lphystudio.app.graphicalmodelpanel.GraphicalModelPanel Maven / Gradle / Ivy
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The GUI for LPhy language.
The newest version!
package lphystudio.app.graphicalmodelpanel;
import jebl.evolution.sequences.SequenceType;
import lphy.core.codebuilder.CanonicalCodeBuilder;
import lphy.core.logger.LoggerUtils;
import lphy.core.model.*;
import lphy.core.parser.LPhyParserDictionary;
import lphy.core.parser.graphicalmodel.GraphicalModel;
import lphy.core.parser.graphicalmodel.GraphicalModelListener;
import lphy.core.simulator.Sampler;
import lphy.core.simulator.SimulatorListener;
import lphy.core.vectorization.VectorizedFunction;
import lphystudio.app.alignmentcomponent.AlignmentComponent;
import lphystudio.app.alignmentcomponent.SequenceTypePanel;
import lphystudio.app.graphicalmodelcomponent.GraphicalModelComponent;
import lphystudio.app.graphicalmodelcomponent.interactive.InteractiveGraphicalModelComponent;
import lphystudio.app.treecomponent.TimeTreeComponent;
import lphystudio.app.treecomponent.TimeTreeExtraPlotComponent;
import lphystudio.core.codecolorizer.LineCodeColorizer;
import lphystudio.core.editor.UndoManagerHelper;
import lphystudio.core.layeredgraph.Layering;
import lphystudio.core.swing.TidyComboBox;
import lphystudio.core.swing.TidyTextField;
import lphystudio.core.valueeditor.Abstract2DEditor;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
/**
* The main panel to include prob graphical model,
* views {@link ViewerPane}, and command line console {@link StudioConsoleInterpreter}.
*/
public class GraphicalModelPanel extends JPanel {
GraphicalModelComponent component;
StudioConsoleInterpreter modelInterpreter;
StudioConsoleInterpreter dataInterpreter;
// default interpreter for console is model tab
final String DEFAULT_INTERPRETER = GraphicalModel.Context.model.toString();
JTabbedPane leftPane;
ViewerPane rightPane;
JToolBar toolbar;
JLabel repsLabel = new JLabel("reps:");
JTextField repsField = new TidyTextField("1", 4);
JButton sampleButton = new JButton("Sample");
JCheckBox showConstantNodes = new JCheckBox("Show constants");
JComboBox layeringAlgorithm = new TidyComboBox<>(new Layering[]{
new Layering.LongestPathFromSinks(), new Layering.LongestPathFromSources()
});
//TODO https://github.com/LinguaPhylo/linguaPhylo/issues/307
// JCheckBox editValues = new JCheckBox("Edit values");
JSplitPane horizSplitPane;
JSplitPane verticalSplitPane;
Object displayedElement;
// Sampler sampler;
CanonicalCodeBuilder codeBuilder = new CanonicalCodeBuilder();
public GraphicalModelPanel(GraphicalModelParserDictionary parser, UndoManagerHelper undoManagerHelper) {
dataInterpreter = new StudioConsoleInterpreter(parser, LPhyParserDictionary.Context.data, undoManagerHelper);
modelInterpreter = new StudioConsoleInterpreter(parser, LPhyParserDictionary.Context.model, undoManagerHelper);
component = new GraphicalModelComponent(parser);
JPanel buttonPanel = new JPanel();
buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.LINE_AXIS));
layeringAlgorithm.addActionListener(new AbstractAction() {
@Override
public void actionPerformed(ActionEvent e) {
component.setLayering((Layering) layeringAlgorithm.getSelectedItem());
}
});
layeringAlgorithm.setPreferredSize(new Dimension(200, 20));
buttonPanel.add(repsLabel);
buttonPanel.add(repsField);
buttonPanel.add(sampleButton);
buttonPanel.add(new JLabel(" Layering:"));
buttonPanel.add(layeringAlgorithm);
buttonPanel.add(showConstantNodes);
// buttonPanel.add(editValues);
sampleButton.addActionListener(e -> sample(getReps()));
showConstantNodes.addActionListener(new AbstractAction() {
@Override
public void actionPerformed(ActionEvent e) {
component.setShowConstantNodes(showConstantNodes.isSelected());
// editValues.setEnabled(showConstantNodes.isSelected());
}
});
showConstantNodes.setSelected(component.getShowConstantNodes());
// editValues.addActionListener(new AbstractAction() {
// @Override
// public void actionPerformed(ActionEvent e) {
// // avoid GraphicalModelComponent depends on GraphicalModelPanel
// component.setEditValues(editValues.isSelected());
// // update currentSelectionContainer
// // take care of selectedNode here, and the rest will update by showObject(...)
// LayeredNode selectedNode = component.getSelectedNode();
// if (selectedNode instanceof LayeredGNode lnode) {
// if (lnode.value() instanceof Value value) {
// showValue(value, false);
// }
// }
// component.repaint();
// }
// });
// editValues.setSelected(component.getEditValues());
// editValues.setToolTipText("Please click Sample button to refresh variables after setting a new value.");
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel, BoxLayout.PAGE_AXIS));
panel.add(component);
panel.add(buttonPanel);
setLayout(new BorderLayout());
GraphicalModelListener listener = new GraphicalModelListener() {
@Override
public void valueSelected(Value value) {
showValue(value);
}
@Override
public void generativeDistributionSelected(GenerativeDistribution g) {
showParameterized(g);
}
@Override
public void functionSelected(DeterministicFunction f) {
showParameterized(f);
}
@Override
public void layout() {
}
};
component.addGraphicalModelListener(listener);
parser.addGraphicalModelChangeListener(component);
//TODO need a new way to deal with this model listener interaction
// parser.addGraphicalModelListener(new GraphicalModelListener() {
// @Override
// public void valueSelected(Value value) {
//
// showValue(value);
// }
//
// @Override
// public void generativeDistributionSelected(GenerativeDistribution g) {
//
// }
//
// @Override
// public void functionSelected(DeterministicFunction f) {
//
// }
// });
rightPane = new ViewerPane(parser, component);
//rightPane.addTab("New Random Variable", new NewRandomVariablePanel(modelInterpreter, ParserUtils.getGenerativeDistributions()));
leftPane = new JTabbedPane();
leftPane.addTab("AutoLayout", panel);
leftPane.addTab("Interactive", new InteractiveGraphicalModelComponent(parser, component));
horizSplitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, leftPane, rightPane);
horizSplitPane.setResizeWeight(0.5);
// horizSplitPane.setOneTouchExpandable(true);
horizSplitPane.setContinuousLayout(true);
JTabbedPane interpreterPane = new JTabbedPane();
interpreterPane.add("data", dataInterpreter);
interpreterPane.add("model", modelInterpreter);
// set default model or model interpreter
if (DEFAULT_INTERPRETER.equals(GraphicalModel.Context.model.toString())) {
interpreterPane.setSelectedComponent(modelInterpreter);
} else {
interpreterPane.setSelectedComponent(dataInterpreter);
}
verticalSplitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, horizSplitPane, interpreterPane);
verticalSplitPane.setResizeWeight(0.75);
// verticalSplitPane.setOneTouchExpandable(true);
verticalSplitPane.setContinuousLayout(true);
add(verticalSplitPane, BorderLayout.CENTER);
if (parser.getModelSinks().size() > 0) {
showValue(parser.getModelSinks().iterator().next());
}
}
// public Sampler getSampler() {
// return this.sampler;
// }
/**
* This is duplicated to {@link LPhyParserDictionary#source(BufferedReader, String[])},
* but has extra code using {@link LineCodeColorizer}
* and panel function.
*
* @param reader
* @throws IOException
*/
public void source(BufferedReader reader) throws IOException {
LPhyParserDictionary metaData = component.getParserDictionary();
metaData.source(reader, null);
repaint();
}
private String consumeForLoop(String firstLine, BufferedReader reader) throws IOException {
StringBuilder builder = new StringBuilder(firstLine);
String line = reader.readLine();
while (!line.trim().startsWith("}")) {
builder.append(line);
line = reader.readLine();
}
builder.append(line);
return builder.toString();
}
private int getReps() {
int reps = 1;
try {
reps = Integer.parseInt(repsField.getText());
} catch (NumberFormatException nfe) {
repsField.setText("1");
reps = 1;
}
return reps;
}
// Key is the replicate index, value is the result of each replicate.
Map> valuesAllRepsMap;
public Map> getValuesAllRepsMap() {
return valuesAllRepsMap;
}
public void sample(int reps) {
sample(reps, new LinkedList<>());
}
public void sample(int reps, List loggers) {
long start = System.currentTimeMillis();
String id = null;
if (displayedElement instanceof Value && !((Value) displayedElement).isAnonymous()) {
id = ((Value) displayedElement).getId();
}
// add Loggers here, to trigger after click Sample button
loggers.addAll(rightPane.getGUISimulatorListener());
// These sync the consoles with GraphicalModelComponent containing the lphy code
// the code may be changed by GUI, such as squared rectangles.
dataInterpreter.clear();
modelInterpreter.clear();
// refresh data and model lines
String text = codeBuilder.getCode(component.getParserDictionary());
dataInterpreter.interpretInput(codeBuilder.getDataLines(), LPhyParserDictionary.Context.data);
modelInterpreter.interpretInput(codeBuilder.getModelLines(), LPhyParserDictionary.Context.model);
// Sample using the lphy code in component.getParser(), and output results to loggers
Sampler sampler = new Sampler(component.getParserDictionary());
// if null then use a random seed
valuesAllRepsMap = sampler.sampleAll(reps, loggers, null);
// this.sampler = sampler;
if (id != null) {
Value selectedValue = component.getParserDictionary().getValue(id, LPhyParserDictionary.Context.model);
if (selectedValue != null) {
showValue(selectedValue, false);
}
} else {
List> sinks = component.getParserDictionary().getModelSinks();
// TODO should not move to tab for all sinks?
// if (sinks.size() > 0) showValue(sinks.get(0), false);
for (Value value : sinks) {
if (value instanceof RandomVariable) {
showValue(value, false);
}
}
}
long end = System.currentTimeMillis();
LoggerUtils.log.info("sample(" + reps + ") took " + (end - start) + " ms.");
rightPane.variableSummary.repaint();
rightPane.repaint();
}
void showValue(Value value) {
showValue(value, true);
}
void showValue(Value value, boolean moveToTab) {
if (value != null) {
String type = value.value().getClass().getSimpleName();
String label = value.getLabel();
showObject(type + " " + label, value, moveToTab);
}
}
private void showParameterized(Generator g) {
showObject(g.codeString(), g, true);
}
// TODO It looks ViewerRegister not store ValueEditor (JTextField),
// so everytime viewer.getViewer(object) creates a new ValueEditor.
private void showObject(String label, Object obj, boolean moveToTab) {
displayedElement = obj;
JComponent viewer = null;
if (obj instanceof Value) {
viewer = ViewerRegister.getJComponentForValue(obj);
if (viewer instanceof TimeTreeComponent timeTreeComponent) {
// if (timeTreeComponent.getTimeTree().isUltrametric()) {
viewer = createTimeTreeSplitPane(timeTreeComponent);
// }
} else if (viewer instanceof AlignmentComponent alignmentComponent) {
SequenceType sequenceType = alignmentComponent.getAlignment().getSequenceType();
SequenceTypePanel sequenceTypePanel = new SequenceTypePanel(sequenceType);
JSplitPane splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, alignmentComponent, sequenceTypePanel);
splitPane.setResizeWeight(1.0);
splitPane.setOneTouchExpandable(true);
splitPane.setContinuousLayout(true);
splitPane.setBorder(null);
splitPane.setBackground(Color.white);
final double ratio = 0.95;
// if (SequenceTypePanel.isShowLegends())
splitPane.setDividerLocation(ratio);
// else
// splitPane.setDividerLocation(1.0);
splitPane.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
if (e.getButton() == MouseEvent.BUTTON1)
AlignmentComponent.setShowTreeInAlignmentViewerIfAvailable(
!AlignmentComponent.getShowTreeInAlignmentViewerIfAvailable());
else if (e.getButton() == MouseEvent.BUTTON3) {
SequenceTypePanel.setShowLegends(!SequenceTypePanel.isShowLegends());
if (SequenceTypePanel.isShowLegends())
splitPane.setDividerLocation(ratio);
else
splitPane.setDividerLocation(1.0);
} else {
AlignmentComponent.showErrorsIfAvailable = !AlignmentComponent.showErrorsIfAvailable;
}
splitPane.repaint();
}
});
viewer = splitPane;
}
} else if (obj instanceof VectorizedFunction) {
viewer = new JLabel(((VectorizedFunction) obj).getComponentFunction(0).getRichDescription(0));
} else if (obj instanceof Generator) {
viewer = new JLabel(((Generator) obj).getRichDescription(0));
} else {
LoggerUtils.log.severe("Trying to show an object that is neither Value nor Generator.");
}
// if (viewer instanceof JTextField textField)
// textField.setEditable(editValues.isSelected());
if (viewer instanceof JTextField || viewer instanceof JLabel || viewer instanceof Abstract2DEditor) {
JPanel viewerPanel = new JPanel();
viewerPanel.setOpaque(false);
viewerPanel.setLayout(new FlowLayout(FlowLayout.LEFT));
viewerPanel.add(viewer);
viewer = viewerPanel;
}
rightPane.currentSelectionContainer.setViewportView(viewer);
rightPane.currentSelectionContainer.setBorder(
BorderFactory.createTitledBorder(
BorderFactory.createMatteBorder(0, 0, 0, 0, viewer.getBackground()),
"" + label + ""));
if (moveToTab) rightPane.setSelectedComponent(rightPane.currentSelectionContainer);
rightPane.repaint();
repaint();
}
private JSplitPane createTimeTreeSplitPane(TimeTreeComponent timeTreeComponent) {
TimeTreeExtraPlotComponent plotComponent = new TimeTreeExtraPlotComponent(timeTreeComponent);
TimeTreeExtraPlotPanel timeTreePlotPanel = new TimeTreeExtraPlotPanel(plotComponent);
JSplitPane treeSplitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, timeTreeComponent, timeTreePlotPanel);
treeSplitPane.setResizeWeight(0.5);
treeSplitPane.setOneTouchExpandable(true);
treeSplitPane.setContinuousLayout(true);
treeSplitPane.setBorder(null);
treeSplitPane.setBackground(Color.white);
// if (TimeTreeExtraPlotComponent.isShowExtraPlot())
// treeSplitPane.setDividerLocation(0.5);
// else
// treeSplitPane.setDividerLocation(1.0);
//TODO not working
// if (TimeTreeExtraPlotComponent.isShowExtraPlot())
// treeSplitPane.setDividerLocation(0.5);
// else
// treeSplitPane.setDividerLocation(1.0);
//TODO not working
// treeSplitPane.addPropertyChangeListener("dividerLocation", evt -> {
// // Get the new divider location of the split pane
// int location = (Integer) evt.getNewValue();
// // getMaximumDividerLocation() NOT return the maximum position of the divider bar when maximized using the arrow
// TimeTreeExtraPlotComponent.setShowExtraPlot(location < treeSplitPane.getMaximumDividerLocation());
// });
treeSplitPane.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
if (e.getButton() == MouseEvent.BUTTON3) {
TimeTreeExtraPlotComponent.setShowExtraPlot(!TimeTreeExtraPlotComponent.isShowExtraPlot());
if (TimeTreeExtraPlotComponent.isShowExtraPlot())
treeSplitPane.setDividerLocation(0.5);
else
treeSplitPane.setDividerLocation(1.0);
}
treeSplitPane.repaint();
}
});
return treeSplitPane;
}
// IO should be in one place
// use LinguaPhyloStudio readFile(File exampleFile)
@Deprecated
public void readScript(File scriptFile) {
Path path = Paths.get(scriptFile.getAbsolutePath());
try {
String mimeType = Files.probeContentType(path);
// bug: NullPointerException: Cannot invoke "String.equals(Object)"
if (mimeType.equals("text/plain")) {
// TODO need to find another way to do this
//parser.clear();
dataInterpreter.clear();
modelInterpreter.clear();
FileReader reader = new FileReader(scriptFile);
BufferedReader bufferedReader = new BufferedReader(reader);
String line = bufferedReader.readLine();
while (line != null) {
dataInterpreter.clear();
modelInterpreter.clear();
line = bufferedReader.readLine();
}
bufferedReader.close();
reader.close();
}
} catch (IOException e) {
e.printStackTrace();
}
}
public GraphicalModelParserDictionary getParserDictionary() {
return component.getParserDictionary();
}
public ViewerPane getRightPane() {
return rightPane;
}
public JTextPane getCanonicalModelPane() {
return rightPane.canonicalModelPanel.pane;
}
public GraphicalModelComponent getComponent() {
return component;
}
/**
* clear panel, parser, and interpreters
*/
public void clear() {
dataInterpreter.clear();
modelInterpreter.clear();
component.clear();
rightPane.clear();
}
public JToolBar getToolbar() {
return toolbar;
}
public void setToolbar(JToolBar toolbar) {
this.toolbar = toolbar;
}
}