Exemplo n.º 1
0
 public void setValueAt(Object aValue, int row, int col) {
   //            PartitionData partition = options.getPartitionDataNoSpecies().get(row);
   PartitionData partition = options.getNonTraitsDataList().get(row);
   switch (col) {
     case 0:
       String name = ((String) aValue).trim();
       if (name.length() > 0) {
         partition.setName(name);
       }
       break;
     case 5:
       //                    partition.setPloidyType((PloidyType) aValue);
       //                    break;
       //                case 6:
       partition.setPartitionSubstitutionModel((PartitionSubstitutionModel) aValue);
       break;
     case 6:
       partition.setPartitionClockModel((PartitionClockModel) aValue);
       break;
     case 7:
       partition.setPartitionTreeModel((PartitionTreeModel) aValue);
       break;
   }
   fireDataChanged();
 }
Exemplo n.º 2
0
  public void unlinkTrees() { // reuse previous PartitionTreePrior
    int[] selRows = dataTable.getSelectedRows();
    for (int row : selRows) {
      PartitionData partition = options.dataPartitions.get(row);

      PartitionTreeModel model = partition.getPartitionTreeModel();
      if (!model.getName().equals(partition.getName())
          && partition.getTraitType() == null) { // not a trait
        PartitionTreeModel newTree = new PartitionTreeModel(options, partition);

        // 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();
    options.taxonSets.clear();
    options.taxonSetsMono.clear();
    repaint();
  }
Exemplo n.º 3
0
  public void linkTrees() { // keep previous PartitionTreePrior for reuse
    int[] selRows = dataTable.getSelectedRows();

    List<PartitionData> selectedPartitionData = new ArrayList<PartitionData>();
    for (int row : selRows) {
      PartitionData partition = options.dataPartitions.get(row);

      if (!selectedPartitionData.contains(partition)) selectedPartitionData.add(partition);
    }

    if (options.allowDifferentTaxa) { // BEAST cannot handle multi <taxa> ref for 1 tree
      if (selectedPartitionData.size() > 1) {
        if (!options.validateDiffTaxa(selectedPartitionData)) {
          JOptionPane.showMessageDialog(
              this,
              "To accommodate different taxa for each partition trees cannot be linked.",
              "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 (PartitionData partition : selectedPartitionData) {
        partition.setPartitionTreeModel(model);
      }
    }

    modelsChanged();

    fireDataChanged();
    options.taxonSets.clear();
    options.taxonSetsMono.clear();
    repaint();
  }