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 writeVertices(ValidateNETFile vmf, PrintWriter pw) {
pw.write(MATFileProperty.HEADER_VERTICES + " " + vmf.getVertices().size() + "\n");
for (int i = 0; i < vmf.getVertices().size(); i++) {
NETVertex mv = (NETVertex) vmf.getVertices().get(i);
String s = "";
for (int j = 0; j < NETVertex.getVertexAttributes().size(); j++) {
try {
NETAttribute ma = (NETAttribute) NETVertex.getVertexAttributes().get(j);
String attr = ma.getAttrName();
String type = ma.getDataType();
String value = mv.getAttribute(attr).toString();
if (value == null) {
s += "";
} else {
if (NETFileFunctions.isInList(attr, noPrintParameters)) {
if (type.equalsIgnoreCase("string")) s += "\"" + mv.getAttribute(attr) + "\" ";
else s += mv.getAttribute(attr) + " ";
} else {
if (type.equalsIgnoreCase("string")) {
if (attr.startsWith("unknown")) s += " \"" + mv.getAttribute(attr) + "\" ";
else s += attr + " \"" + mv.getAttribute(attr) + "\" ";
} else s += attr + " " + mv.getAttribute(attr) + " ";
}
}
} catch (NullPointerException ex) {
s += "";
}
}
// System.out.println(s);
pw.println(s);
}
// System.out.println("done here");
}
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");
}