Esempio n. 1
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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();
  }
Esempio n. 2
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  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();
  }
Esempio n. 3
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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();
  }
Esempio n. 4
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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();
  }
Esempio n. 5
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  public void selectionChanged() {
    int[] selRows = dataTable.getSelectedRows();
    boolean hasSelection = (selRows != null && selRows.length != 0);
    frame.dataSelectionChanged(hasSelection);

    boolean canUnlink = options.dataPartitions.size() > 1 && hasSelection;
    boolean canLink = options.dataPartitions.size() > 1 && hasSelection && selRows.length > 1;

    unlinkModelsAction.setEnabled(canUnlink);
    linkModelsAction.setEnabled(canLink);

    unlinkClocksAction.setEnabled(canUnlink);
    linkClocksAction.setEnabled(canLink);

    unlinkTreesAction.setEnabled(canUnlink);
    linkTreesAction.setEnabled(canLink);
  }
 public void fireModelChanged() {
   frame.setDirty();
 }
Esempio n. 7
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 public void createFromTraits() {
   frame.createImportTraits();
   dataTableModel.fireTableDataChanged();
 }
Esempio n. 8
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 private void fireDataChanged() {
   options.updatePartitionAllLinks();
   frame.setDirty();
 }