private void updateBorder() {
String title;
switch (currentPartition.getDataType().getType()) {
case DataType.NUCLEOTIDES:
title = "Nucleotide";
break;
case DataType.AMINO_ACIDS:
title = "Amino Acid";
break;
case DataType.TWO_STATES:
title = "Binary";
break;
case DataType.GENERAL:
title = "Discrete Traits";
break;
case DataType.CONTINUOUS:
title = "Continuous Traits";
break;
case DataType.MICRO_SAT:
title = "Microsatellite";
break;
default:
throw new IllegalArgumentException("Unsupported data type");
}
optionsBorder.setTitle(title + " Partition - " + currentPartition.getName());
repaint();
}
public void setValueAt(Object aValue, int row, int col) {
AbstractPartitionData partition = options.dataPartitions.get(row);
switch (col) {
case 0:
String name = ((String) aValue).trim();
if (options.hasPartitionData(name)) {
JOptionPane.showMessageDialog(
frame,
"Duplicate partition name.",
"Illegal Argument Exception",
JOptionPane.ERROR_MESSAGE);
return;
}
if (name.length() > 0) {
options.renamePartition(partition, name);
}
break;
case 5:
// partition.setPloidyType((PloidyType) aValue);
// break;
// case 6:
if (((PartitionSubstitutionModel) aValue).getDataType().equals(partition.getDataType())) {
partition.setPartitionSubstitutionModel((PartitionSubstitutionModel) aValue);
}
break;
case 6:
partition.setPartitionClockModel((PartitionClockModel) aValue);
break;
case 7:
partition.setPartitionTreeModel((PartitionTreeModel) aValue);
break;
}
fireDataChanged();
}
public boolean isCellEditable(int row, int col) {
boolean editable;
AbstractPartitionData partition = options.dataPartitions.get(row);
switch (col) {
case 0: // name
editable = true;
break;
// case 5:// ploidy type selection menu
// editable = true;
// break;
case 5: // substitution model selection menu
editable = partition.getDataType().getType() != DataType.CONTINUOUS;
break;
case 6: // clock model selection menu
editable = partition.getDataType().getType() != DataType.CONTINUOUS;
break;
case 7: // tree selection menu
editable = true;
break;
default:
editable = false;
}
return editable;
}
public void linkClocks() { // keep previous PartitionTreePrior for reuse
int[] selRows = dataTable.getSelectedRows();
List<AbstractPartitionData> selectedPartitionData = new ArrayList<AbstractPartitionData>();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
Object[] modelArray = options.getPartitionClockModels(selectedPartitionData).toArray();
if (selectClockDialog == null) {
selectClockDialog = new SelectClockDialog(frame);
}
int result = selectClockDialog.showDialog(modelArray);
if (result != JOptionPane.CANCEL_OPTION) {
PartitionClockModel model = selectClockDialog.getModel();
if (selectClockDialog.getMakeCopy()) {
model.setName(selectClockDialog.getName());
}
for (AbstractPartitionData partition : selectedPartitionData) {
partition.setPartitionClockModel(model);
}
}
modelsChanged();
fireDataChanged();
repaint();
}
public Object getValueAt(int row, int col) {
AbstractPartitionData partition = options.getDataPartitions().get(row);
switch (col) {
case 0:
return partition.getName();
default:
throw new IllegalArgumentException("unknown column, " + col);
}
}
public void linkTrees() { // keep previous PartitionTreePrior for reuse
int[] selRows = dataTable.getSelectedRows();
List<AbstractPartitionData> selectedPartitionData = new ArrayList<AbstractPartitionData>();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
if (selectedPartitionData.size() > 1) {
if (!options.hasIdenticalTaxa(selectedPartitionData)) {
String errMsg = "To share a tree, partitions need to have identical taxa.";
if (selectedPartitionData.get(0).getDataType().getType() == DataType.MICRO_SAT)
errMsg += "\nThe data must be all diploid or all haploid when you want to link the tree.";
JOptionPane.showMessageDialog(
this, errMsg, "Illegal Configuration", JOptionPane.ERROR_MESSAGE);
return;
}
}
Object[] treeArray = options.getPartitionTreeModels(selectedPartitionData).toArray();
if (selectTreeDialog == null) {
selectTreeDialog = new SelectTreeDialog(frame);
}
int result = selectTreeDialog.showDialog(treeArray);
if (result != JOptionPane.CANCEL_OPTION) {
PartitionTreeModel model = selectTreeDialog.getTree();
if (selectTreeDialog.getMakeCopy()) {
model.setName(selectTreeDialog.getName());
}
PartitionTreePrior prior = model.getPartitionTreePrior();
options.linkTreePriors(prior);
for (AbstractPartitionData partition : selectedPartitionData) {
partition.setPartitionTreeModel(model);
}
for (Taxa taxa :
options.taxonSets) { // Issue 454: all the taxon sets are deleted when link/unlink tree
PartitionTreeModel prevModel = options.taxonSetsTreeModel.get(taxa);
if (prevModel != model) options.taxonSetsTreeModel.put(taxa, model);
}
}
modelsChanged();
fireDataChanged();
repaint();
}
public void linkModels() {
int[] selRows = dataTable.getSelectedRows();
List<AbstractPartitionData> selectedPartitionData = new ArrayList<AbstractPartitionData>();
DataType dateType = null;
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
if (dateType == null) {
dateType = partition.getDataType();
} else {
if (partition.getDataType() != dateType) {
JOptionPane.showMessageDialog(
this,
"Can only link the models for data partitions \n"
+ "of the same data type (e.g., nucleotides)",
"Unable to link models",
JOptionPane.ERROR_MESSAGE);
return;
}
}
if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
}
Object[] modelArray = options.getPartitionSubstitutionModels(selectedPartitionData).toArray();
if (selectModelDialog == null) {
selectModelDialog = new SelectModelDialog(frame);
}
int result = selectModelDialog.showDialog(modelArray);
if (result != JOptionPane.CANCEL_OPTION) {
PartitionSubstitutionModel model = selectModelDialog.getModel();
if (selectModelDialog.getMakeCopy()) {
model.setName(selectModelDialog.getName());
}
for (AbstractPartitionData partition : selectedPartitionData) {
partition.setPartitionSubstitutionModel(model);
}
}
if (options.getPartitionSubstitutionModels(Microsatellite.INSTANCE).size() <= 1) {
options.shareMicroSat = true;
}
modelsChanged();
fireDataChanged();
repaint();
}
public void unlinkClocks() { // reuse previous PartitionTreePrior
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
PartitionClockModel model = partition.getPartitionClockModel();
if (!model.getName().equals(partition.getName())) {
PartitionClockModel newModel = new PartitionClockModel(options, partition.getName(), model);
partition.setPartitionClockModel(newModel);
newModel.setClockModelGroup(model.getClockModelGroup()); // set clock model group
}
}
modelsChanged();
fireDataChanged();
repaint();
}
public void unlinkModels() {
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
PartitionSubstitutionModel model = partition.getPartitionSubstitutionModel();
if (!model.getName().equals(partition.getName())) {
PartitionSubstitutionModel newModel =
new PartitionSubstitutionModel(options, partition.getName(), model);
partition.setPartitionSubstitutionModel(newModel);
}
}
modelsChanged();
fireDataChanged();
repaint();
}
public void unlinkTrees() { // reuse previous PartitionTreePrior
int[] selRows = dataTable.getSelectedRows();
for (int row : selRows) {
AbstractPartitionData partition = options.dataPartitions.get(row);
PartitionTreeModel model = partition.getPartitionTreeModel();
if (!model.getName().equals(partition.getName())
&& partition.getTraits() == null) { // not a trait
PartitionTreeModel newTree = new PartitionTreeModel(options, partition.getName(), model);
// this prevents partition not broken, and used for unsharing tree prior only,
// because sharing uses shareSameTreePrior, unsharing uses getPartitionTreePrior
// newTree.setPartitionTreePrior(newPrior); // important
partition.setPartitionTreeModel(newTree);
}
}
options.linkTreePriors(frame.getCurrentPartitionTreePrior());
modelsChanged();
fireDataChanged();
repaint();
}
public Object getValueAt(int row, int col) {
// PartitionData partition = options.getPartitionDataNoSpecies().get(row);
AbstractPartitionData partition = options.dataPartitions.get(row);
switch (col) {
case 0:
return partition.getName();
case 1:
return partition.getFileName();
case 2:
return "" + (partition.getTaxonCount() >= 0 ? partition.getTaxonCount() : "-");
case 3:
return "" + (partition.getSiteCount() >= 0 ? partition.getSiteCount() : "-");
case 4:
return partition.getDataDescription();
case 5:
// return partition.getPloidyType();
// case 6:
return partition.getPartitionSubstitutionModel().getName();
case 6:
return ""
+ (partition.getPartitionClockModel() != null
? partition.getPartitionClockModel().getName()
: "-");
case 7:
return partition.getPartitionTreeModel().getName();
default:
throw new IllegalArgumentException("unknown column, " + col);
}
}