public PartitionModelPanel(final PartitionSubstitutionModel partitionModel) {
super(12, (OSType.isMac() ? 6 : 24));
this.model = partitionModel;
initCodonPartitionComponents();
PanelUtils.setupComponent(nucSubstCombo);
nucSubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setNucSubstitutionModel((NucModelType) nucSubstCombo.getSelectedItem());
}
});
nucSubstCombo.setToolTipText("<html>Select the type of nucleotide substitution model.</html>");
PanelUtils.setupComponent(aaSubstCombo);
aaSubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
model.setAaSubstitutionModel(type);
citationText.setText(type.getCitation().toString());
}
});
aaSubstCombo.setToolTipText("<html>Select the type of amino acid substitution model.</html>");
PanelUtils.setupComponent(binarySubstCombo);
binarySubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setBinarySubstitutionModel((BinaryModelType) binarySubstCombo.getSelectedItem());
useAmbiguitiesTreeLikelihoodCheck.setSelected(
binarySubstCombo.getSelectedItem() == BinaryModelType.BIN_COVARION);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(
binarySubstCombo.getSelectedItem() != BinaryModelType.BIN_COVARION);
}
});
binarySubstCombo.setToolTipText("<html>Select the type of binary substitution model.</html>");
PanelUtils.setupComponent(useAmbiguitiesTreeLikelihoodCheck);
useAmbiguitiesTreeLikelihoodCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUseAmbiguitiesTreeLikelihood(useAmbiguitiesTreeLikelihoodCheck.isSelected());
}
});
useAmbiguitiesTreeLikelihoodCheck.setToolTipText(
"<html>Detemine useAmbiguities in < treeLikelihood > .</html>");
PanelUtils.setupComponent(frequencyCombo);
frequencyCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setFrequencyPolicy((FrequencyPolicyType) frequencyCombo.getSelectedItem());
}
});
frequencyCombo.setToolTipText(
"<html>Select the policy for determining the base frequencies.</html>");
PanelUtils.setupComponent(heteroCombo);
heteroCombo.setToolTipText(
"<html>Select the type of site-specific rate<br>heterogeneity model.</html>");
heteroCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
boolean gammaHetero =
heteroCombo.getSelectedIndex() == 1 || heteroCombo.getSelectedIndex() == 3;
model.setGammaHetero(gammaHetero);
model.setInvarHetero(
heteroCombo.getSelectedIndex() == 2 || heteroCombo.getSelectedIndex() == 3);
if (gammaHetero) {
gammaCatLabel.setEnabled(true);
gammaCatCombo.setEnabled(true);
} else {
gammaCatLabel.setEnabled(false);
gammaCatCombo.setEnabled(false);
}
if (codingCombo.getSelectedIndex() != 0) {
heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 0);
heteroUnlinkCheck.setSelected(heteroCombo.getSelectedIndex() != 0);
}
}
});
PanelUtils.setupComponent(gammaCatCombo);
gammaCatCombo.setToolTipText(
"<html>Select the number of categories to use for<br>the discrete gamma rate heterogeneity model.</html>");
gammaCatCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setGammaCategories(gammaCatCombo.getSelectedIndex() + 4);
}
});
setYang96Button = new JButton("Use Yang96 model");
setYang96Button.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ev) {
setYang96Model();
}
});
PanelUtils.setupComponent(setYang96Button);
setYang96Button.setToolTipText(
"<html>Sets a 3 codon-position model with independent GTR and Gamma as described in<br>"
+ "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587–596. This model is named 3' in this paper.</html>");
setSRD06Button = new JButton("Use SRD06 model");
setSRD06Button.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ev) {
setSRD06Model();
}
});
PanelUtils.setupComponent(setSRD06Button);
setSRD06Button.setToolTipText(
"<html>Sets the SRD06 model as described in<br>"
+ "Shapiro, Rambaut & Drummond (2006) <i>MBE</i> <b>23</b>: 7-9.</html>");
citationText = new JTextArea(1, 40);
citationText.setLineWrap(true);
citationText.setWrapStyleWord(true);
citationText.setEditable(false);
citationText.setFont(this.getFont());
citationText.setOpaque(false);
AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
citationText.setText(type.getCitation().toString());
dolloCheck.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
if (dolloCheck.isSelected()) {
binarySubstCombo.setSelectedIndex(0);
binarySubstCombo.setEnabled(false);
useAmbiguitiesTreeLikelihoodCheck.setSelected(true);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(false);
frequencyCombo.setEnabled(false);
frequencyCombo.setSelectedItem(FrequencyPolicyType.EMPIRICAL);
heteroCombo.setSelectedIndex(0);
heteroCombo.setEnabled(false);
model.setBinarySubstitutionModel(BinaryModelType.BIN_DOLLO);
model.setDolloModel(true);
DolloComponentOptions comp =
(DolloComponentOptions)
model.getOptions().getComponentOptions(DolloComponentOptions.class);
comp.createParameters(model.getOptions());
comp.setActive(true);
} else {
binarySubstCombo.setEnabled(true);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(true);
frequencyCombo.setEnabled(true);
heteroCombo.setEnabled(true);
model.setBinarySubstitutionModel(
(BinaryModelType) binarySubstCombo.getSelectedItem());
model.setDolloModel(false);
}
}
});
PanelUtils.setupComponent(dolloCheck);
// dolloCheck.addChangeListener(new ChangeListener() {
// public void stateChanged(ChangeEvent e) {
// model.setDolloModel(true);
// }
// });
dolloCheck.setEnabled(true);
dolloCheck.setToolTipText(
"<html>Activates a Stochastic Dollo model as described in<br>"
+ "Alekseyenko, Lee & Suchard (2008) <i>Syst Biol</i> <b>57</b>: 772-784.</html>");
PanelUtils.setupComponent(discreteTraitSiteModelCombo);
discreteTraitSiteModelCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setDiscreteSubstType(
(DiscreteSubstModelType) discreteTraitSiteModelCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(continuousTraitSiteModelCombo);
continuousTraitSiteModelCombo.setToolTipText(
"<html>Select the model of continuous random walk, either homogenous<br>"
+ "or relaxed random walk (RRW) with a choice of distributions.</html>");
continuousTraitSiteModelCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setContinuousSubstModelType(
(ContinuousSubstModelType) continuousTraitSiteModelCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(latLongCheck);
latLongCheck.setToolTipText(
"<html>Specify whether this is a geographical trait representing <br>"
+ "latitude and longitude. Provides appropriate statistics to log file.</html>");
latLongCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setIsLatitudeLongitude(latLongCheck.isSelected());
}
});
latLongCheck.setEnabled(false);
PanelUtils.setupComponent(useLambdaCheck);
useLambdaCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
ContinuousComponentOptions component =
(ContinuousComponentOptions)
model.getOptions().getComponentOptions(ContinuousComponentOptions.class);
component.setUseLambda(model, useLambdaCheck.isSelected());
}
});
useLambdaCheck.setToolTipText(
"<html>Estimate degree of phylogenetic correlation in continuous traits using <br>"
+ "a tree transform. Inspired by Pagel (1999), described in Lemey et al (2013) <i>in prep</i></html>");
PanelUtils.setupComponent(activateBSSVS);
activateBSSVS.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setActivateBSSVS(activateBSSVS.isSelected());
}
});
activateBSSVS.setToolTipText(
"<html>Activates Bayesian stochastic search variable selection on the rates as described in<br>"
+ "Lemey, Rambaut, Drummond & Suchard (2009) <i>PLoS Computational Biology</i> <b>5</b>: e1000520</html>");
// ============ micro-sat ================
microsatName.setColumns(30);
microsatName.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setName(microsatName.getText());
}
});
microsatMax.setColumns(10);
microsatMax.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setMax(Integer.parseInt(microsatMax.getText()));
}
});
microsatMin.setColumns(10);
microsatMin.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setMin(Integer.parseInt(microsatMin.getText()));
}
});
PanelUtils.setupComponent(shareMicroSatCheck);
shareMicroSatCheck.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
model.getOptions().shareMicroSat = shareMicroSatCheck.isSelected();
if (shareMicroSatCheck.isSelected()) {
model.getOptions().shareMicroSat();
} else {
model.getOptions().unshareMicroSat();
}
setOptions();
}
});
PanelUtils.setupComponent(rateProportionCombo);
rateProportionCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setRatePorportion(
(MicroSatModelType.RateProportionality) rateProportionCombo.getSelectedItem());
}
});
// rateProportionCombo.setToolTipText("<html>Select the type of microsatellite substitution
// model.</html>");
PanelUtils.setupComponent(mutationBiasCombo);
mutationBiasCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setMutationBias(
(MicroSatModelType.MutationalBias) mutationBiasCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(phaseCombo);
phaseCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setPhase((MicroSatModelType.Phase) phaseCombo.getSelectedItem());
}
});
setupPanel();
setOpaque(false);
}
/**
* @author Alexei Drummond
* @author Andrew Rambaut
* @author Walter Xie
*/
public class PartitionModelPanel extends OptionsPanel {
private static final boolean ENABLE_STOCHASTIC_DOLLO = true;
// Components
private static final long serialVersionUID = -1645661616353099424L;
private JComboBox nucSubstCombo =
new JComboBox(EnumSet.range(NucModelType.HKY, NucModelType.TN93).toArray());
private JComboBox aaSubstCombo = new JComboBox(AminoAcidModelType.values());
private JComboBox binarySubstCombo =
new JComboBox(
new BinaryModelType[] {BinaryModelType.BIN_SIMPLE, BinaryModelType.BIN_COVARION});
private JCheckBox useAmbiguitiesTreeLikelihoodCheck =
new JCheckBox("Use ambiguities in the tree likelihood associated with this model");
private JComboBox frequencyCombo = new JComboBox(FrequencyPolicyType.values());
private JComboBox heteroCombo =
new JComboBox(new String[] {"None", "Gamma", "Invariant Sites", "Gamma + Invariant Sites"});
private JComboBox gammaCatCombo =
new JComboBox(new String[] {"4", "5", "6", "7", "8", "9", "10"});
private JLabel gammaCatLabel;
private JComboBox codingCombo =
new JComboBox(
new String[] {
"Off", "2 partitions: positions (1 + 2), 3", "3 partitions: positions 1, 2, 3"
});
private JCheckBox substUnlinkCheck =
new JCheckBox("Unlink substitution rate parameters across codon positions");
private JCheckBox heteroUnlinkCheck =
new JCheckBox("Unlink rate heterogeneity model across codon positions");
private JCheckBox freqsUnlinkCheck =
new JCheckBox("Unlink base frequencies across codon positions");
private JButton setYang96Button;
private JButton setSRD06Button;
private JCheckBox dolloCheck = new JCheckBox("Use stochastic Dollo model");
// private JComboBox dolloCombo = new JComboBox(new String[]{"Analytical",
// "Sample"});
private JComboBox discreteTraitSiteModelCombo = new JComboBox(DiscreteSubstModelType.values());
private JCheckBox activateBSSVS =
new JCheckBox(
// "Activate BSSVS"
"Infer social network with BSSVS");
private JComboBox continuousTraitSiteModelCombo =
new JComboBox(ContinuousSubstModelType.values());
private JCheckBox latLongCheck =
new JCheckBox("Bivariate trait represents latitude and longitude");
private JCheckBox useLambdaCheck =
new JCheckBox("Estimate phylogenetic signal using tree transform");
private JTextArea citationText;
// =========== micro sat ===========
private JTextField microsatName = new JTextField();
private WholeNumberField microsatMax = new WholeNumberField(2, Integer.MAX_VALUE);
private WholeNumberField microsatMin = new WholeNumberField(1, Integer.MAX_VALUE);
private JComboBox rateProportionCombo =
new JComboBox(MicroSatModelType.RateProportionality.values());
private JComboBox mutationBiasCombo = new JComboBox(MicroSatModelType.MutationalBias.values());
private JComboBox phaseCombo = new JComboBox(MicroSatModelType.Phase.values());
JCheckBox shareMicroSatCheck =
new JCheckBox("Share one microsatellite among all substitution model(s)");
protected final PartitionSubstitutionModel model;
public PartitionModelPanel(final PartitionSubstitutionModel partitionModel) {
super(12, (OSType.isMac() ? 6 : 24));
this.model = partitionModel;
initCodonPartitionComponents();
PanelUtils.setupComponent(nucSubstCombo);
nucSubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setNucSubstitutionModel((NucModelType) nucSubstCombo.getSelectedItem());
}
});
nucSubstCombo.setToolTipText("<html>Select the type of nucleotide substitution model.</html>");
PanelUtils.setupComponent(aaSubstCombo);
aaSubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
model.setAaSubstitutionModel(type);
citationText.setText(type.getCitation().toString());
}
});
aaSubstCombo.setToolTipText("<html>Select the type of amino acid substitution model.</html>");
PanelUtils.setupComponent(binarySubstCombo);
binarySubstCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setBinarySubstitutionModel((BinaryModelType) binarySubstCombo.getSelectedItem());
useAmbiguitiesTreeLikelihoodCheck.setSelected(
binarySubstCombo.getSelectedItem() == BinaryModelType.BIN_COVARION);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(
binarySubstCombo.getSelectedItem() != BinaryModelType.BIN_COVARION);
}
});
binarySubstCombo.setToolTipText("<html>Select the type of binary substitution model.</html>");
PanelUtils.setupComponent(useAmbiguitiesTreeLikelihoodCheck);
useAmbiguitiesTreeLikelihoodCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUseAmbiguitiesTreeLikelihood(useAmbiguitiesTreeLikelihoodCheck.isSelected());
}
});
useAmbiguitiesTreeLikelihoodCheck.setToolTipText(
"<html>Detemine useAmbiguities in < treeLikelihood > .</html>");
PanelUtils.setupComponent(frequencyCombo);
frequencyCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setFrequencyPolicy((FrequencyPolicyType) frequencyCombo.getSelectedItem());
}
});
frequencyCombo.setToolTipText(
"<html>Select the policy for determining the base frequencies.</html>");
PanelUtils.setupComponent(heteroCombo);
heteroCombo.setToolTipText(
"<html>Select the type of site-specific rate<br>heterogeneity model.</html>");
heteroCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
boolean gammaHetero =
heteroCombo.getSelectedIndex() == 1 || heteroCombo.getSelectedIndex() == 3;
model.setGammaHetero(gammaHetero);
model.setInvarHetero(
heteroCombo.getSelectedIndex() == 2 || heteroCombo.getSelectedIndex() == 3);
if (gammaHetero) {
gammaCatLabel.setEnabled(true);
gammaCatCombo.setEnabled(true);
} else {
gammaCatLabel.setEnabled(false);
gammaCatCombo.setEnabled(false);
}
if (codingCombo.getSelectedIndex() != 0) {
heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 0);
heteroUnlinkCheck.setSelected(heteroCombo.getSelectedIndex() != 0);
}
}
});
PanelUtils.setupComponent(gammaCatCombo);
gammaCatCombo.setToolTipText(
"<html>Select the number of categories to use for<br>the discrete gamma rate heterogeneity model.</html>");
gammaCatCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setGammaCategories(gammaCatCombo.getSelectedIndex() + 4);
}
});
setYang96Button = new JButton("Use Yang96 model");
setYang96Button.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ev) {
setYang96Model();
}
});
PanelUtils.setupComponent(setYang96Button);
setYang96Button.setToolTipText(
"<html>Sets a 3 codon-position model with independent GTR and Gamma as described in<br>"
+ "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587–596. This model is named 3' in this paper.</html>");
setSRD06Button = new JButton("Use SRD06 model");
setSRD06Button.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent ev) {
setSRD06Model();
}
});
PanelUtils.setupComponent(setSRD06Button);
setSRD06Button.setToolTipText(
"<html>Sets the SRD06 model as described in<br>"
+ "Shapiro, Rambaut & Drummond (2006) <i>MBE</i> <b>23</b>: 7-9.</html>");
citationText = new JTextArea(1, 40);
citationText.setLineWrap(true);
citationText.setWrapStyleWord(true);
citationText.setEditable(false);
citationText.setFont(this.getFont());
citationText.setOpaque(false);
AminoAcidModelType type = (AminoAcidModelType) aaSubstCombo.getSelectedItem();
citationText.setText(type.getCitation().toString());
dolloCheck.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent actionEvent) {
if (dolloCheck.isSelected()) {
binarySubstCombo.setSelectedIndex(0);
binarySubstCombo.setEnabled(false);
useAmbiguitiesTreeLikelihoodCheck.setSelected(true);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(false);
frequencyCombo.setEnabled(false);
frequencyCombo.setSelectedItem(FrequencyPolicyType.EMPIRICAL);
heteroCombo.setSelectedIndex(0);
heteroCombo.setEnabled(false);
model.setBinarySubstitutionModel(BinaryModelType.BIN_DOLLO);
model.setDolloModel(true);
DolloComponentOptions comp =
(DolloComponentOptions)
model.getOptions().getComponentOptions(DolloComponentOptions.class);
comp.createParameters(model.getOptions());
comp.setActive(true);
} else {
binarySubstCombo.setEnabled(true);
useAmbiguitiesTreeLikelihoodCheck.setEnabled(true);
frequencyCombo.setEnabled(true);
heteroCombo.setEnabled(true);
model.setBinarySubstitutionModel(
(BinaryModelType) binarySubstCombo.getSelectedItem());
model.setDolloModel(false);
}
}
});
PanelUtils.setupComponent(dolloCheck);
// dolloCheck.addChangeListener(new ChangeListener() {
// public void stateChanged(ChangeEvent e) {
// model.setDolloModel(true);
// }
// });
dolloCheck.setEnabled(true);
dolloCheck.setToolTipText(
"<html>Activates a Stochastic Dollo model as described in<br>"
+ "Alekseyenko, Lee & Suchard (2008) <i>Syst Biol</i> <b>57</b>: 772-784.</html>");
PanelUtils.setupComponent(discreteTraitSiteModelCombo);
discreteTraitSiteModelCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setDiscreteSubstType(
(DiscreteSubstModelType) discreteTraitSiteModelCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(continuousTraitSiteModelCombo);
continuousTraitSiteModelCombo.setToolTipText(
"<html>Select the model of continuous random walk, either homogenous<br>"
+ "or relaxed random walk (RRW) with a choice of distributions.</html>");
continuousTraitSiteModelCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setContinuousSubstModelType(
(ContinuousSubstModelType) continuousTraitSiteModelCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(latLongCheck);
latLongCheck.setToolTipText(
"<html>Specify whether this is a geographical trait representing <br>"
+ "latitude and longitude. Provides appropriate statistics to log file.</html>");
latLongCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setIsLatitudeLongitude(latLongCheck.isSelected());
}
});
latLongCheck.setEnabled(false);
PanelUtils.setupComponent(useLambdaCheck);
useLambdaCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
ContinuousComponentOptions component =
(ContinuousComponentOptions)
model.getOptions().getComponentOptions(ContinuousComponentOptions.class);
component.setUseLambda(model, useLambdaCheck.isSelected());
}
});
useLambdaCheck.setToolTipText(
"<html>Estimate degree of phylogenetic correlation in continuous traits using <br>"
+ "a tree transform. Inspired by Pagel (1999), described in Lemey et al (2013) <i>in prep</i></html>");
PanelUtils.setupComponent(activateBSSVS);
activateBSSVS.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setActivateBSSVS(activateBSSVS.isSelected());
}
});
activateBSSVS.setToolTipText(
"<html>Activates Bayesian stochastic search variable selection on the rates as described in<br>"
+ "Lemey, Rambaut, Drummond & Suchard (2009) <i>PLoS Computational Biology</i> <b>5</b>: e1000520</html>");
// ============ micro-sat ================
microsatName.setColumns(30);
microsatName.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setName(microsatName.getText());
}
});
microsatMax.setColumns(10);
microsatMax.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setMax(Integer.parseInt(microsatMax.getText()));
}
});
microsatMin.setColumns(10);
microsatMin.addKeyListener(
new java.awt.event.KeyListener() {
public void keyTyped(KeyEvent e) {}
public void keyPressed(KeyEvent e) {}
public void keyReleased(KeyEvent e) {
model.getMicrosatellite().setMin(Integer.parseInt(microsatMin.getText()));
}
});
PanelUtils.setupComponent(shareMicroSatCheck);
shareMicroSatCheck.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
model.getOptions().shareMicroSat = shareMicroSatCheck.isSelected();
if (shareMicroSatCheck.isSelected()) {
model.getOptions().shareMicroSat();
} else {
model.getOptions().unshareMicroSat();
}
setOptions();
}
});
PanelUtils.setupComponent(rateProportionCombo);
rateProportionCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setRatePorportion(
(MicroSatModelType.RateProportionality) rateProportionCombo.getSelectedItem());
}
});
// rateProportionCombo.setToolTipText("<html>Select the type of microsatellite substitution
// model.</html>");
PanelUtils.setupComponent(mutationBiasCombo);
mutationBiasCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setMutationBias(
(MicroSatModelType.MutationalBias) mutationBiasCombo.getSelectedItem());
}
});
PanelUtils.setupComponent(phaseCombo);
phaseCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setPhase((MicroSatModelType.Phase) phaseCombo.getSelectedItem());
}
});
setupPanel();
setOpaque(false);
}
/**
* Sets the components up according to the partition model - but does not layout the top level
* options panel.
*/
public void setOptions() {
if (SiteModelsPanel.DEBUG) {
String modelName = (model == null) ? "null" : model.getName();
Logger.getLogger("dr.app.beauti").info("ModelsPanel.setModelOptions(" + modelName + ")");
}
if (model == null) {
return;
}
int dataType = model.getDataType().getType();
switch (dataType) {
case DataType.NUCLEOTIDES:
nucSubstCombo.setSelectedItem(model.getNucSubstitutionModel());
frequencyCombo.setSelectedItem(model.getFrequencyPolicy());
break;
case DataType.AMINO_ACIDS:
aaSubstCombo.setSelectedItem(model.getAaSubstitutionModel());
break;
case DataType.TWO_STATES:
case DataType.COVARION:
binarySubstCombo.setSelectedItem(model.getBinarySubstitutionModel());
useAmbiguitiesTreeLikelihoodCheck.setSelected(model.isUseAmbiguitiesTreeLikelihood());
break;
case DataType.GENERAL:
discreteTraitSiteModelCombo.setSelectedItem(model.getDiscreteSubstType());
activateBSSVS.setSelected(model.isActivateBSSVS());
break;
case DataType.CONTINUOUS:
continuousTraitSiteModelCombo.setSelectedItem(model.getContinuousSubstModelType());
ContinuousComponentOptions component =
(ContinuousComponentOptions)
model.getOptions().getComponentOptions(ContinuousComponentOptions.class);
latLongCheck.setSelected(model.isLatitudeLongitude());
latLongCheck.setEnabled(model.getContinuousTraitCount() == 2);
useLambdaCheck.setSelected(component.useLambda(model));
break;
case DataType.MICRO_SAT:
microsatName.setText(model.getMicrosatellite().getName());
microsatMax.setText(Integer.toString(model.getMicrosatellite().getMax()));
microsatMin.setText(Integer.toString(model.getMicrosatellite().getMin()));
shareMicroSatCheck.setSelected(model.getOptions().shareMicroSat);
rateProportionCombo.setSelectedItem(model.getRatePorportion());
mutationBiasCombo.setSelectedItem(model.getMutationBias());
phaseCombo.setSelectedItem(model.getPhase());
shareMicroSatCheck.setEnabled(
model.getOptions().getPartitionSubstitutionModels(Microsatellite.INSTANCE).size() > 1);
break;
default:
throw new IllegalArgumentException("Unknown data type");
}
if (model.isGammaHetero() && !model.isInvarHetero()) {
heteroCombo.setSelectedIndex(1);
} else if (!model.isGammaHetero() && model.isInvarHetero()) {
heteroCombo.setSelectedIndex(2);
} else if (model.isGammaHetero() && model.isInvarHetero()) {
heteroCombo.setSelectedIndex(3);
} else {
heteroCombo.setSelectedIndex(0);
}
gammaCatCombo.setSelectedIndex(model.getGammaCategories() - 4);
if (model.getCodonHeteroPattern() == null) {
codingCombo.setSelectedIndex(0);
} else if (model.getCodonHeteroPattern().equals("112")) {
codingCombo.setSelectedIndex(1);
} else {
codingCombo.setSelectedIndex(2);
}
substUnlinkCheck.setSelected(model.isUnlinkedSubstitutionModel());
heteroUnlinkCheck.setSelected(model.isUnlinkedHeterogeneityModel());
freqsUnlinkCheck.setSelected(model.isUnlinkedFrequencyModel());
dolloCheck.setSelected(model.isDolloModel());
}
/** Configure this panel for the Yang 96 codon position model */
private void setYang96Model() {
nucSubstCombo.setSelectedIndex(1);
heteroCombo.setSelectedIndex(1);
codingCombo.setSelectedIndex(2);
substUnlinkCheck.setSelected(true);
heteroUnlinkCheck.setSelected(true);
freqsUnlinkCheck.setSelected(true);
}
/** Configure this panel for the Shapiro, Rambaut and Drummond 2006 codon position model */
private void setSRD06Model() {
nucSubstCombo.setSelectedIndex(0);
heteroCombo.setSelectedIndex(1);
codingCombo.setSelectedIndex(1);
substUnlinkCheck.setSelected(true);
heteroUnlinkCheck.setSelected(true);
freqsUnlinkCheck.setSelected(false);
}
/** Lays out the appropriate components in the panel for this partition model. */
private void setupPanel() {
switch (model.getDataType().getType()) {
case DataType.NUCLEOTIDES:
addComponentWithLabel("Substitution Model:", nucSubstCombo);
addComponentWithLabel("Base frequencies:", frequencyCombo);
addComponentWithLabel("Site Heterogeneity Model:", heteroCombo);
heteroCombo.setSelectedIndex(0);
gammaCatLabel = addComponentWithLabel("Number of Gamma Categories:", gammaCatCombo);
gammaCatCombo.setEnabled(false);
addSeparator();
addComponentWithLabel("Partition into codon positions:", codingCombo);
JPanel panel2 = new JPanel();
panel2.setOpaque(false);
panel2.setLayout(new BoxLayout(panel2, BoxLayout.PAGE_AXIS));
panel2.setBorder(BorderFactory.createTitledBorder("Link/Unlink parameters:"));
panel2.add(substUnlinkCheck);
panel2.add(heteroUnlinkCheck);
panel2.add(freqsUnlinkCheck);
addComponent(panel2);
addComponent(setYang96Button);
addComponent(setSRD06Button);
break;
case DataType.AMINO_ACIDS:
addComponentWithLabel("Substitution Model:", aaSubstCombo);
addComponentWithLabel("Citation:", citationText);
addComponentWithLabel("Site Heterogeneity Model:", heteroCombo);
heteroCombo.setSelectedIndex(0);
gammaCatLabel = addComponentWithLabel("Number of Gamma Categories:", gammaCatCombo);
gammaCatCombo.setEnabled(false);
break;
case DataType.TWO_STATES:
case DataType.COVARION:
addComponentWithLabel("Substitution Model:", binarySubstCombo);
addComponentWithLabel("Base frequencies:", frequencyCombo);
addComponentWithLabel("Site Heterogeneity Model:", heteroCombo);
heteroCombo.setSelectedIndex(0);
gammaCatLabel = addComponentWithLabel("Number of Gamma Categories:", gammaCatCombo);
gammaCatCombo.setEnabled(false);
addSeparator();
addComponentWithLabel("", useAmbiguitiesTreeLikelihoodCheck);
// Easy XML specification is currently only available for binary models
if (ENABLE_STOCHASTIC_DOLLO) {
addSeparator();
addComponent(dolloCheck);
}
break;
case DataType.GENERAL:
addComponentWithLabel("Discrete Trait Substitution Model:", discreteTraitSiteModelCombo);
addComponent(activateBSSVS);
break;
case DataType.CONTINUOUS:
addComponentWithLabel("Continuous Trait Model:", continuousTraitSiteModelCombo);
addComponent(latLongCheck);
addSeparator();
addComponent(useLambdaCheck);
break;
case DataType.MICRO_SAT:
addComponentWithLabel("Microsatellite Name:", microsatName);
addComponentWithLabel("Max of Length:", microsatMax);
addComponentWithLabel("Min of Length:", microsatMin);
addComponent(shareMicroSatCheck);
addSeparator();
addComponentWithLabel("Rate Proportionality:", rateProportionCombo);
addComponentWithLabel("Mutational Bias:", mutationBiasCombo);
addComponentWithLabel("Phase:", phaseCombo);
break;
default:
throw new IllegalArgumentException("Unknown data type");
}
setOptions();
}
/** Initializes and binds the components related to modeling codon positions. */
private void initCodonPartitionComponents() {
PanelUtils.setupComponent(substUnlinkCheck);
substUnlinkCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUnlinkedSubstitutionModel(substUnlinkCheck.isSelected());
}
});
substUnlinkCheck.setEnabled(false);
substUnlinkCheck.setToolTipText(
""
+ "<html>Gives each codon position partition different<br>"
+ "substitution model parameters.</html>");
PanelUtils.setupComponent(heteroUnlinkCheck);
heteroUnlinkCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUnlinkedHeterogeneityModel(heteroUnlinkCheck.isSelected());
}
});
heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 0);
heteroUnlinkCheck.setToolTipText(
"<html>Gives each codon position partition different<br>rate heterogeneity model parameters.</html>");
PanelUtils.setupComponent(freqsUnlinkCheck);
freqsUnlinkCheck.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
model.setUnlinkedFrequencyModel(freqsUnlinkCheck.isSelected());
}
});
freqsUnlinkCheck.setEnabled(false);
freqsUnlinkCheck.setToolTipText(
"<html>Gives each codon position partition different<br>nucleotide frequency parameters.</html>");
PanelUtils.setupComponent(codingCombo);
codingCombo.setToolTipText("<html>Select how to partition the codon positions.</html>");
codingCombo.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent ev) {
switch (codingCombo.getSelectedIndex()) {
case 0:
model.setCodonHeteroPattern(null);
break;
case 1:
model.setCodonHeteroPattern("112");
break;
default:
model.setCodonHeteroPattern("123");
break;
}
if (codingCombo.getSelectedIndex() != 0) {
// codon position partitioning
substUnlinkCheck.setEnabled(true);
heteroUnlinkCheck.setEnabled(heteroCombo.getSelectedIndex() != 3);
freqsUnlinkCheck.setEnabled(true);
substUnlinkCheck.setSelected(true);
heteroUnlinkCheck.setSelected(heteroCombo.getSelectedIndex() != 0);
freqsUnlinkCheck.setSelected(true);
} else {
substUnlinkCheck.setEnabled(false);
substUnlinkCheck.setSelected(false);
heteroUnlinkCheck.setEnabled(false);
heteroUnlinkCheck.setSelected(false);
freqsUnlinkCheck.setEnabled(false);
freqsUnlinkCheck.setSelected(false);
}
}
});
}
}
/**
* Parses an element from an DOM document into a DemographicModel. Recognises ConstantPopulation and
* ExponentialGrowth.
*/
public class EmpiricalAminoAcidModelParser extends AbstractXMLObjectParser {
public static final String EMPIRICAL_AMINO_ACID_MODEL = "aminoAcidModel";
public static final String FREQUENCIES = "frequencies";
public static final String TYPE = "type";
public String getParserName() {
return EMPIRICAL_AMINO_ACID_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
FrequencyModel freqModel = null;
if (xo.hasAttribute(FREQUENCIES)) {
XMLObject cxo = xo.getChild(FREQUENCIES);
freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
}
EmpiricalRateMatrix rateMatrix = null;
String type = xo.getStringAttribute(TYPE);
if (type.equals(AminoAcidModelType.BLOSUM_62.getXMLName())) {
rateMatrix = Blosum62.INSTANCE;
} else if (type.equals(AminoAcidModelType.DAYHOFF.getXMLName())) {
rateMatrix = Dayhoff.INSTANCE;
} else if (type.equals(AminoAcidModelType.JTT.getXMLName())) {
rateMatrix = dr.evomodel.substmodel.JTT.INSTANCE;
} else if (type.equals(AminoAcidModelType.MT_REV_24.getXMLName())) {
rateMatrix = MTREV.INSTANCE;
} else if (type.equals(AminoAcidModelType.CP_REV_45.getXMLName())) {
rateMatrix = CPREV.INSTANCE;
} else if (type.equals(AminoAcidModelType.WAG.getXMLName())) {
rateMatrix = dr.evomodel.substmodel.WAG.INSTANCE;
} else if (type.equals(AminoAcidModelType.FLU.getXMLName())) {
rateMatrix = dr.evomodel.substmodel.FLU.INSTANCE;
}
return new EmpiricalAminoAcidModel(rateMatrix, freqModel);
}
// ************************************************************************
// AbstractXMLObjectParser implementation
// ************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules =
new XMLSyntaxRule[] {
new StringAttributeRule(
TYPE,
"The type of empirical amino-acid rate matrix",
AminoAcidModelType.xmlNames(),
false),
new ElementRule(
FREQUENCIES,
FrequencyModel.class,
"If the frequencies are omitted than the empirical frequencies associated with the selected model are used.",
true)
};
public String getParserDescription() {
return "An empirical amino acid substitution model.";
}
public Class getReturnType() {
return EmpiricalAminoAcidModel.class;
}
}
