/**
* Write out the state for the given attributes
*
* @param selectedRows
* @return number of files successfully saved, the better way to do this would just be to throw
* the error and display a specific message for each failure, but oh well.
* @throws IOException
*/
public void writeAttributes() throws IOException {
final String className;
final byte dataType =
cyAttributes.getMultiHashMapDefinition().getAttributeValueType(attributeName);
if ((dataType == CyAttributes.TYPE_COMPLEX)
|| (dataType == CyAttributes.TYPE_SIMPLE_MAP)
|| (dataType == CyAttributes.TYPE_UNDEFINED))
throw new IOException("Unsupported Datatype.");
if (dataType == MultiHashMapDefinition.TYPE_BOOLEAN) className = "java.lang.Boolean";
else if (dataType == MultiHashMapDefinition.TYPE_INTEGER) className = "java.lang.Integer";
else if (dataType == MultiHashMapDefinition.TYPE_FLOATING_POINT) className = "java.lang.Double";
else className = "java.lang.String";
try {
fileWriter.write(attributeName + " (class=" + className + ")" + newline);
final MultiHashMap attributeMap = cyAttributes.getMultiHashMap();
if (attributeMap != null) {
final Iterator<String> keys = cyAttributes.getMultiHashMap().getObjectKeys(attributeName);
String key;
Object value;
Iterator objIt;
String vs;
StringBuilder result = new StringBuilder();
while (keys.hasNext()) {
key = keys.next();
if (cyAttributes.getType(attributeName) == CyAttributes.TYPE_SIMPLE_LIST)
value = cyAttributes.getListAttribute(key, attributeName);
else value = cyAttributes.getAttribute(key, attributeName);
key = encodeString(key);
if (value != null) {
if (value instanceof List) {
result.append(key + " = ");
if (((Collection) value).size() > 0) {
Object o;
objIt = ((Collection) value).iterator();
result.append("(");
o = objIt.next();
vs = o.toString();
vs = slashEncodeString(vs);
vs = encodeString(vs);
result.append(vs);
while (objIt.hasNext()) {
o = objIt.next();
vs = o.toString();
vs = slashEncodeString(vs);
vs = encodeString(vs);
result.append("::" + vs);
}
result.append(")" + newline);
fileWriter.write(result.toString());
result = new StringBuilder();
}
} else {
vs = value.toString();
vs = slashEncodeString(vs);
vs = encodeString(vs);
fileWriter.write(key + " = " + vs + newline);
}
}
}
fileWriter.flush();
}
} finally {
if (fileWriter != null) {
fileWriter.close();
}
}
}
@SuppressWarnings("unchecked")
@Override
public void actionPerformed(ActionEvent ae) {
String action = ae.getActionCommand();
LinkTriple[] addNodes = null;
if (action.equals("Fetch")) {
addNodes = iSparql.ExploreURI(urlText.getText());
addLinks(addNodes);
// Cytoscape.getCurrentNetwork().addNode( Cytoscape.getCyNode( urlText.getText(), true ) );
}
if (action.equals("Fetch Selected")) {
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<LinkTriple> nodeList = new LinkedList<LinkTriple>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
for (LinkTriple newNode : iSparql.ExploreURI(node.getIdentifier())) {
nodeList.add(newNode);
}
}
if (filterCheckbox.getState())
addLinks(iSparql.NodeFilter(null, nodeList.toArray(new LinkTriple[0])));
else addLinks(nodeList.toArray(new LinkTriple[0]));
}
if (action.equals("Find Nodes")) {
CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<Map<String, Object>> nodeList = new LinkedList<Map<String, Object>>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
Map<String, Object> map = new HashMap<String, Object>();
String id = node.getIdentifier();
map.put("ID", id);
for (String attr : nodeAttr.getAttributeNames()) {
if (nodeAttr.hasAttribute(id, attr)) {
System.out.println(id + " " + attr + " " + nodeAttr.getType(attr));
if (nodeAttr.getType(attr) == CyAttributes.TYPE_STRING) {
Object iAttr = nodeAttr.getAttribute(id, attr);
map.put(attr, iAttr);
}
}
}
nodeList.add(map);
}
LinkTriple[] links = iSparql.NodeSearch(null, nodeList, "ID");
addLinks(links);
}
if (action.equals("Edit Namespaces")) {
Map<String, String> nameMap = prefs.getNameSpaces();
Map<String, String> newMap = NameSpaceEditor.EditDialog(nameMap);
for (String key : nameMap.keySet()) {
prefs.removeNameSpace(key);
}
for (String key : newMap.keySet()) {
prefs.addNameSpace(key, newMap.get(key));
}
}
}