Example 21 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class InitialConditionsPanel method initialize.
/**
* Initialize the class.
*/
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void initialize() {
try {
// user code begin {1}
// user code end
setName("InitialConditionsPanel");
setLayout(new BorderLayout());
add(getRadioButtonAndCheckboxPanel(), BorderLayout.NORTH);
add(getScrollPaneTable().getEnclosingScrollPane(), BorderLayout.CENTER);
getScrollPaneTable().getSelectionModel().addListSelectionListener(ivjEventHandler);
getJMenuItemPaste().addActionListener(ivjEventHandler);
getJMenuItemCopy().addActionListener(ivjEventHandler);
getJMenuItemCopyAll().addActionListener(ivjEventHandler);
getJMenuItemPasteAll().addActionListener(ivjEventHandler);
getAmountRadioButton().addActionListener(ivjEventHandler);
getConcentrationRadioButton().addActionListener(ivjEventHandler);
getRandomizeInitCondnCheckbox().addActionListener(ivjEventHandler);
DefaultTableCellRenderer renderer = new DefaultScrollTableCellRenderer() {
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
setIcon(null);
defaultToolTipText = null;
if (value instanceof Species) {
setText(((Species) value).getCommonName());
defaultToolTipText = getText();
setToolTipText(defaultToolTipText);
} else if (value instanceof SpeciesContext) {
setText(((SpeciesContext) value).getName());
defaultToolTipText = getText();
setToolTipText(defaultToolTipText);
} else if (value instanceof Structure) {
setText(((Structure) value).getName());
defaultToolTipText = getText();
setToolTipText(defaultToolTipText);
} else if (value instanceof ScopedExpression) {
SpeciesContextSpec scSpec = tableModel.getValueAt(row);
VCUnitDefinition unit = null;
if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_INITIAL.label)) {
SpeciesContextSpecParameter initialConditionParameter = scSpec.getInitialConditionParameter();
unit = initialConditionParameter.getUnitDefinition();
} else if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_DIFFUSION.label)) {
SpeciesContextSpecParameter diffusionParameter = scSpec.getDiffusionParameter();
unit = diffusionParameter.getUnitDefinition();
}
if (unit != null) {
setHorizontalTextPosition(JLabel.LEFT);
setIcon(new TextIcon("[" + unit.getSymbolUnicode() + "]", DefaultScrollTableCellRenderer.uneditableForeground));
}
int rgb = 0x00ffffff & DefaultScrollTableCellRenderer.uneditableForeground.getRGB();
defaultToolTipText = "<html>" + StringEscapeUtils.escapeHtml4(getText()) + " <font color=#" + Integer.toHexString(rgb) + "> [" + unit.getSymbolUnicode() + "] </font></html>";
setToolTipText(defaultToolTipText);
if (unit != null) {
setText(defaultToolTipText);
}
}
TableModel tableModel = table.getModel();
if (tableModel instanceof SortTableModel) {
DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
setHorizontalTextPosition(JLabel.TRAILING);
}
return this;
}
};
DefaultTableCellRenderer 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 SpeciesContextSpec) {
SpeciesContextSpec scs = (SpeciesContextSpec) selectedObject;
SpeciesContext sc = scs.getSpeciesContext();
// sp may be null for "plain" species contexts
SpeciesPattern sp = sc.getSpeciesPattern();
Graphics panelContext = table.getGraphics();
spss = new SpeciesPatternSmallShape(4, 2, sp, shapeManager, 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);
}
}
};
getScrollPaneTable().setDefaultRenderer(SpeciesContext.class, renderer);
getScrollPaneTable().setDefaultRenderer(Structure.class, renderer);
getScrollPaneTable().setDefaultRenderer(SpeciesPattern.class, rbmSpeciesShapeDepictionCellRenderer);
getScrollPaneTable().setDefaultRenderer(Species.class, renderer);
getScrollPaneTable().setDefaultRenderer(ScopedExpression.class, renderer);
getScrollPaneTable().setDefaultRenderer(Boolean.class, new ScrollTableBooleanCellRenderer());
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
Also used :
VCellSortTableModel(cbit.vcell.client.desktop.biomodel.VCellSortTableModel)
SortTableModel(org.vcell.util.gui.sorttable.SortTableModel)
TextIcon(cbit.vcell.mapping.gui.StructureMappingTableRenderer.TextIcon)
SpeciesPatternSmallShape(cbit.vcell.graph.SpeciesPatternSmallShape)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
ScrollTableBooleanCellRenderer(org.vcell.util.gui.ScrollTable.ScrollTableBooleanCellRenderer)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
DefaultTableCellRenderer(javax.swing.table.DefaultTableCellRenderer)
Graphics(java.awt.Graphics)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
ScopedExpression(cbit.gui.ScopedExpression)
BorderLayout(java.awt.BorderLayout)
VCellSortTableModel(cbit.vcell.client.desktop.biomodel.VCellSortTableModel)
JTable(javax.swing.JTable)
DefaultScrollTableCellRenderer(org.vcell.util.gui.DefaultScrollTableCellRenderer)
Structure(cbit.vcell.model.Structure)
Species(cbit.vcell.model.Species)
TableModel(javax.swing.table.TableModel)
VCellSortTableModel(cbit.vcell.client.desktop.biomodel.VCellSortTableModel)
SortTableModel(org.vcell.util.gui.sorttable.SortTableModel)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
Example 22 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class InitialConditionsPanel method jMenuItemCopy_ActionPerformed.
/**
* Comment
*/
private void jMenuItemCopy_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
if (actionEvent.getSource() == getJMenuItemCopy() || actionEvent.getSource() == getJMenuItemCopyAll()) {
try {
//
// Copy Symbols and Values Init Conditions
//
int[] rows = null;
if (actionEvent.getSource() == getJMenuItemCopyAll()) {
rows = new int[getScrollPaneTable().getRowCount()];
for (int i = 0; i < rows.length; i += 1) {
rows[i] = i;
}
} else {
rows = getScrollPaneTable().getSelectedRows();
}
MathSymbolMapping msm = null;
try {
msm = getSimulationContext().createNewMathMapping().getMathSymbolMapping();
} catch (Exception e) {
e.printStackTrace(System.out);
DialogUtils.showWarningDialog(this, "current math not valid, some paste operations will be limited\n\nreason: " + e.getMessage());
}
StringBuffer sb = new StringBuffer();
sb.append("initial Conditions Parameters for (BioModel)" + getSimulationContext().getBioModel().getName() + " (App)" + getSimulationContext().getName() + "\n");
java.util.Vector<SymbolTableEntry> primarySymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
java.util.Vector<SymbolTableEntry> alternateSymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
java.util.Vector<Expression> resolvedValuesV = new java.util.Vector<Expression>();
for (int i = 0; i < rows.length; i += 1) {
SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
if (scs.isConstant()) {
// need to change
primarySymbolTableEntriesV.add(scs.getInitialConditionParameter());
if (msm != null) {
alternateSymbolTableEntriesV.add(msm.getVariable(scs.getSpeciesContext()));
} else {
alternateSymbolTableEntriesV.add(null);
}
resolvedValuesV.add(new Expression(scs.getInitialConditionParameter().getExpression()));
sb.append(scs.getSpeciesContext().getName() + "\t" + scs.getInitialConditionParameter().getName() + "\t" + scs.getInitialConditionParameter().getExpression().infix() + "\n");
} else {
for (int j = 0; j < scs.getParameters().length; j += 1) {
SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[j];
if (VCellCopyPasteHelper.isSCSRoleForDimension(scsp.getRole(), getSimulationContext().getGeometry().getDimension())) {
Expression scspExpression = scsp.getExpression();
sb.append(scs.getSpeciesContext().getName() + "\t" + scsp.getName() + "\t" + (scspExpression != null ? scspExpression.infix() : "") + "\n");
if (scspExpression != null) {
// "Default" boundary conditions can't be copied
primarySymbolTableEntriesV.add(scsp);
if (msm != null) {
alternateSymbolTableEntriesV.add(msm.getVariable(scsp));
} else {
alternateSymbolTableEntriesV.add(null);
}
resolvedValuesV.add(new Expression(scspExpression));
}
}
}
}
}
//
// Send to clipboard
//
VCellTransferable.ResolvedValuesSelection rvs = new VCellTransferable.ResolvedValuesSelection((SymbolTableEntry[]) BeanUtils.getArray(primarySymbolTableEntriesV, SymbolTableEntry.class), (SymbolTableEntry[]) BeanUtils.getArray(alternateSymbolTableEntriesV, SymbolTableEntry.class), (Expression[]) BeanUtils.getArray(resolvedValuesV, Expression.class), sb.toString());
VCellTransferable.sendToClipboard(rvs);
} catch (Throwable e) {
PopupGenerator.showErrorDialog(InitialConditionsPanel.this, "InitialConditionsPanel Copy failed. " + e.getMessage(), e);
}
}
}
Also used :
VCellTransferable(cbit.vcell.desktop.VCellTransferable)
MathSymbolMapping(cbit.vcell.mapping.MathSymbolMapping)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
ScopedExpression(cbit.gui.ScopedExpression)
Expression(cbit.vcell.parser.Expression)
Vector(java.util.Vector)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
Example 23 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class SimulationContextDbDriver method assignSpeciesContextSpecsSQL.
/**
* This method was created in VisualAge.
* @param simContextKey cbit.sql.KeyValue
* @param simContext cbit.vcell.mapping.SimulationContext
*/
private void assignSpeciesContextSpecsSQL(Connection con, KeyValue simContextKey, SimulationContext simContext) throws SQLException, DataAccessException {
String sql;
sql = " SELECT " + "*" + " FROM " + speciesContextSpecTable.getTableName() + " WHERE " + speciesContextSpecTable.simContextRef + " = " + simContextKey + " ORDER BY " + speciesContextSpecTable.id;
Statement stmt = con.createStatement();
Boolean bUseConcentration = null;
try {
ResultSet rset = stmt.executeQuery(sql);
while (rset.next()) {
KeyValue speciesContextRef = new KeyValue(rset.getBigDecimal(speciesContextSpecTable.specContextRef.toString()));
// KeyValue simContextRef = new KeyValue(rset.getBigDecimal(speciesContextSpecTable.simContextRef.toString()));
boolean bEnableDiffusing = rset.getBoolean(speciesContextSpecTable.bEnableDif.toString());
boolean bForceConstant = rset.getBoolean(speciesContextSpecTable.bForceConst.toString());
// boolean bForceIndep = rset.getBoolean(speciesContextSpecTable.bForceIndep.toString());
String initCondConcExpS = null;
String initCondCountExpS = null;
initCondConcExpS = rset.getString(speciesContextSpecTable.initCondExp.toString());
if (rset.wasNull()) {
initCondConcExpS = null;
initCondCountExpS = rset.getString(speciesContextSpecTable.initCondCountExp.toString());
if (rset.wasNull()) {
throw new DataAccessException("Not expecting both initialCondition expressions types to be NULL");
}
if (bUseConcentration == null) {
bUseConcentration = false;
} else if (bUseConcentration) {
throw new DataAccessException("Not expecting both Concentration and Count in initialConditions");
}
} else {
if (bUseConcentration == null) {
bUseConcentration = true;
} else if (!bUseConcentration) {
throw new DataAccessException("Not expecting both Concentration and Count in initialConditions");
}
}
String diffRateString = rset.getString(speciesContextSpecTable.diffRateExp.toString());
String boundaryXmString = rset.getString(speciesContextSpecTable.boundaryXmExp.toString());
if (rset.wasNull()) {
boundaryXmString = null;
}
String boundaryXpString = rset.getString(speciesContextSpecTable.boundaryXpExp.toString());
if (rset.wasNull()) {
boundaryXpString = null;
}
String boundaryYmString = rset.getString(speciesContextSpecTable.boundaryYmExp.toString());
if (rset.wasNull()) {
boundaryYmString = null;
}
String boundaryYpString = rset.getString(speciesContextSpecTable.boundaryYpExp.toString());
if (rset.wasNull()) {
boundaryYpString = null;
}
String boundaryZmString = rset.getString(speciesContextSpecTable.boundaryZmExp.toString());
if (rset.wasNull()) {
boundaryZmString = null;
}
String boundaryZpString = rset.getString(speciesContextSpecTable.boundaryZpExp.toString());
if (rset.wasNull()) {
boundaryZpString = null;
}
String velocityXString = rset.getString(speciesContextSpecTable.velocityXExp.toString());
if (rset.wasNull()) {
velocityXString = null;
}
String velocityYString = rset.getString(speciesContextSpecTable.velocityYExp.toString());
if (rset.wasNull()) {
velocityYString = null;
}
String velocityZString = rset.getString(speciesContextSpecTable.velocityZExp.toString());
if (rset.wasNull()) {
velocityZString = null;
}
String wellMixedString = rset.getString(speciesContextSpecTable.bWellMixed.toString());
if (rset.wasNull()) {
wellMixedString = null;
}
String forceContinuousString = rset.getString(speciesContextSpecTable.bForceContinuous.toString());
if (rset.wasNull()) {
forceContinuousString = null;
}
//
SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec scs = speciesContextSpecs[i];
if (scs.getSpeciesContext().getKey().compareEqual(speciesContextRef)) {
try {
// scs.setEnableDiffusing(bEnableDiffusing);
scs.setConstant(bForceConstant);
if (initCondConcExpS != null) {
scs.getInitialConcentrationParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(initCondConcExpS)));
scs.getInitialCountParameter().setExpression(null);
} else {
scs.getInitialCountParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(initCondCountExpS)));
scs.getInitialConcentrationParameter().setExpression(null);
}
scs.getDiffusionParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(diffRateString)));
if (boundaryXmString != null) {
scs.getBoundaryXmParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(boundaryXmString)));
} else {
scs.getBoundaryXmParameter().setExpression(null);
}
if (boundaryXpString != null) {
scs.getBoundaryXpParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(boundaryXpString)));
} else {
scs.getBoundaryXpParameter().setExpression(null);
}
if (boundaryYmString != null) {
scs.getBoundaryYmParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(boundaryYmString)));
} else {
scs.getBoundaryYmParameter().setExpression(null);
}
if (boundaryYpString != null) {
scs.getBoundaryYpParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(boundaryYpString)));
} else {
scs.getBoundaryYpParameter().setExpression(null);
}
if (boundaryZmString != null) {
scs.getBoundaryZmParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(boundaryZmString)));
} else {
scs.getBoundaryZmParameter().setExpression(null);
}
if (boundaryZpString != null) {
scs.getBoundaryZpParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(boundaryZpString)));
} else {
scs.getBoundaryZpParameter().setExpression(null);
}
if (velocityXString != null) {
scs.getVelocityXParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(velocityXString)));
} else {
scs.getVelocityXParameter().setExpression(null);
}
if (velocityYString != null) {
scs.getVelocityYParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(velocityYString)));
} else {
scs.getVelocityYParameter().setExpression(null);
}
if (velocityZString != null) {
scs.getVelocityZParameter().setExpression(new Expression(TokenMangler.getSQLRestoredString(velocityZString)));
} else {
scs.getVelocityZParameter().setExpression(null);
}
if (wellMixedString != null) {
int value = Integer.parseInt(wellMixedString);
if (value != 0 && value != 1) {
throw new DataAccessException("unexpected value for bSpatial column in SimulationCOntextDbDriver: \"" + wellMixedString + "\", expecting 0 or 1");
}
boolean bWellMixed = (value == 1) ? true : false;
scs.setWellMixed(bWellMixed);
}
if (forceContinuousString != null) {
int value = Integer.parseInt(forceContinuousString);
if (value != 0 && value != 1) {
throw new DataAccessException("unexpected value for bForceContinuous column in SimulationCOntextDbDriver: \"" + forceContinuousString + "\", expecting 0 or 1");
}
boolean bForceContinuous = (value == 1) ? true : false;
scs.setForceContinuous(bForceContinuous);
}
} catch (Exception e) {
throw new DataAccessException("Error setting SpeciesContextSpec info for SimulationContext:" + simContext.getVersion().getName() + " id=" + simContextKey);
}
break;
}
}
}
} finally {
stmt.close();
}
if (bUseConcentration != null) {
simContext.setUsingConcentration(bUseConcentration);
}
}
Also used :
KeyValue(org.vcell.util.document.KeyValue)
Expression(cbit.vcell.parser.Expression)
PreparedStatement(java.sql.PreparedStatement)
Statement(java.sql.Statement)
ResultSet(java.sql.ResultSet)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
DataAccessException(org.vcell.util.DataAccessException)
PropertyVetoException(java.beans.PropertyVetoException)
DependencyException(org.vcell.util.DependencyException)
RecordChangedException(cbit.sql.RecordChangedException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
PermissionException(org.vcell.util.PermissionException)
ObjectNotFoundException(org.vcell.util.ObjectNotFoundException)
IllegalMappingException(cbit.vcell.mapping.IllegalMappingException)
SQLException(java.sql.SQLException)
DataAccessException(org.vcell.util.DataAccessException)
ExpressionException(cbit.vcell.parser.ExpressionException)
MappingException(cbit.vcell.mapping.MappingException)
MathException(cbit.vcell.math.MathException)
Example 24 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class InitialConditionsPanel method jMenuItemPaste_ActionPerformed.
/**
* Comment
*/
private void jMenuItemPaste_ActionPerformed(final java.awt.event.ActionEvent actionEvent) {
final Vector<String> pasteDescriptionsV = new Vector<String>();
final Vector<Expression> newExpressionsV = new Vector<Expression>();
final Vector<SpeciesContextSpec.SpeciesContextSpecParameter> changedParametersV = new Vector<SpeciesContextSpec.SpeciesContextSpecParameter>();
AsynchClientTask task1 = new AsynchClientTask("validating", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
MathSymbolMapping msm = null;
Exception mathMappingException = null;
try {
MathMapping mm = null;
mm = getSimulationContext().createNewMathMapping();
msm = mm.getMathSymbolMapping();
} catch (Exception e) {
mathMappingException = e;
e.printStackTrace(System.out);
}
int[] rows = null;
if (actionEvent.getSource() == getJMenuItemPasteAll()) {
rows = new int[getScrollPaneTable().getRowCount()];
for (int i = 0; i < rows.length; i += 1) {
rows[i] = i;
}
} else {
rows = getScrollPaneTable().getSelectedRows();
}
//
// Check paste
//
StringBuffer errors = null;
for (int i = 0; i < rows.length; i += 1) {
SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
try {
if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
SpeciesContextSpec.SpeciesContextSpecParameter pasteDestination = null;
SpeciesContextSpec.SpeciesContextSpecParameter clipboardBiologicalParameter = null;
if (rvs.getPrimarySymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getPrimarySymbolTableEntries()[j];
} else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getAlternateSymbolTableEntries()[j];
}
if (clipboardBiologicalParameter == null) {
Variable pastedMathVariable = null;
if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
} else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
}
if (pastedMathVariable != null) {
if (msm == null) {
throw mathMappingException;
}
Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
if (localMathVariable == null) {
// try if localMathVariable is a speciesContext init parameter
String initSuffix = DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX + TokenMangler.fixTokenStrict(scs.getInitialConcentrationParameter().getUnitDefinition().getSymbol());
localMathVariable = msm.findVariableByName(pastedMathVariable.getName() + initSuffix);
}
if (localMathVariable != null) {
SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
if (localBiologicalSymbolArr[k] instanceof SpeciesContext && scs.getSpeciesContext() == localBiologicalSymbolArr[k]) {
// need to change
pasteDestination = scs.getInitialConditionParameter();
} else if (localBiologicalSymbolArr[k] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
for (int l = 0; l < scs.getParameters().length; l += 1) {
if (scs.getParameters()[l] == localBiologicalSymbolArr[k]) {
pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) localBiologicalSymbolArr[k];
break;
}
}
}
if (pasteDestination != null) {
break;
}
}
}
}
} else {
for (int k = 0; k < scs.getParameters().length; k += 1) {
SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[k];
if (scsp.getRole() == clipboardBiologicalParameter.getRole() && scs.getSpeciesContext().compareEqual(((SpeciesContextSpec) clipboardBiologicalParameter.getNameScope().getScopedSymbolTable()).getSpeciesContext())) {
pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) scsp;
}
}
}
if (pasteDestination != null) {
changedParametersV.add(pasteDestination);
newExpressionsV.add(rvs.getExpressionValues()[j]);
pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(scs.getSpeciesContext().getName(), pasteDestination.getName(), pasteDestination.getExpression().infix(), rvs.getExpressionValues()[j].infix()));
}
}
}
} catch (Throwable e) {
if (errors == null) {
errors = new StringBuffer();
}
errors.append(scs.getSpeciesContext().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n\n");
}
}
if (errors != null) {
throw new Exception(errors.toString());
}
}
}
};
AsynchClientTask task2 = new AsynchClientTask("pasting", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
// Do paste
if (pasteDescriptionsV.size() > 0) {
String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
pasteDescriptionsV.copyInto(pasteDescriptionArr);
SpeciesContextSpec.SpeciesContextSpecParameter[] changedParametersArr = new SpeciesContextSpec.SpeciesContextSpecParameter[changedParametersV.size()];
changedParametersV.copyInto(changedParametersArr);
Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
newExpressionsV.copyInto(newExpressionsArr);
VCellCopyPasteHelper.chooseApplyPaste(InitialConditionsPanel.this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
} else {
PopupGenerator.showInfoDialog(InitialConditionsPanel.this, "No paste items match the destination (no changes made).");
}
}
};
ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}
Also used :
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
Variable(cbit.vcell.math.Variable)
VCellTransferable(cbit.vcell.desktop.VCellTransferable)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
Vector(java.util.Vector)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
Hashtable(java.util.Hashtable)
MathSymbolMapping(cbit.vcell.mapping.MathSymbolMapping)
ScopedExpression(cbit.gui.ScopedExpression)
Expression(cbit.vcell.parser.Expression)
DiffEquMathMapping(cbit.vcell.mapping.DiffEquMathMapping)
MathMapping(cbit.vcell.mapping.MathMapping)
Example 25 with SpeciesContextSpec
use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.
the class SpeciesContextSpecPanel method onSelectedObjectsChange.
@Override
protected void onSelectedObjectsChange(Object[] selectedObjects) {
SpeciesContextSpec speciesContextSpec = null;
if (selectedObjects != null && selectedObjects.length == 1 && selectedObjects[0] instanceof SpeciesContextSpec) {
speciesContextSpec = (SpeciesContextSpec) selectedObjects[0];
}
setSpeciesContextSpec(speciesContextSpec);
}
Also used :
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
Aggregations
SpeciesContextSpec (cbit.vcell.mapping.SpeciesContextSpec)58
Expression (cbit.vcell.parser.Expression)33
SpeciesContext (cbit.vcell.model.SpeciesContext)28
SimulationContext (cbit.vcell.mapping.SimulationContext)23
Model (cbit.vcell.model.Model)21
BioModel (cbit.vcell.biomodel.BioModel)19
StructureMapping (cbit.vcell.mapping.StructureMapping)17
ReactionStep (cbit.vcell.model.ReactionStep)16
Simulation (cbit.vcell.solver.Simulation)13
ReactionSpec (cbit.vcell.mapping.ReactionSpec)12
SpeciesContextSpecParameter (cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)12
KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)12
Structure (cbit.vcell.model.Structure)12
ExpressionException (cbit.vcell.parser.ExpressionException)12
MathDescription (cbit.vcell.math.MathDescription)11
ModelParameter (cbit.vcell.model.Model.ModelParameter)11
FeatureMapping (cbit.vcell.mapping.FeatureMapping)10
SpeciesContextMapping (cbit.vcell.mapping.SpeciesContextMapping)10
Feature (cbit.vcell.model.Feature)10
Parameter (cbit.vcell.model.Parameter)10
