Created new class CastingUtils, and moved appropriate calls from Bean…

…Utils to CastingUtils. Additionally, small changes to some remaining functions in BeanUtils.
virtualcell · Nov 8, 2023 · 035dc9b · 035dc9b
1 parent 3c12cb2
commit 035dc9b
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Showing 33 changed files with 872 additions and 1,023 deletions.
diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/VCDocumentDecorator.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/VCDocumentDecorator.java
@@ -9,11 +9,8 @@
 import java.util.Objects;
 import java.util.Set;
 
-import org.vcell.util.BeanUtils;
-import org.vcell.util.Issue;
+import org.vcell.util.*;
 import org.vcell.util.Issue.IssueCategory;
-import org.vcell.util.IssueContext;
-import org.vcell.util.ProgrammingException;
 import org.vcell.util.document.VCDocument;
 
 import cbit.vcell.biomodel.BioModel;
@@ -277,7 +274,7 @@ void setSolverDescription(SolverDescription sd) {
 
 		@Override
 		public void activateView(SelectionManager selectionManager) {
-			SimulationContext sc = BeanUtils.downcast(SimulationContext.class, simulation.getSimulationOwner());
+			SimulationContext sc = CastingUtils.downcast(SimulationContext.class, simulation.getSimulationOwner());
 			Window activated = null;
 			if (sc != null ) {
 				ActiveView av = new ActiveView(sc, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.simulations);

diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/IssueTableModel.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/IssueTableModel.java
@@ -18,13 +18,10 @@
 import org.vcell.model.rbm.MolecularComponent;
 import org.vcell.model.rbm.MolecularType;
 import org.vcell.model.rbm.SpeciesPattern;
-import org.vcell.util.BeanUtils;
-import org.vcell.util.Issue;
+import org.vcell.util.*;
 import org.vcell.util.Issue.IssueCategory;
 import org.vcell.util.Issue.IssueOrigin;
 import org.vcell.util.Issue.Severity;
-import org.vcell.util.ObjectNotFoundException;
-import org.vcell.util.VCAssert;
 import org.vcell.util.document.VCDocument;
 import org.vcell.util.gui.GuiUtils;
 import org.vcell.util.gui.ScrollTable;
@@ -210,7 +207,7 @@ private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue
 		VCAssert.assertValid(issue);
 		Object source = issue.getSource();
 		{
-			IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
+			IssueOrigin io = CastingUtils.downcast(IssueOrigin.class, source);
 			if (io != null) {
 				return io.getDescription();
 			}
@@ -358,7 +355,7 @@ private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
 		if (vcDocument instanceof BioModel){
 			Object object = issue.getSource();
 			{
-				DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
+				DecoratedIssueSource dis = CastingUtils.downcast(DecoratedIssueSource.class, object);
 				if (dis != null) {
 					return dis.getSourcePath();
 				}

diff --git a/...l-client/src/main/java/cbit/vcell/client/desktop/simulation/SimulationListTableModel.java b/...l-client/src/main/java/cbit/vcell/client/desktop/simulation/SimulationListTableModel.java
@@ -214,12 +214,6 @@ public void propertyChange(java.beans.PropertyChangeEvent evt) {
 	}
 }
 
-
-/**
- * Insert the method's description here.
- * Creation date: (5/10/2004 6:32:09 PM)
- * @param newSimContext cbit.vcell.mapping.SimulationContext
- */
 public void setSimulationWorkspace(SimulationWorkspace newSimulationWorkspace) {
 	SimulationWorkspace oldValue = this.simulationWorkspace;
 	simulationWorkspace = newSimulationWorkspace;
@@ -282,7 +276,7 @@ public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
 										suggestedInterval = timeStep;
 										bValid = false;
 									} else {
-										if (!BeanUtils.isIntegerMultiple(outputTime, timeStep)) {
+										if (BeanUtils.isNotAnIntegerMultiple(outputTime, timeStep)) {
 											double n = outputTime/timeStep;
 											int intn = (int)Math.round(n);
 											suggestedInterval = (intn * timeStep);

diff --git a/vcell-client/src/main/java/cbit/vcell/client/task/ClientTaskDispatcher.java b/vcell-client/src/main/java/cbit/vcell/client/task/ClientTaskDispatcher.java
@@ -438,7 +438,7 @@ public void finished() {
 				}
 				if (lg.isInfoEnabled()) {
 					Object obj = hash.get(STACK_TRACE_ARRAY);
-					StackTraceElement ste[] = BeanUtils.downcast(StackTraceElement[].class, obj);
+					StackTraceElement ste[] = CastingUtils.downcast(StackTraceElement[].class, obj);
 					if (ste != null) {
 						String stackTraceString = StringUtils.join(ste,'\n');
 						lg.info(stackTraceString,(Throwable)hash.get(TASK_ABORTED_BY_ERROR));
@@ -641,7 +641,7 @@ private static void runTask(AsynchClientTask currentTask, Hashtable<String, Obje
 		String msg = "Thread " + Thread.currentThread().getName() + " calling task " + currentTask.getTaskName();
 		if (lg.isDebugEnabled()) {
 			Object obj = hash.get(STACK_TRACE_ARRAY);
-			StackTraceElement ste[] = BeanUtils.downcast(StackTraceElement[].class, obj);
+			StackTraceElement ste[] = CastingUtils.downcast(StackTraceElement[].class, obj);
 			if (ste != null) {
 				msg += '\n' + StringUtils.join(ste,'\n');
 			}

diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/OutputOptionsPanel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/OutputOptionsPanel.java
@@ -803,7 +803,7 @@ public boolean shouldYieldFocus(JComponent input) {
 						if (outputTime < timeStep) {
 							suggestedInterval = timeStep;
 							bValid = false;
-						} else if (!BeanUtils.isIntegerMultiple(outputTime, timeStep)) {
+						} else if (BeanUtils.isNotAnIntegerMultiple(outputTime, timeStep)) {
 							double n = outputTime/timeStep;
 							int intn = (int)Math.round(n);
 							if (intn != n) {

diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/TimeStepPanel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/TimeStepPanel.java
@@ -94,7 +94,7 @@ public void correctUniformOutputTimeStep() {
 			if (outputTime < timeStep) {
 				suggestedInterval = timeStep;
 				bValid = false;
-			} else if (!BeanUtils.isIntegerMultiple(outputTime, timeStep)){
+			} else if (BeanUtils.isNotAnIntegerMultiple(outputTime, timeStep)){
 				double n = outputTime/timeStep;
 				int intn = (int)Math.round(n);
 				if (intn != n) {
@@ -120,9 +120,9 @@ public void correctUniformOutputTimeStep() {
 public void setNewTimeStep() {
 	try {
 		TimeStep oldTimeStep = solverTaskDescription.getTimeStep();
-		double defaultTimeStep = !getDefaultTimeStepTextField().isEnabled() ? oldTimeStep.getDefaultTimeStep() : new Double(getDefaultTimeStepTextField().getText()).doubleValue();
-		double minTimeStep = !getMinimumTimeStepTextField().isEnabled() ? oldTimeStep.getMinimumTimeStep() : new Double(getMinimumTimeStepTextField().getText()).doubleValue();
-		double maxTimeStep = !getMaximumTimeStepTextField().isEnabled() ? oldTimeStep.getMaximumTimeStep() : new Double(getMaximumTimeStepTextField().getText()).doubleValue();
+		double defaultTimeStep = !getDefaultTimeStepTextField().isEnabled() ? oldTimeStep.getDefaultTimeStep() : Double.parseDouble(getDefaultTimeStepTextField().getText());
+		double minTimeStep = !getMinimumTimeStepTextField().isEnabled() ? oldTimeStep.getMinimumTimeStep() : Double.parseDouble(getMinimumTimeStepTextField().getText());
+		double maxTimeStep = !getMaximumTimeStepTextField().isEnabled() ? oldTimeStep.getMaximumTimeStep() : Double.parseDouble(getMaximumTimeStepTextField().getText());
 		TimeStep newTimeStep = new TimeStep(minTimeStep, defaultTimeStep, maxTimeStep);
 		solverTaskDescription.setTimeStep(newTimeStep);
 	} catch (java.lang.Throwable ivjExc) {
@@ -383,12 +383,6 @@ public void windowClosing(java.awt.event.WindowEvent e) {
 	}
 }
 
-/**
- * Sets the timeStep property (cbit.vcell.solver.TimeStep) value.
- * @param timeStep The new value for the property.
- * @exception java.beans.PropertyVetoException The exception description.
- * @see #getTimeStep
- */
 public void setSolverTaskDescription(SolverTaskDescription newValue) throws java.beans.PropertyVetoException {
 	SolverTaskDescription oldValue = solverTaskDescription;
 	/* Stop listening for events from the current object */

diff --git a/vcell-client/src/main/java/org/vcell/client/logicalwindow/LWNamespace.java b/vcell-client/src/main/java/org/vcell/client/logicalwindow/LWNamespace.java
@@ -18,9 +18,9 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.client.logicalwindow.LWHandle.LWModality;
-import org.vcell.util.BeanUtils;
 
 import edu.uchc.connjur.wb.ExecutionTrace;
+import org.vcell.util.CastingUtils;
 
 /**
  * utility methods for package
@@ -111,7 +111,7 @@ public static void stagger(Container reference, Window positioned) {
 	 */
 	public static <T> T findOwnerOfType(Class<? extends T> clzz,Component swingParent) {
 		final Logger lg = LGHolder.LG; 
-		T t = BeanUtils.downcast(clzz, swingParent);
+		T t = CastingUtils.downcast(clzz, swingParent);
 		if (t != null) {
 			return t;
 		}

diff --git a/vcell-client/src/main/java/org/vcell/util/gui/DialogUtils.java b/vcell-client/src/main/java/org/vcell/util/gui/DialogUtils.java
@@ -300,10 +300,10 @@ public static Dimension getScreenSize( ) {
 	private static void setInternalNotCancelEnabled(final JOptionPane jop,final  boolean bEnabled, boolean bClickOK) {
 		VCAssert.assertTrue(!bClickOK || bEnabled, "bEnabled must be true if bClickOK is true");
 	  	for(Component topLevel : jop.getComponents() ) {
-	  		Container cntr = BeanUtils.downcast(Container.class, topLevel); 
+	  		Container cntr = CastingUtils.downcast(Container.class, topLevel);
 	  		if (cntr != null) {
 	  			for (Component cmpt : cntr.getComponents()) {
-	  				JButton btn = BeanUtils.downcast(JButton.class, cmpt); 
+	  				JButton btn = CastingUtils.downcast(JButton.class, cmpt);
 	  				if (btn != null && !btn.getText().equalsIgnoreCase(getCancelText())) {
 				  		btn.setEnabled(bEnabled);
 					  	if(bEnabled && bClickOK) {
@@ -757,7 +757,7 @@ public static void showErrorDialog(final Component requester, final String messa
 				dialog.setVisible(true);
 				if (goingToEmail ) {
 					Object ro = pane.getValue( );
-					Integer reply = BeanUtils.downcast(Integer.class, ro);
+					Integer reply = CastingUtils.downcast(Integer.class, ro);
 					boolean userSaidYes = reply != null ? reply == JOptionPane.YES_OPTION : false;
 					if (userSaidYes) {
 						Throwable throwableToSend = exception; 

diff --git a/vcell-client/src/main/java/org/vcell/util/gui/GuiUtils.java b/vcell-client/src/main/java/org/vcell/util/gui/GuiUtils.java
@@ -33,7 +33,7 @@
 import javax.swing.tree.TreePath;
 
 import org.apache.commons.lang3.StringUtils;
-import org.vcell.util.BeanUtils;
+import org.vcell.util.CastingUtils;
 import org.vcell.util.ISize;
 
 import cbit.vcell.desktop.BioModelNode;
@@ -219,7 +219,7 @@ private static void prefSize(StringBuilder destination, int level, Component cmp
 		Dimension dim = cmpnt.getPreferredSize();
 		destination.append(StringUtils.repeat(' ', level) + ExecutionTrace.justClassName(cmpnt) + " prefers " + dim);
 		destination.append('\n');
-		Container container = BeanUtils.downcast(Container.class, cmpnt);
+		Container container = CastingUtils.downcast(Container.class, cmpnt);
 		if (container != null) {
 			for ( Component c : container.getComponents()) {
 				prefSize(destination, level + 1, c);
@@ -246,11 +246,11 @@ public static String getPreferredSizes(Component container) {
 	public static String describe(Window w) {
 		if (w != null) {
 			String className = ExecutionTrace.justClassName(w) + " ";
-			Frame f = BeanUtils.downcast(Frame.class, w);
+			Frame f = CastingUtils.downcast(Frame.class, w);
 			if (f != null) {
 				return className + f.getTitle();
 			}
-			Dialog d = BeanUtils.downcast(Dialog.class, w);
+			Dialog d = CastingUtils.downcast(Dialog.class, w);
 			if (d != null) {
 				return className + d.getTitle();
 			}

diff --git a/vcell-client/src/main/java/org/vcell/util/gui/IndefiniteProgressDialog.java b/vcell-client/src/main/java/org/vcell/util/gui/IndefiniteProgressDialog.java
@@ -28,7 +28,7 @@
 import javax.swing.Timer;
 
 import org.vcell.client.logicalwindow.LWContainerHandle;
-import org.vcell.util.BeanUtils;
+import org.vcell.util.CastingUtils;
 
 @SuppressWarnings("serial")
 
@@ -219,7 +219,7 @@ public void actionPerformed(ActionEvent arg0) {
 		private boolean isModelDialogPresent( ) {
 			for (Window w: Window.getWindows()) {
 				if (w.isShowing()) {
-					Dialog d = BeanUtils.downcast(Dialog.class, w);
+					Dialog d = CastingUtils.downcast(Dialog.class, w);
 					if (d != null && d != IndefiniteProgressDialog.this) {
 						switch (d.getModalityType()) {
 						case MODELESS:

diff --git a/vcell-client/src/main/java/org/vcell/util/gui/LinearDefiniteProgressDialog.java b/vcell-client/src/main/java/org/vcell/util/gui/LinearDefiniteProgressDialog.java
@@ -26,7 +26,7 @@
 import javax.swing.Timer;
 
 import org.vcell.client.logicalwindow.LWContainerHandle;
-import org.vcell.util.BeanUtils;
+import org.vcell.util.CastingUtils;
 
 @SuppressWarnings("serial")
 
@@ -251,7 +251,7 @@ public void actionPerformed(ActionEvent arg0) {
 		private boolean isModelDialogPresent( ) {
 			for (Window w: Window.getWindows()) {
 				if (w.isShowing()) {
-					Dialog d = BeanUtils.downcast(Dialog.class, w);
+					Dialog d = CastingUtils.downcast(Dialog.class, w);
 					if (d != null && d != LinearDefiniteProgressDialog.this) {
 						switch (d.getModalityType()) {
 						case MODELESS:

diff --git a/vcell-client/src/test/java/org/vcell/client/logicalwindow/TestPanel.java b/vcell-client/src/test/java/org/vcell/client/logicalwindow/TestPanel.java
@@ -7,7 +7,7 @@
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 
-import org.vcell.util.BeanUtils;
+import org.vcell.util.CastingUtils;
 import org.vcell.util.gui.DialogUtils;
 
 @SuppressWarnings("serial")
@@ -95,7 +95,7 @@ private void optionPaneDialogs( ) {
 		//		int r = JOptionPane.showConfirmDialog(this, "What say ye?","A question", JOptionPane.YES_NO_OPTION);
 		Object v = jop.getValue(); 
 		System.out.println(v);
-		Integer rval = BeanUtils.downcast(Integer.class, v);
+		Integer rval = CastingUtils.downcast(Integer.class, v);
 		if (rval != null) {
 			int r = rval;
 			switch (r) {

diff --git a/vcell-core/src/main/java/cbit/vcell/export/server/ASCIIExporter.java b/vcell-core/src/main/java/cbit/vcell/export/server/ASCIIExporter.java
@@ -25,11 +25,7 @@
 import org.apache.logging.log4j.Logger;
 import org.vcell.solver.smoldyn.SmoldynVCellMapper;
 import org.vcell.solver.smoldyn.SmoldynVCellMapper.SmoldynKeyword;
-import org.vcell.util.BeanUtils;
-import org.vcell.util.Coordinate;
-import org.vcell.util.DataAccessException;
-import org.vcell.util.NumberUtils;
-import org.vcell.util.VCAssert;
+import org.vcell.util.*;
 import org.vcell.util.document.TSJobResultsNoStats;
 import org.vcell.util.document.TimeSeriesJobSpec;
 import org.vcell.util.document.User;
@@ -1248,7 +1244,7 @@ private FileDataContainerID getSlice(SliceHelper sliceHelper, CartesianMesh mesh
 public Collection<ExportOutput >makeASCIIData(OutputContext outputContext,JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs,FileDataContainerManager fileDataContainerManager) 
 		throws DataAccessException, IOException {
 	FormatSpecificSpecs formatSpecs = exportSpecs.getFormatSpecificSpecs( );
-	ASCIISpecs asciiSpecs = BeanUtils.downcast(ASCIISpecs.class, formatSpecs);
+	ASCIISpecs asciiSpecs = CastingUtils.downcast(ASCIISpecs.class, formatSpecs);
 	if (asciiSpecs != null) {
 		switch (asciiSpecs.getDataType()) {
 		case PDE_VARIABLE_DATA: