/**
* Creates the mgf file object from an existing mgf file with a pre-parsed index of ms2 spectra.
* The index must hold the offsets of all "BEGIN IONS" lines in the order they appear in the file.
*
* @param file The mgf file
* @param index An ArrayList holding the
* @throws JMzReaderException
*/
public MgfFile(File file, List<IndexElement> index) throws JMzReaderException {
// open the file
try {
// save the file
sourceFile = file;
// save the index
this.index = index;
BufferedRandomAccessFile reader = new BufferedRandomAccessFile(sourceFile, "r", 1024 * 1000);
// process the file line by line
String line;
boolean inHeader = true; // indicates whether we're still in the attribute section
while ((line = reader.getNextLine()) != null) {
// remove any comments from the line (if the line will be processed)
line = line.replaceAll(mgfCommentRegex, "").trim();
// ignore empty lines
if (line.length() < 1) {
continue;
}
// break the loop as soon as a ms2 query is encountered
if (line.contains("BEGIN IONS")) break;
// check if it's an attribute line
if (inHeader && line.contains("=")) {
Matcher matcher = attributePattern.matcher(line);
if (!matcher.find()) throw new JMzReaderException("Malformatted attribute encountered");
if (matcher.groupCount() != 2)
throw new JMzReaderException("Malformatted attribute encountered");
// process the attribute
processAttribute(matcher.group(1), matcher.group(2));
continue;
} else if (!inHeader && line.contains("=")) {
throw new JMzReaderException(
"Attribute encountered at illegal position. Attributes must all be at the beginning of the file");
} else {
inHeader = false;
}
// if we're not in the header and it's not a ms2 it must be a pmf query
if (!inHeader) {
PmfQuery query = new PmfQuery(line);
pmfQueries.add(query);
}
}
reader.close();
} catch (FileNotFoundException e) {
throw new JMzReaderException("MgfFile does not exist.", e);
} catch (IOException e) {
throw new JMzReaderException("Failed to read from mgf file.", e);
}
}
/**
* Creates the mgf file object from an existing mgf file.
*
* @param file The mgf file
* @param allowCustomTags Indicates if the parser should throw an exception when encountering
* non-standard tags
* @throws JMzReaderException
*/
public MgfFile(File file, boolean allowCustomTags) throws JMzReaderException {
setAllowCustomTags(allowCustomTags);
// open the file
try {
// save the file
sourceFile = file;
BufferedRandomAccessFile braf =
new BufferedRandomAccessFile(sourceFile.getAbsolutePath(), "r", 1024 * 100);
// process the file line by line
String line;
boolean inHeader = true; // indicates whether we're still in the attribute section
boolean inMs2 = false;
long lastPosition = 0;
long beginIonsIndex = 0; // the index where the last "BEGIN IONS" was encountered
while ((line = braf.getNextLine()) != null) {
// remove any comments from the line (if the line will be processed)
if (!inMs2) line = line.replaceAll(mgfCommentRegex, "").trim();
// ignore empty lines
if (line.length() < 1) {
// always update file pointer before continue
lastPosition = braf.getFilePointer();
continue;
}
// check if a ms2 block started
if (!inMs2 && line.contains("BEGIN IONS")) {
// save the offset of the spectrum
beginIonsIndex = lastPosition;
inMs2 = true;
}
if (inMs2 && line.contains("END IONS")) {
inMs2 = false;
// index.add(new IndexElement(beginIonsIndex, reader.getFilePointer()));
int size = (int) (braf.getFilePointer() - beginIonsIndex);
index.add(new IndexElementImpl(beginIonsIndex, size));
// always update file pointer before continue
lastPosition = braf.getFilePointer();
continue;
}
if (inMs2) {
// always update file pointer before continue
lastPosition = braf.getFilePointer();
continue;
}
// check if it's an attribute line
if (inHeader && line.contains("=")) {
Matcher matcher = attributePattern.matcher(line);
if (!matcher.find()) throw new JMzReaderException("Malformatted attribute encountered");
if (matcher.groupCount() != 2)
throw new JMzReaderException("Malformatted attribute encountered");
// process the attribute
processAttribute(matcher.group(1), matcher.group(2));
// always update file pointer before continue
lastPosition = braf.getFilePointer();
continue;
} else if (!inHeader && line.contains("=")) {
throw new JMzReaderException(
"Attribute encountered at illegal position. Attributes must all be at the beginning of the file");
} else {
inHeader = false;
}
// if we're not in the header and it's not a ms2 it must be a pmf query
if (!inHeader) {
PmfQuery query = new PmfQuery(line);
pmfQueries.add(query);
}
// always update file pointer before continue
lastPosition = braf.getFilePointer();
}
braf.close();
} catch (FileNotFoundException e) {
throw new JMzReaderException("MgfFile does not exist.", e);
} catch (IOException e) {
throw new JMzReaderException("Failed to read from mgf file.", e);
}
}
