private static String addFileList(String script, String tag) {
String fileList = "";
int i = -1;
while ((i = script.indexOf(tag, i + 1)) >= 0) {
fileList += Parser.getNextQuotedString(script, i) + "\n";
}
return fileList;
}
protected void readAtomCountAndOrigin() throws Exception {
String atomLine = br.readLine();
String[] tokens = Parser.getTokens(atomLine, 0);
atomCount = parseInt(tokens[0]);
negativeAtomCount = (atomCount < 0); // MO list
if (negativeAtomCount) atomCount = -atomCount;
volumetricOrigin.set(parseFloat(tokens[1]), parseFloat(tokens[2]), parseFloat(tokens[3]));
JvxlReader.jvxlCheckAtomLine(
isXLowToHigh, isAngstroms, tokens[0], atomLine, jvxlFileHeaderBuffer);
if (!isAngstroms) volumetricOrigin.scale(ANGSTROMS_PER_BOHR);
}
static String determineFileType(BufferedReader bufferedReader) {
// JVXL should be on the FIRST line of the file, but it may be
// after comments or missing.
// Apbs, Jvxl, or Cube
String line;
LimitedLineReader br = new LimitedLineReader(bufferedReader, 16000);
// sure bets, but not REQUIRED:
if ((line = br.info()).indexOf("#JVXL+") == 0) return "Jvxl+";
if (line.indexOf("#JVXL") == 0) return "Jvxl";
if (line.indexOf("&plot") == 0) return "Jaguar";
if (line.indexOf("!NTITLE") >= 0 || line.indexOf("REMARKS ") >= 0) return "Xplor";
line = br.readNonCommentLine();
if (line.indexOf("object 1 class gridpositions counts") == 0) return "Apbs";
// Jvxl, or Cube, maybe formatted Plt
String[] tokens = Parser.getTokens(line);
line = br.readNonCommentLine(); // second line
if (tokens.length == 2
&& Parser.parseInt(tokens[0]) == 3
&& Parser.parseInt(tokens[1]) != Integer.MIN_VALUE) {
tokens = Parser.getTokens(line);
if (tokens.length == 3
&& Parser.parseInt(tokens[0]) != Integer.MIN_VALUE
&& Parser.parseInt(tokens[1]) != Integer.MIN_VALUE
&& Parser.parseInt(tokens[2]) != Integer.MIN_VALUE) return "PltFormatted";
}
line = br.readNonCommentLine(); // third line
// next line should be the atom line
int nAtoms = Parser.parseInt(line);
if (nAtoms == Integer.MIN_VALUE) return (line.indexOf("+") == 0 ? "Jvxl+" : "UNKNOWN");
if (nAtoms >= 0) return "Cube"; // Can't be a Jvxl file
nAtoms = -nAtoms;
for (int i = 4 + nAtoms; --i >= 0; )
if ((line = br.readNonCommentLine()) == null) return "UNKNOWN";
int nSurfaces = Parser.parseInt(line);
if (nSurfaces == Integer.MIN_VALUE) return "UNKNOWN";
return (nSurfaces < 0 ? "Jvxl" : "Cube"); // Final test looks at surface definition line
}
int parseInt(String s) {
next[0] = 0;
return Parser.parseInt(s, next);
}
int parseInt() {
return Parser.parseInt(line, next);
}
float parseFloatNext(String s) {
return Parser.parseFloat(s, next);
}
float parseFloat(String s) {
next[0] = 0;
return Parser.parseFloat(s, next);
}
float parseFloat() {
return Parser.parseFloat(line, next);
}
public static String[] getTokens(String s) {
return Parser.getTokens(s);
}
protected String parseToken(String s, int iStart, int iEnd) {
next[0] = iStart;
return Parser.parseToken(s, iEnd, next);
}
protected static String parseTrimmed(String s, int iStart, int iEnd) {
return Parser.parseTrimmed(s, iStart, iEnd);
}
protected String parseToken(String s) {
next[0] = 0;
return Parser.parseToken(s, next);
}
protected String parseTokenNext(String s) {
return Parser.parseToken(s, next);
}
protected String parseToken() {
return Parser.parseToken(line, next);
}
protected int parseInt(String s, int iStart, int iEnd) {
next[0] = iStart;
return Parser.parseInt(s, iEnd, next);
}
protected static String[] getTokens(String s, int iStart) {
return Parser.getTokens(s, iStart);
}
int parseIntNext(String s) {
return Parser.parseInt(s, next);
}
protected String[] getTokens() {
return Parser.getTokens(line);
}
int parseInt(String s, int iStart) {
next[0] = iStart;
return Parser.parseInt(s, next);
}
String[] getTokens() {
return Parser.getTokens(line, 0);
}
protected void parseStringInfestedFloatArray(String s, float[] data) {
Parser.parseStringInfestedFloatArray(s, null, data);
}
protected static float[] getTokensFloat(String s, float[] f, int n) {
if (f == null) f = new float[n];
Parser.parseFloatArray(getTokens(s), f, n);
return f;
}