private int findAttr(String attrName, List attrList) {
for (int i = 0; i < attrList.size(); i++) {
NWBAttribute attr = (NWBAttribute) attrList.get(i);
if (attr.getAttrName().equalsIgnoreCase(attrName)) {
return i;
}
}
return -1;
}
private void writeNodes(
String s, PrintWriter out, ValidateNWBFile validator, List nodeAttrList, int mapper) {
out.flush();
String[] columns = NETFileFunctions.processTokens(s);
int i = 0;
for (Iterator ii = nodeAttrList.iterator(); ii.hasNext(); ) {
NWBAttribute na = (NWBAttribute) ii.next();
String value = columns[i];
// System.out.print(value + "::");
// value.replace("\"", "");
if (value.equalsIgnoreCase("*")) {
} else if (NETFileFunctions.isInList(na.getAttrName(), noPrintParameters)) {
if (na.getDataType().equalsIgnoreCase(NWBFileProperty.TYPE_STRING)) {
String[] sa = value.split(" ");
if (sa.length > 1) out.print(" \"" + value + "\" ");
else out.print(value + " ");
} else {
if (na.getAttrName().equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_ID)) {
this.vertexToIdMap.put(new Integer(value), new Integer(mapper));
out.print(mapper + " ");
} else out.print(value + " ");
}
} else if (na.getDataType().equalsIgnoreCase("float")
|| na.getDataType().equalsIgnoreCase("int")) {
if (!value.equalsIgnoreCase("")) {
// System.out.print(na.getAttrName() + " " + value + " ");
String ss = na.getAttrName();
if (ss.matches("[bil]?c1")) {
ss = ss.replace("1", "");
ss += " " + value + " ";
for (int j = 1; j < 3; j++) {
ss += columns[j + i] + " ";
ii.next();
}
i = i + 2;
out.print(ss);
} else out.print(na.getAttrName() + " " + value + " ");
}
} else if (na.getDataType().equalsIgnoreCase("string")) {
if (!value.equalsIgnoreCase("")) {
if (na.getAttrName().startsWith("unknown")) {
String[] sa = value.split(" ");
if (sa.length > 1) out.print(" \"" + value + "\" ");
else out.print(value + " ");
} else out.print(na.getAttrName() + " \"" + value + "\" ");
}
} else ;
i++;
}
out.print("\r\n");
}
private void printGraph(PrintWriter out, ValidateNWBFile validator, BufferedReader reader)
throws IOException {
if (validator.getHasTotalNumOfNodes() && validator.getSkipNodeList()) {
int totalNumOfNodes = validator.getTotalNumOfNodes();
for (int i = 1; i <= totalNumOfNodes; i++) {
out.println("<node id=\"" + i + "\">");
out.println("<data key=\"label\">" + i + "</data></node>");
}
}
// read from nwb file and write to the graphml file
boolean inNodesSection = false;
boolean inDirectededgesSection = false;
boolean inUndirectededgesSection = false;
String line = reader.readLine();
int edgeID = 0;
while (line != null) {
if (line.length() == 0) {
line = reader.readLine();
continue;
}
String line_lower = line.toLowerCase();
// find node section header that looks like
// *nodes or *nodes 1000
if (line_lower.startsWith(NWBFileProperty.HEADER_NODE)) {
inNodesSection = true;
inDirectededgesSection = false;
inUndirectededgesSection = false;
line = reader.readLine();
continue;
}
if (line_lower.startsWith(NWBFileProperty.HEADER_DIRECTED_EDGES)) {
inDirectededgesSection = true;
inNodesSection = false;
inUndirectededgesSection = false;
line = reader.readLine();
continue;
}
if (line_lower.startsWith(NWBFileProperty.HEADER_UNDIRECTED_EDGES)) {
inUndirectededgesSection = true;
inNodesSection = false;
inDirectededgesSection = false;
line = reader.readLine();
continue;
}
if (inNodesSection) { // ignore attribute list line or comment line(s)
if (line_lower.startsWith(NWBFileProperty.ATTRIBUTE_ID)
|| line_lower.startsWith(NWBFileProperty.PREFIX_COMMENTS + NWBFileProperty.ATTRIBUTE_ID)
|| line_lower.startsWith(NWBFileProperty.PREFIX_COMMENTS)) {
line = reader.readLine();
continue;
} else {
StringTokenizer st = new StringTokenizer(line);
String[] columns = validator.processTokens(st);
List nodeAttrList = validator.getNodeAttrList();
out.println("<node id=\"" + columns[0] + "\">");
for (int i = 1; i < nodeAttrList.size(); i++) {
NWBAttribute attr = (NWBAttribute) nodeAttrList.get(i);
String value = columns[i];
if (attr.getDataType().equalsIgnoreCase(NWBFileProperty.TYPE_STRING)) {
if (value.startsWith("\"")) {
value = value.substring(1);
}
if (value.endsWith("\"")) {
value = value.substring(0, value.length() - 1);
}
}
out.println("<data key=\"" + attr.getAttrName() + "\">" + value + "</data>");
}
out.println("</node>");
}
} // end if (inNodesSection)
if (inDirectededgesSection || inUndirectededgesSection) {
// ignore attribute list line or comment line(s)
if (line_lower.startsWith(NWBFileProperty.ATTRIBUTE_SOURCE)
|| line_lower.startsWith(
NWBFileProperty.PREFIX_COMMENTS + NWBFileProperty.ATTRIBUTE_SOURCE)
|| line_lower.startsWith(NWBFileProperty.PREFIX_COMMENTS)) {
line = reader.readLine();
continue;
} else {
List edgeAttrList = new ArrayList();
StringTokenizer st = new StringTokenizer(line);
String[] columns = validator.processTokens(st);
if (inDirectededgesSection) edgeAttrList = validator.getDirectedEdgeAttrList();
else if (inUndirectededgesSection) edgeAttrList = validator.getUndirectedEdgeAttrList();
edgeID++;
// find if there is an id attribute
int idColumnNumber = findAttr(NWBFileProperty.ATTRIBUTE_ID, edgeAttrList);
int sourceColumnNumber = findAttr(NWBFileProperty.ATTRIBUTE_SOURCE, edgeAttrList);
int targetColumnNumber = findAttr(NWBFileProperty.ATTRIBUTE_TARGET, edgeAttrList);
if (idColumnNumber == -1) {
if (edgeAttrList.size() > 2) {
out.println(
"<edge id=\""
+ edgeID
+ "\" source=\""
+ columns[sourceColumnNumber]
+ "\" target=\""
+ columns[targetColumnNumber]
+ "\">");
for (int i = 0; i < edgeAttrList.size(); i++) {
NWBAttribute attr = (NWBAttribute) edgeAttrList.get(i);
String attrName = attr.getAttrName();
if (!(attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_SOURCE)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_TARGET)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_ID))) {
String value = columns[i];
if (attr.getDataType().equalsIgnoreCase(NWBFileProperty.TYPE_STRING)) {
if (value.startsWith("\"")) {
value = value.substring(1);
}
if (value.endsWith("\"")) {
value = value.substring(0, value.length() - 1);
}
}
out.println("<data key=\"" + attr.getAttrName() + "\">" + value + "</data>");
}
}
out.println("</edge>");
} else {
out.println(
"<edge id=\""
+ edgeID
+ "\" source=\""
+ columns[sourceColumnNumber]
+ "\" target=\""
+ columns[targetColumnNumber]
+ "\"/>");
}
} else {
if (edgeAttrList.size() > 3) {
out.println(
"<edge id=\""
+ columns[idColumnNumber]
+ "\" source=\""
+ columns[sourceColumnNumber]
+ "\" target=\""
+ columns[targetColumnNumber]
+ "\">");
for (int i = 0; i < edgeAttrList.size(); i++) {
NWBAttribute attr = (NWBAttribute) edgeAttrList.get(i);
String attrName = attr.getAttrName();
if (!(attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_SOURCE)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_TARGET)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_ID))) {
out.println("<data key=\"" + attr.getAttrName() + "\">" + columns[i] + "</data>");
}
}
out.println("</edge>");
} else {
out.println(
"<edge id=\""
+ columns[idColumnNumber]
+ "\" source=\""
+ columns[sourceColumnNumber]
+ "\" target=\""
+ columns[targetColumnNumber]
+ "\"/>");
}
}
}
} // end if (inDirectededgesSection || inUndirectededgesSection)
line = reader.readLine();
} // end while
}
// write GraphML-Attributes
private void writeAttributes(PrintWriter out, ValidateNWBFile validator) {
// first handle node attributes
List array = validator.getNodeAttrList();
for (int i = 0; i < array.size(); i++) {
NWBAttribute attr = (NWBAttribute) array.get(i);
String attrName = attr.getAttrName();
if (attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_ID)) {
continue;
}
out.println(
"<key id=\""
+ attr.getAttrName()
+ "\" for=\"node\" attr.name=\""
+ attr.getAttrName()
+ "\" attr.type=\""
+ attr.getDataType()
+ "\" /> ");
}
if (validator.isDirectedGraph() && !validator.isUndirectedGraph()) {
// this is a directed graph
array = validator.getDirectedEdgeAttrList();
for (int i = 0; i < array.size(); i++) {
NWBAttribute attr = (NWBAttribute) array.get(i);
String attrName = attr.getAttrName();
if (attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_SOURCE)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_TARGET)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_ID)) {
continue;
}
out.println(
"<key id=\""
+ attr.getAttrName()
+ "\" for=\"edge\" attr.name=\""
+ attr.getAttrName()
+ "\" attr.type=\""
+ attr.getDataType()
+ "\" />");
}
out.println("<graph edgedefault=\"directed\">");
} else if (!validator.isDirectedGraph() && validator.isUndirectedGraph()) {
// this is a undirected graph
array = validator.getUndirectedEdgeAttrList();
for (int i = 0; i < array.size(); i++) {
NWBAttribute attr = (NWBAttribute) array.get(i);
String attrName = attr.getAttrName();
if (attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_SOURCE)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_TARGET)
|| attrName.equalsIgnoreCase(NWBFileProperty.ATTRIBUTE_ID)) {
continue;
}
out.println(
"<key id=\""
+ attr.getAttrName()
+ "\" for=\"edge\" attr.name=\""
+ attr.getAttrName()
+ "\" attr.type=\""
+ attr.getDataType()
+ "\" /> ");
}
out.println("<graph edgedefault=\"undirected\">");
} else if (validator.isDirectedGraph() && validator.isUndirectedGraph()) {
// hybrid graph, don't know how to handle it???
}
}
private void writeEdges(String s, PrintWriter out, ValidateNWBFile validator, List edgeAttrList)
throws Exception {
// System.out.println(s);
out.flush();
int i = 0;
String[] columns = NETFileFunctions.processTokens(s);
/*if (inDirectededgesSection)
edgeAttrList = validator.getDirectedEdgeAttrList();
else if (inUndirectededgesSection)
edgeAttrList = validator.getUndirectedEdgeAttrList();*/
for (Iterator ii = edgeAttrList.iterator(); ii.hasNext(); ) {
NWBAttribute na = (NWBAttribute) ii.next();
String value = columns[i];
// System.out.println(value);
// System.out.print(na.getAttrName()+ " ");
if (value.equalsIgnoreCase("*")) {
} else if (na.getAttrName().equals(NETFileProperty.ATTRIBUTE_LABEL)
|| na.getAttrName().equals(ARCEDGEParameter.PARAMETER_LABEL)) {
out.print(ARCEDGEParameter.PARAMETER_LABEL + " \"" + value + "\" ");
} else if ((NETFileFunctions.isInList(na.getAttrName(), noPrintParameters))
&& !(na.getAttrName().equals(NETFileProperty.ATTRIBUTE_LABEL))) {
if (na.getDataType().equalsIgnoreCase(NWBFileProperty.TYPE_STRING)) {
String[] sa = value.split(" ");
if (sa.length > 1) out.print(" \"" + value + "\" ");
else out.print(value + " ");
} else {
if (na.getAttrName().equals(NWBFileProperty.ATTRIBUTE_SOURCE)
|| na.getAttrName().equals(NWBFileProperty.ATTRIBUTE_TARGET)) {
try {
value = ((Integer) this.vertexToIdMap.get(new Integer(value))).toString();
} catch (NullPointerException npe) {
throw new Exception("Edge references an undefined node " + value);
}
}
out.print(value + " ");
}
} else if (na.getDataType().equalsIgnoreCase("float")
|| na.getDataType().equalsIgnoreCase("int")) {
if (!value.equalsIgnoreCase("")) {
// System.out.print(na.getAttrName() + " " + value + " ");
String ss = na.getAttrName();
if (ss.matches("[bil]?c1")) {
ss = ss.replace("1", "");
ss += " " + value + " ";
for (int j = 1; j < 3; j++) {
ss += columns[j + i] + " ";
ii.next();
}
i = i + 2;
out.print(ss);
} else out.print(na.getAttrName() + " " + value + " ");
}
} else if (na.getDataType().equalsIgnoreCase("string")) {
if (!value.equalsIgnoreCase("")) {
if (na.getAttrName().startsWith("unknown")) {
String[] sa = value.split(" ");
if (sa.length > 1) out.print(" \"" + value + "\" ");
else out.print(value + " ");
} else out.print(na.getAttrName() + " \"" + value + "\" ");
}
} else ;
i++;
}
out.print("\r\n");
}