/**
* Check whether s qualifier string exists in a StringVector for that qualifier. If the
* StringVector contains the hit, organism, description & e-value then return true.
*
* @param qualStr
* @param qualStringVector
* @return
*/
public static boolean containsStringInStringVector(
final String qualStr, final StringVector qualStringVector) {
StringVector sim1 = StringVector.getStrings(qualStr, ";");
for (int i = 0; i < qualStringVector.size(); i++) {
String thisStr = (String) qualStringVector.get(i);
StringVector sim2 = StringVector.getStrings(thisStr, ";");
// hit
if (!((String) sim1.get(1)).equals((String) sim2.get(1))) continue;
// organism
if (!((String) sim1.get(2)).equals((String) sim2.get(2))) continue;
// description
if (!((String) sim1.get(3)).equals((String) sim2.get(3))) continue;
// e-value
final String evalueString1 = getField("E()=", qualStr);
final String evalueString2 = getField("E()=", thisStr);
if (!(evalueString1.equals(evalueString2))) continue;
return true;
}
return false;
}
/**
* 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;
}
/**
* Add a new qualifier to a list of qualifiers
*
* @param qualifiers
* @param newQualifier
*/
private void addNewQualifier(QualifierVector qualifiers, Qualifier newQualifier) {
Qualifier qualifier;
if ((qualifier = qualifiers.getQualifierByName(newQualifier.getName())) != null) {
final StringVector newValues = newQualifier.getValues();
final StringVector values = qualifier.getValues();
if (newValues == null) return;
for (int j = 0; j < newValues.size(); j++) {
String newValue = (String) newValues.get(j);
if (!values.contains(newValue)) qualifier.addValue(newValue);
}
} else qualifiers.addElement(newQualifier);
}
/**
* Optionally transfer GO fields with evidence code ISO and link back to the original source in
* the WITH/FROM column.
*
* @param setEvidenceAndWithFrom
* @param feature
* @param qName
* @param values
* @return
*/
private static StringVector getTransferValues(
final boolean setEvidenceAndWithFrom,
final Feature feature,
final String qName,
final StringVector values) {
if (!setEvidenceAndWithFrom) return values;
if (qName.equals("GO") || qName.equals("product")) {
final StringVector tvalues = new StringVector();
final String gene = getGeneName(feature);
for (int i = 0; i < values.size(); i++) {
String val =
changeField("evidence=", "Inferred from Sequence Orthology", null, values.get(i));
if (gene != null) val = changeField("with=", "GeneDB:" + gene, "|", val);
tvalues.add(val);
}
return tvalues;
}
return values;
}
/**
* 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;
}
/** Read key and qualifier mappings for CHADO to EMBL */
private static void initDatabaseMappings() {
InputStream keyStream = Options.class.getResourceAsStream("/key_mapping");
if (keyStream == null) keyStream = Options.class.getResourceAsStream("/etc/key_mapping");
InputStream qualifierStream = Options.class.getResourceAsStream("/qualifier_mapping");
if (qualifierStream == null)
qualifierStream = Options.class.getResourceAsStream("/etc/qualifier_mapping");
final Properties keyMapProperties = new Properties();
final Properties qualifierMapProperties = new Properties();
try {
keyMapProperties.load(keyStream);
qualifierMapProperties.load(qualifierStream);
if (System.getProperty("nohistory") != null)
qualifierMapProperties.setProperty("history", "");
} catch (IOException e) {
e.printStackTrace();
}
// parse the keyMapProperties
DATABASE_MAP_KEYS = new Object[keyMapProperties.size()][3];
final Enumeration keysenum = keyMapProperties.propertyNames();
int n = 0;
while (keysenum.hasMoreElements()) {
String current_map_name = (String) keysenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(keyMapProperties, current_map_name);
DATABASE_MAP_KEYS[n][0] = current_map_name;
DATABASE_MAP_KEYS[n][1] = property_values.get(0);
if (property_values.size() == 2) {
String qualifierString[] = ((String) property_values.get(1)).split("=");
final uk.ac.sanger.artemis.io.Qualifier qualifier;
if (qualifierString.length == 2)
qualifier = new uk.ac.sanger.artemis.io.Qualifier(qualifierString[0], qualifierString[1]);
else qualifier = new uk.ac.sanger.artemis.io.Qualifier(qualifierString[0]);
DATABASE_MAP_KEYS[n][2] = qualifier;
} else DATABASE_MAP_KEYS[n][2] = null;
n++;
}
// parse the qualifier mappings
Enumeration qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
Vector qualifiersToRemove = new Vector();
while (qualifiersenum.hasMoreElements()) {
String current_map_name = (String) qualifiersenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(qualifierMapProperties, current_map_name);
if (property_values == null || property_values.size() == 0)
qualifiersToRemove.add(current_map_name);
else n++;
}
DATABASE_QUALIFIERS_TO_MAP = new String[n][2];
DATABASE_QUALIFIERS_TO_REMOVE = qualifiersToRemove.toArray();
qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
while (qualifiersenum.hasMoreElements()) {
String current_map_name = (String) qualifiersenum.nextElement();
final StringVector property_values =
Options.getPropertyValues(qualifierMapProperties, current_map_name);
if (property_values != null && property_values.size() > 0) {
DATABASE_QUALIFIERS_TO_MAP[n][0] = current_map_name;
DATABASE_QUALIFIERS_TO_MAP[n][1] = (String) property_values.get(0);
n++;
}
}
}
/**
* Merge qualifiers
*
* @param qualifiers
* @param newQualifiers
*/
private void combineQualifiers(
final QualifierVector qualifiers, final QualifierVector newQualifiers, final boolean isGene) {
for (int i = 0; i < newQualifiers.size(); i++) {
Qualifier newQualifier = (Qualifier) newQualifiers.get(i);
if (newQualifier.getName().equals("ID") && !isGene) {
continue;
}
// convert GO evidence to codes (e.g. ND=No biological Data available)
if (newQualifier.getName().equals("GO")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
String val = GoBox.getEvidenceCodeGoTextFromText((String) newValues.get(j));
tmpNewValues.add(val);
}
newQualifier = new Qualifier("GO", tmpNewValues);
}
if (newQualifier.getName().equals("product")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
String val = (String) newValues.get(j);
int ind = 0;
if ((ind = val.indexOf(";db_xref=")) > -1) val = val.substring(0, ind);
if ((ind = val.indexOf(";evidence=")) > -1) val = val.substring(0, ind);
if (val.startsWith("term=")) val = val.substring(5, val.length());
if (val.endsWith(";")) val = val.substring(0, val.length() - 1);
tmpNewValues.add(val);
}
newQualifier = new Qualifier("product", tmpNewValues);
}
if (newQualifier.getName().equals("orthologous_to")
|| newQualifier.getName().equals("paralogous_to")) {
final StringVector newValues = newQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
for (int j = 0; j < newValues.size(); j++) {
if (!newValues.get(j).equals("")) tmpNewValues.add(newValues.get(j));
}
if (tmpNewValues.size() == 0) continue;
Pattern p = Pattern.compile("\\w+:link=\\w+");
for (int j = 0; j < tmpNewValues.size(); j++) {
String valueStr = (String) tmpNewValues.get(j);
String newValueStr;
int indexEnd = valueStr.indexOf(';');
String endStr = "";
if (indexEnd > -1) endStr = valueStr.substring(indexEnd);
Matcher m = p.matcher(valueStr);
while (m.find()) {
int index = valueStr.indexOf("link=", m.start());
newValueStr =
valueStr.substring(m.start(), index)
+ valueStr.substring(index + 5, m.end())
+ endStr;
if (newQualifier.getName().equals("orthologous_to"))
newQualifier = new Qualifier("orthologous_to", newValueStr);
else newQualifier = new Qualifier("paralogous_to", newValueStr);
qualifiers.addElement(newQualifier);
}
}
continue;
}
addNewQualifier(qualifiers, newQualifier);
}
}
/**
* 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));
}
/**
* Build a vector of the row data
*
* @param similarityString
* @return
*/
private Vector getRowData(String similarityString, final Vector tableData) {
Vector row = new Vector(NUMBER_COLUMNS);
row.setSize(NUMBER_COLUMNS);
if (similarityString.startsWith("\"")) similarityString = similarityString.substring(1);
if (similarityString.endsWith("\""))
similarityString = similarityString.substring(0, similarityString.length() - 1);
StringVector sim = StringVector.getStrings(similarityString, ";");
// organism
if (sim.size() >= 3) {
int columnIndex = tableData.indexOf(ORGANISM_COL);
row.setElementAt(((String) sim.get(2)).trim(), columnIndex);
}
// hit
if (sim.size() >= 2) {
int columnIndex = tableData.indexOf(HIT_COL);
String hit = ((String) sim.get(1)).trim();
if (hit.startsWith("with=")) hit = hit.substring(5);
final String hits[] = hit.split(" ");
row.setElementAt(hits[0], columnIndex);
if (hits.length > 1) {
// dbxref
columnIndex = tableData.indexOf(HIT_DBXREF_COL);
if (hits[1].startsWith("(") && hits[1].endsWith(")"))
hits[1] = hits[1].substring(1, hits[1].length() - 1);
row.setElementAt(hits[1], columnIndex);
}
}
// description
if (sim.size() >= 4) {
int columnIndex = tableData.indexOf(DESCRIPTION_COL);
row.setElementAt(((String) sim.get(3)).trim(), columnIndex);
}
// e-value
String evalueString;
if (!(evalueString = getField("E()=", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(EVALUE_COL);
row.setElementAt(evalueString, columnIndex);
}
// length
String lenString;
if (!(lenString = getField("length=", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(LENGTH_COL);
row.setElementAt(lenString, columnIndex);
} else if (!(lenString = getField("length", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(LENGTH_COL);
row.setElementAt(lenString, columnIndex);
}
String ungappedId;
if (!(ungappedId = getField("ungapped id", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(ID_COL);
row.setElementAt(ungappedId, columnIndex);
}
String query;
if (!(query = getField("query", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(QUERY_COL);
row.setElementAt(query, columnIndex);
}
String subject;
if (!(subject = getField("subject", similarityString).trim()).equals("")) {
int columnIndex = tableData.indexOf(SUBJECT_COL);
row.setElementAt(subject, columnIndex);
}
String score;
if (!(score = getField("score=", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(SCORE_COL);
row.setElementAt(score, columnIndex);
}
String overlap;
if (!(overlap = getField("overlap=", similarityString)).equals("")) {
int columnIndex = tableData.indexOf(OVERLAP_COL);
row.setElementAt(overlap, columnIndex);
} else if (similarityString.indexOf("overlap;") > -1) {
overlap = null;
for (int i = 0; i < sim.size(); i++) {
String val = (String) sim.get(i);
if (val.endsWith("overlap")) {
overlap = val;
break;
}
}
if (overlap != null) {
int columnIndex = tableData.indexOf(OVERLAP_COL);
row.setElementAt(overlap, columnIndex);
}
}
int columnIndex = tableData.indexOf(METHOD_COL);
row.setElementAt(((String) sim.get(0)).trim(), columnIndex);
return row;
}