public void startElement(String namespaceURI, String localName, String qName, Attributes atts) {
// first clear the character buffer
m_sbuf.delete(0, m_sbuf.length());
if (qName.equals(GRAPH)) {
// parse directedness default
String edef = atts.getValue(EDGEDEF);
m_directed = DIRECTED.equalsIgnoreCase(edef);
m_graphid = atts.getValue(ID);
} else if (qName.equals(KEY)) {
if (!inSchema) {
error(
"\""
+ KEY
+ "\" elements can not"
+ " occur after the first node or edge declaration.");
}
m_for = atts.getValue(FOR);
m_id = atts.getValue(ID);
m_name = atts.getValue(ATTRNAME);
m_type = atts.getValue(ATTRTYPE);
} else if (qName.equals(NODE)) {
schemaCheck();
m_row = m_nodes.addRow();
String id = atts.getValue(ID);
m_nodeMap.put(id, new Integer(m_row));
m_table = m_nodes;
} else if (qName.equals(EDGE)) {
schemaCheck();
m_row = m_edges.addRow();
// do not use the id value
// String id = atts.getValue(ID);
// if ( id != null ) {
// if ( !m_edges.canGetString(ID) )
// m_edges.addColumn(ID, String.class);
// m_edges.setString(m_row, ID, id);
// }
m_edges.setString(m_row, SRCID, atts.getValue(SRC));
m_edges.setString(m_row, TRGID, atts.getValue(TRG));
// currently only global directedness is used
// ignore directed edge value for now
// String dir = atts.getValue(DIRECTED);
// boolean d = m_directed;
// if ( dir != null ) {
// d = dir.equalsIgnoreCase("false");
// }
// m_edges.setBoolean(m_row, DIRECTED, d);
m_table = m_edges;
} else if (qName.equals(DATA)) {
m_key = atts.getValue(KEY);
}
}
public Graph toGraph() {
Table edgeTable = new Table();
Table nodeTable = new Table();
HashMap<String, Integer> unique = new HashMap<String, Integer>();
edgeTable.addColumn("Node1", int.class);
edgeTable.addColumn("Node2", int.class);
nodeTable.addColumn("key", int.class);
nodeTable.addColumn("name", String.class);
nodeTable.addColumn("type", String.class);
nodeTable.addColumn("indeterminate", int.class);
int idx = 0;
for (Protein prot : minProteins.values()) {
int row = nodeTable.addRow();
unique.put(prot.getName(), idx);
nodeTable.setInt(row, "key", idx++);
nodeTable.setString(row, "name", prot.getName());
nodeTable.setString(row, "type", "protein");
nodeTable.setInt(row, "indeterminate", 0);
}
for (Peptide pep : minPeptides.values()) {
int row = nodeTable.addRow();
unique.put(pep.getSequence(), idx);
nodeTable.setInt(row, "key", idx++);
nodeTable.setString(row, "name", pep.getSequence());
nodeTable.setString(row, "type", "peptide");
if (pep.getIndeterminateType() == PeptideIndeterminacyType.NONE) {
nodeTable.setInt(row, "indeterminate", 0);
} else {
nodeTable.setInt(row, "indeterminate", 1);
}
}
for (Protein prot : minProteins.values()) {
int id1 = unique.get(prot.getName());
for (String pep : prot.getPeptides()) {
int id2 = unique.get(pep);
int row = edgeTable.addRow();
edgeTable.setInt(row, "Node1", id1);
edgeTable.setInt(row, "Node2", id2);
}
}
Graph g = new Graph(nodeTable, edgeTable, false, "key", "Node1", "Node2");
// System.err.println(g.getEdgeCount());
return g;
}
private Table populateTable(Table t, Graph g) {
for (final Iterator it = g.nodes(); it.hasNext(); ) {
final Node n = (Node) it.next();
t.addRow();
for (int i = 0; i < n.getColumnCount(); i++) {
t.set(t.getRowCount() - 1, i, n.get(i));
}
t.set(t.getRowCount() - 1, UNIQUE_INDEX_COLUMN_NAME, new Integer(t.getRowCount()));
}
return t;
}
/**
* Adds a menu item to the fisheye menu.
*
* @param name the menu label to use
* @param action the ActionListener to notify when the item is clicked The prefuse VisualItem
* corresponding to this menu item will be returned by the ActionEvent's getSource() method.
*/
public void addMenuItem(String name, ActionListener listener) {
int row = m_items.addRow();
m_items.set(row, LABEL, name);
m_items.set(row, ACTION, listener);
}
/**
* Adds a edge.
*
* @param node1
* @param node2
* @param weight
*/
public void addEdge(long node1, long node2, double weight) {
int row = edges.addRow();
edges.set(row, EHEADERS[0], node1);
edges.set(row, EHEADERS[1], node2);
edges.set(row, EHEADERS[2], weight);
}
/**
* Adds a node.
*
* @param id
* @param name
* @param picture
*/
public void addNode(long id, String name, String picture) {
int row = nodes.addRow();
nodes.set(row, NHEADERS[0], id);
nodes.set(row, NHEADERS[1], name);
nodes.set(row, NHEADERS[2], picture);
}
/*
* Input data from the "Place_Column_Name" is obtained from the original table & Lookups
* are made to appropriate maps. After processing all rows, the new output table is
* returned having original data and 2 new columns for Latitude & Longitude.
*/
public static Table compute(
String locationColumnName, Table originalTable, LogService logger, Geocoder geocoder) {
/*
* Create Blank new output table using the schema from the original table.
*/
Table outputTable = originalTable.getSchema().instantiate();
String outputTableLatitudeColumnName =
TableUtilities.formNonConflictingNewColumnName(
originalTable.getSchema(), LATITUDE_COLUMN_NAME_SUGGESTIONS);
String outputTableLongitudeColumnName =
TableUtilities.formNonConflictingNewColumnName(
originalTable.getSchema(), LONGITUDE_COLUMN_NAME_SUGGESTIONS);
outputTable.addColumn(outputTableLatitudeColumnName, Double.class);
outputTable.addColumn(outputTableLongitudeColumnName, Double.class);
logger.log(
LogService.LOG_INFO,
String.format(
"Latitude & Longitude values added to %s & %s, respectively.",
outputTableLatitudeColumnName, outputTableLongitudeColumnName));
int locationColumnNumber = originalTable.getColumnNumber(locationColumnName);
int latitudeColumnNumber = outputTable.getColumnNumber(outputTableLatitudeColumnName);
int longitudeColumnNumber = outputTable.getColumnNumber(outputTableLongitudeColumnName);
Map<String, Geolocation> geocodedAddressToGeoLocation = new HashMap<String, Geolocation>();
FrequencyMap<String> failedFrequency = new FrequencyMap<String>(true);
Iterator<?> locationColumnIterator = originalTable.iterator();
while (locationColumnIterator.hasNext()) {
int currentRowNumber = Integer.parseInt(locationColumnIterator.next().toString());
/* Start geocoding */
Geolocation geolocation = DEFAULT_NO_LOCATION_VALUE;
String currentLocation = "";
Object currentLocationObject = originalTable.get(currentRowNumber, locationColumnNumber);
if (currentLocationObject != null) {
currentLocation = currentLocationObject.toString();
String currentLocationUppercase = currentLocation.toUpperCase();
/* Avoid re-geocoding the same place */
if (geocodedAddressToGeoLocation.containsKey(currentLocationUppercase)) {
geolocation = geocodedAddressToGeoLocation.get(currentLocationUppercase);
if (geolocation == DEFAULT_NO_LOCATION_VALUE) {
failedFrequency.add(currentLocation);
}
} else {
try {
geolocation = geocoder.geocodingFullForm(currentLocationUppercase);
} catch (GeoCoderException e) {
try {
/* Try lookup in the abbreviation */
geolocation = geocoder.geocodingAbbreviation(currentLocationUppercase);
} catch (GeoCoderException e1) {
/* No result is found */
failedFrequency.add(currentLocation);
}
}
/* Add to geocoded map */
geocodedAddressToGeoLocation.put(currentLocationUppercase, geolocation);
}
} else {
failedFrequency.add(currentLocation);
}
/*
* Add the new row to the new table
* by copying the original row & then adding 2 new columns to it.
*/
outputTable.addRow();
TableUtilities.copyTableRow(currentRowNumber, currentRowNumber, outputTable, originalTable);
outputTable.set(currentRowNumber, latitudeColumnNumber, geolocation.getLatitude());
outputTable.set(currentRowNumber, longitudeColumnNumber, geolocation.getLongitude());
}
/* Warning user about failure */
if (!failedFrequency.isEmpty()) {
printWarningMessage(logger, locationColumnName, failedFrequency);
}
/* Show statistic information */
int totalRow = originalTable.getRowCount();
NumberFormat numberFormat = NumberFormat.getInstance();
logger.log(
LogService.LOG_INFO,
String.format(
"Successfully geocoded %s out of %s locations to geographic coordinates",
numberFormat.format(totalRow - failedFrequency.sum()), numberFormat.format(totalRow)));
return outputTable;
}
