;
try {
SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
description = "App(" + simulationContext.getName() + ") / Simulations";
} catch (ObjectNotFoundException e) {
e.printStackTrace();
description = "App(" + "unknown" + ") / Simulations";
}
} else if (source instanceof UnmappedGeometryClass) {
UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
} else if (source instanceof GeometryContext) {
description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
} else if (source instanceof ModelOptimizationSpec) {
description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
} else if (source instanceof MicroscopeMeasurement) {
description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
} else if (source instanceof SpatialObject) {
description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
} else if (source instanceof SpatialProcess) {
description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
} else if (source instanceof SpeciesContextSpec) {
SpeciesContextSpec scs = (SpeciesContextSpec) source;
description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
} else if (source instanceof ReactionCombo) {
ReactionCombo rc = (ReactionCombo) source;
description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
} else if (source instanceof RbmModelContainer) {
IssueCategory ic = issue.getCategory();
switch(ic) {
case RbmMolecularTypesTableBad:
description = "Model / " + MolecularType.typeName + "s";
break;
case RbmReactionRulesTableBad:
description = "Model / Reactions";
break;
case RbmObservablesTableBad:
description = "Model / Observables";
break;
case RbmNetworkConstraintsBad:
description = "Network Constrains";
break;
default:
description = "Model";
break;
}
} else if (source instanceof SimulationContext) {
SimulationContext sc = (SimulationContext) source;
IssueCategory ic = issue.getCategory();
switch(ic) {
case RbmNetworkConstraintsBad:
description = "Specifications / Network";
break;
default:
description = "Application";
break;
}
} else if (source instanceof Model) {
description = "Model";
} else if (source instanceof BioEvent) {
return "Protocols / Events";
} else if (source instanceof MathDescription) {
return "Math Description";
} else {
System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
}
return description;
} else if (vcDocument instanceof MathModel) {
if (source instanceof Geometry) {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
} else if (source instanceof OutputFunctionIssueSource) {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
} else if (source instanceof Simulation) {
return "Simulation(" + ((Simulation) source).getName() + ")";
} else {
return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
}
} else {
System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
return "";
}
}
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