/**
   * @param features
   * @param qualifiersToTransfer
   * @param key
   * @param sameKey
   * @param isDatabaseEntry
   * @param geneNames
   * @return
   */
  private static String[] transfer(
      final FeatureVector features,
      final QualifierVector qualifiersToTransfer,
      final String key,
      final boolean sameKey,
      final boolean overwrite,
      final boolean isDatabaseEntry,
      String[] geneNames,
      final StringBuffer genesUpdated) {
    final TransferFeaturePredicate predicate =
        new TransferFeaturePredicate(key, sameKey, isDatabaseEntry, geneNames);

    for (int i = 0; i < features.size(); i++) {
      Feature thisFeature = features.elementAt(i);
      if (predicate.testPredicate(thisFeature)) {
        StringBuffer qualifierBuffer = new StringBuffer();
        for (int j = 0; j < qualifiersToTransfer.size(); j++) {
          Qualifier newQualifier = qualifiersToTransfer.elementAt(j);
          String qualifierName = newQualifier.getName();
          try {
            if (overwrite) {
              thisFeature.setQualifier(newQualifier);
              qualifierBuffer.append(
                  "  "
                      + qualifierName
                      + " (overwritten)\n"
                      + parseStringVector(newQualifier.getValues()));
            } else {
              final StringVector oldValues;
              if (thisFeature.getQualifierByName(newQualifier.getName()) == null) oldValues = null;
              else oldValues = thisFeature.getQualifierByName(newQualifier.getName()).getValues();

              final Qualifier newQualifierTmp =
                  getQualifierWithoutDuplicateValues(newQualifier, oldValues);
              if (newQualifierTmp == null) continue;
              thisFeature.addQualifierValues(newQualifierTmp);
              qualifierBuffer.append(
                  "  "
                      + qualifierName
                      + " (added)\n"
                      + parseStringVector(newQualifier.getValues()));
            }
          } catch (Exception e1) {
            e1.printStackTrace();
          }
        }

        geneNames = removeArrayElement(geneNames, predicate.getGeneName());
        if (qualifierBuffer.length() > 0)
          genesUpdated.append(
              thisFeature.getSystematicName() + " (" + key + ")\n" + qualifierBuffer);
      }
    }
    return geneNames;
  }
Exemplo n.º 2
0
  private void updateFromFeature(Feature feature) {
    GridBagConstraints c = new GridBagConstraints();
    JPanel gridPanel = new JPanel(new GridBagLayout());
    gridPanel.setBackground(Color.white);

    //
    // literature & dbxref
    literatureTextArea = new QualifierTextArea();
    literatureTextArea.setBorder(BorderFactory.createLineBorder(Color.gray));
    dbxrefTextArea = new QualifierTextArea();
    dbxrefTextArea.setBorder(BorderFactory.createLineBorder(Color.gray));

    literatureTextArea
        .getDocument()
        .addDocumentListener(new TextAreaDocumentListener(literatureTextArea));

    dbxrefTextArea.getDocument().addDocumentListener(new TextAreaDocumentListener(dbxrefTextArea));

    final QualifierVector qualifiers = feature.getQualifiers().copy();
    final StringBuffer litBuffer = new StringBuffer();
    final StringBuffer dbxrefBuffer = new StringBuffer();

    for (int i = 0; i < qualifiers.size(); ++i) {
      Qualifier this_qualifier = (Qualifier) qualifiers.elementAt(i);
      if (this_qualifier.getName().equals("literature"))
        appendToBuffer(this_qualifier.getValues(), litBuffer);
      else if (this_qualifier.getName().equalsIgnoreCase("Dbxref"))
        appendToBuffer(this_qualifier.getValues(), dbxrefBuffer);
    }

    c.gridx = 0;
    c.gridy = 0;
    c.ipadx = 5;
    c.ipady = 5;
    c.anchor = GridBagConstraints.NORTHWEST;
    c.fill = GridBagConstraints.NONE;
    gridPanel.add(new JLabel("Literature"), c);
    c.gridx = 1;
    gridPanel.add(literatureTextArea, c);

    c.gridx = 0;
    c.gridy = 1;
    gridPanel.add(new JLabel("Dbxref"), c);
    c.gridx = 1;
    gridPanel.add(dbxrefTextArea, c);

    add(gridPanel);

    literatureTextArea.setText(litBuffer.toString() + "\n");
    dbxrefTextArea.setText(dbxrefBuffer.toString() + "\n");
  }
  /**
   * Return a qualifier copy of the qualifier provided that does not contain any of the values in
   * the StringVector.
   *
   * @param newQualifier
   * @param oldValues
   * @return
   * @throws InvalidRelationException
   */
  protected static Qualifier getQualifierWithoutDuplicateValues(
      final Qualifier qualifier, final StringVector values) throws InvalidRelationException {
    final Qualifier newQualifier;
    if (values == null || values.size() < 1) newQualifier = qualifier;
    else {
      StringVector newValues = qualifier.getValues();
      StringVector valuesToAdd = new StringVector();

      for (int k = 0; k < newValues.size(); k++) {
        if (!values.contains(newValues.get(k))) {
          if (qualifier.getName().equals("history")) {
            if (!uk.ac.sanger.artemis.components.genebuilder.cv.HistoryBox.contains(
                values, (String) newValues.get(k))) valuesToAdd.add(newValues.get(k));
          } else valuesToAdd.add(newValues.get(k));
        }
      }

      if (valuesToAdd.size() == 0) return null;
      newQualifier = new Qualifier(qualifier.getName(), valuesToAdd);
    }
    return newQualifier;
  }
  /**
   * Set up the expander button to display qualifier values.
   *
   * @param butt - expander button
   * @param qualifier - the qualifer that is being displayed
   * @param qualifierValueBox - Box containing the values
   * @param qualifierNameCheckBox - JCheckBox for the given qualifier
   * @param pane
   * @return
   */
  private Vector<JCheckBox> setExpanderButton(
      final JButton butt,
      final Qualifier qualifier,
      final Box qualifierValueBox,
      final JCheckBox qualifierNameCheckBox) {
    butt.setMargin(new Insets(0, 0, 0, 0));
    butt.setHorizontalAlignment(SwingConstants.RIGHT);
    butt.setHorizontalTextPosition(SwingConstants.RIGHT);
    butt.setBorderPainted(false);
    butt.setFont(butt.getFont().deriveFont(Font.BOLD));
    butt.setForeground(TransferAnnotationTool.STEEL_BLUE);

    butt.addActionListener(
        new ActionListener() {
          public void actionPerformed(ActionEvent e) {
            if (butt.getText().equals("+")) butt.setText("-");
            else butt.setText("+");

            qualifierValueBox.setVisible(butt.getText().equals("-"));
            revalidate();
          }
        });

    // set-up qualifier values list
    qualifierValueBox.setVisible(false);
    final Vector<JCheckBox> qualifierValuesCheckBox = new Vector<JCheckBox>();
    final StringVector values = qualifier.getValues();
    if (values != null) {
      for (int i = 0; i < values.size(); i++) {
        final JCheckBox cb = new JCheckBox(values.get(i), qualifierNameCheckBox.isSelected());
        cb.setFont(cb.getFont().deriveFont(Font.ITALIC));
        qualifierValueBox.add(cb);
        qualifierValuesCheckBox.add(cb);
      }
    }
    return qualifierValuesCheckBox;
  }
Exemplo n.º 5
0
  /**
   * Contruct a component for a similarity line
   *
   * @param similarity
   * @param similarityString
   */
  protected SimilarityTable(final Qualifier simQualifier, final DatabaseDocument doc) {
    this.origQualifiers = new QualifierVector();
    this.origQualifiers.add(simQualifier);

    infoLevelButton.setOpaque(false);
    infoLevelButton.setHorizontalAlignment(SwingConstants.LEFT);
    tableData.setSize(NUMBER_COLUMNS);

    tableData.setElementAt(ORGANISM_COL, 0);
    tableData.setElementAt(HIT_COL, 1);
    tableData.setElementAt(HIT_DBXREF_COL, 2);
    tableData.setElementAt(DESCRIPTION_COL, 3);
    tableData.setElementAt(EVALUE_COL, 4);
    tableData.setElementAt(LENGTH_COL, 5);
    tableData.setElementAt(ID_COL, 6);
    tableData.setElementAt(QUERY_COL, 7);
    tableData.setElementAt(SUBJECT_COL, 8);
    tableData.setElementAt(SCORE_COL, 9);
    tableData.setElementAt(OVERLAP_COL, 10);
    tableData.setElementAt(METHOD_COL, 11);
    tableData.setElementAt(REMOVE_BUTTON_COL, 12);

    // add rows of similarity
    StringVector sims = simQualifier.getValues();
    for (int i = 0; i < sims.size(); i++) rowData.add(getRowData((String) sims.get(i), tableData));

    JTable similarityTable = new JTable(rowData, tableData);
    setTable(similarityTable);

    // set hand cursor
    similarityTable.addMouseMotionListener(
        new MouseMotionAdapter() {
          private Cursor handCursor = Cursor.getPredefinedCursor(Cursor.HAND_CURSOR);

          public void mouseMoved(MouseEvent e) {
            int col = table.columnAtPoint(e.getPoint());

            String colName = table.getColumnName(col);

            if (colName.equals(HIT_COL)
                || colName.equals(HIT_DBXREF_COL)
                || colName.equals(REMOVE_BUTTON_COL)) table.setCursor(handCursor);
            else table.setCursor(Cursor.getDefaultCursor());
          }
        });

    similarityTable.setColumnSelectionAllowed(false);
    similarityTable.setRowSelectionAllowed(true);

    packColumn(similarityTable, getColumnIndex(LENGTH_COL), 4);
    packColumn(similarityTable, getColumnIndex(EVALUE_COL), 4);
    packColumn(similarityTable, getColumnIndex(ID_COL), 4);
    packColumn(similarityTable, getColumnIndex(HIT_COL), 6);
    packColumn(similarityTable, getColumnIndex(HIT_DBXREF_COL), 6);

    final TableColumn[] hideColumns = new TableColumn[5];
    hideColumns[0] = similarityTable.getColumn(QUERY_COL);
    hideColumns[1] = similarityTable.getColumn(SUBJECT_COL);
    hideColumns[2] = similarityTable.getColumn(SCORE_COL);
    hideColumns[3] = similarityTable.getColumn(OVERLAP_COL);
    hideColumns[4] = similarityTable.getColumn(METHOD_COL);

    for (int i = 0; i < hideColumns.length; i++) {
      hideColumns[i].setMinWidth(0);
      hideColumns[i].setMaxWidth(0);
    }

    infoLevelButton.addActionListener(
        new ActionListener() {
          private boolean show = true;

          public void actionPerformed(ActionEvent e) {
            // change the column size
            for (int i = 0; i < hideColumns.length; i++) {
              if (show)
                packColumn(getTable(), getColumnIndex((String) hideColumns[i].getHeaderValue()), 2);
              else {
                hideColumns[i].setMinWidth(0);
                hideColumns[i].setMaxWidth(0);
              }
            }
            show = !show;

            if (infoLevelButton.getText().equals("Details"))
              infoLevelButton.setText("Hide Details");
            else infoLevelButton.setText("Details");
          }
        });

    TableModel tableModel = getTable().getModel();
    // remove button column
    TableColumn col = getTable().getColumn(REMOVE_BUTTON_COL);
    col.setMinWidth(35);
    col.setMaxWidth(40);
    col.setPreferredWidth(40);

    final SimilarityRenderer renderer = new SimilarityRenderer();

    for (int columnIndex = 0; columnIndex < tableModel.getColumnCount(); columnIndex++) {
      col = getTable().getColumnModel().getColumn(columnIndex);
      col.setCellRenderer(renderer);
      col.setCellEditor(new CellEditing(new JTextField()));
    }

    col = getTable().getColumn(HIT_COL);
    col.setCellEditor(
        new LinkEditor(new JCheckBox(), (DefaultTableModel) getTable().getModel(), null));

    col = getTable().getColumn(HIT_DBXREF_COL);
    col.setCellEditor(
        new LinkEditor(new JCheckBox(), (DefaultTableModel) getTable().getModel(), null));

    // remove JButton column
    col = getTable().getColumn(REMOVE_BUTTON_COL);
    col.setCellEditor(
        new ButtonEditor(new JCheckBox(), (DefaultTableModel) getTable().getModel(), "X", doc));
  }