/**
* @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;
}
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;
}
/**
* 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));
}