Exemplo n.º 1
0
  public void removeSelection() {
    int[] selRows = dataTable.getSelectedRows();
    Set<AbstractPartitionData> partitionsToRemove = new HashSet<AbstractPartitionData>();
    for (int row : selRows) {
      partitionsToRemove.add(options.dataPartitions.get(row));
    }

    boolean hasIdenticalTaxa =
        options.hasIdenticalTaxa(); // need to check this before removing partitions

    // TODO: would probably be a good idea to check if the user wants to remove the last partition
    options.dataPartitions.removeAll(partitionsToRemove);

    if (options.dataPartitions.size() == 0) {
      // all data partitions removed so reset the taxa
      options.reset();
      useStarBEASTCheck.setSelected(false);
      frame.setupStarBEAST(false);
      frame.statusLabel.setText("");
      frame.setAllOptions();
      frame.getExportAction().setEnabled(false);
    } else if (!hasIdenticalTaxa) {
      options.updateTaxonList();
    }

    dataTableModel.fireTableDataChanged();

    fireDataChanged();
  }
Exemplo n.º 2
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  public void removeSelection() {
    int[] selRows = dataTable.getSelectedRows();
    Set<PartitionData> partitionsToRemove = new HashSet<PartitionData>();
    for (int row : selRows) {
      partitionsToRemove.add(options.dataPartitions.get(row));
    }

    // TODO: would probably be a good idea to check if the user wants to remove the last partition
    options.dataPartitions.removeAll(partitionsToRemove);

    //        if (options.allowDifferentTaxa && options.dataPartitions.size() < 2) {
    //            uncheckAllowDifferentTaxa();
    //        }

    if (options.getNonTraitsDataList().size() == 0) {
      // all data partitions removed so reset the taxa
      options.reset();
      useStarBEASTCheck.setSelected(false);
      frame.statusLabel.setText("");
      frame.setAllOptions();
      frame.getExportAction().setEnabled(false);
    }

    dataTableModel.fireTableDataChanged();

    fireDataChanged();
  }
Exemplo n.º 3
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  public void setOptions(BeautiOptions options) {

    this.options = options;

    modelsChanged();

    useStarBEASTCheck.setEnabled(
        options.getNonTraitsDataList().size() > 0); // single partition is allowed
    createImportTraitButton.setEnabled(options.getNonTraitsDataList().size() > 0);

    dataTableModel.fireTableDataChanged();
  }
Exemplo n.º 4
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  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();
  }
Exemplo n.º 5
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  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();
  }
Exemplo n.º 6
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  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();
  }
Exemplo n.º 7
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  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 8
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  public void linkClocks() { // 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);
    }
    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 (PartitionData partition : selectedPartitionData) {
        partition.setPartitionClockModel(model);
      }
    }

    modelsChanged();

    fireDataChanged();
    repaint();
  }
Exemplo n.º 9
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  public boolean createFromTraits(List<TraitData> traits) {
    int selRow = -1;

    if (selectTraitDialog == null) {
      selectTraitDialog = new SelectTraitDialog(frame);
    }

    if (traits == null || traits.size() == 0) {
      int result = selectTraitDialog.showDialog(options.traits, null);
      if (result != JOptionPane.CANCEL_OPTION) {
        TraitData trait = selectTraitDialog.getTrait();
        String name = trait.getName();
        if (selectTraitDialog.getMakeCopy()) {
          name = selectTraitDialog.getName();
        }

        selRow = options.createPartitionForTraits(name, trait);
      } else {
        return false;
      }
    } else {
      if (traits.size() > 1) {
        // a set of traits have been passed to the function
        int result = selectTraitDialog.showDialog(null, null);
        if (result != JOptionPane.CANCEL_OPTION) {
          String name = selectTraitDialog.getName();
          selRow = options.createPartitionForTraits(name, traits);
        } else {
          return false;
        }
      } else {
        selRow = options.createPartitionForTraits(traits.get(0).getName(), traits);
      }
    }

    modelsChanged();
    dataTableModel.fireTableDataChanged();

    if (selRow != -1) {
      dataTable.getSelectionModel().setSelectionInterval(selRow, selRow);
    }
    fireDataChanged();
    repaint();

    return true;
  }
Exemplo n.º 10
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  private void modelsChanged() {
    TableColumn col = dataTable.getColumnModel().getColumn(5);
    col.setCellEditor(new ComboBoxCellEditor());

    col = dataTable.getColumnModel().getColumn(6);
    col.setCellEditor(new ComboBoxCellEditor());

    col = dataTable.getColumnModel().getColumn(7);
    col.setCellEditor(
        new DefaultCellEditor(new JComboBox(options.getNonTraitPartitionTreeModels().toArray())));
  }
Exemplo n.º 11
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  private void fireDataChanged() {
    //        options.updateLinksBetweenPDPCMPSMPTMPTPP();
    options.updatePartitionAllLinks();

    if (!(options.clockModelOptions.getRateOptionClockModel() == FixRateType.TIP_CALIBRATED
        || options.clockModelOptions.getRateOptionClockModel() == FixRateType.NODE_CALIBRATED
        || options.clockModelOptions.getRateOptionClockModel() == FixRateType.RATE_CALIBRATED)) {
      // TODO correct?
      options.clockModelOptions.fixRateOfFirstClockPartition();
    }

    frame.setDirty();
  }
Exemplo n.º 12
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 private void fireDataChanged() {
   options.updatePartitionAllLinks();
   frame.setDirty();
 }