| Package | Description |
|---|---|
| umich.ms.fileio.filetypes.mzml | |
| umich.ms.fileio.filetypes.mzxml | |
| umich.ms.fileio.filetypes.xmlbased |
| Modifier and Type | Method and Description |
|---|---|
protected InputStream |
MZMLRunHeaderParser.getRunHeaderInputStream(OffsetLength msRunLocation) |
| Constructor and Description |
|---|
MZMLIndexElement(int num,
int numRaw,
String id,
OffsetLength offlen) |
| Modifier and Type | Method and Description |
|---|---|
protected OffsetLength |
XmlBasedRunHeaderParser.locateRunHeader(String firstTag,
boolean firstTagIsStart,
boolean firstTagGetStartLoc,
String lastTag,
boolean lastTagIsStart,
boolean lastTagGetStartLoc)
Reads the run header from the file, locating positions of
<firstTag> and first <lastTag> tags. |
| Modifier and Type | Method and Description |
|---|---|
protected abstract InputStream |
XmlBasedRunHeaderParser.getRunHeaderInputStream(OffsetLength msRunLocation)
Be sure to include all the correct tags in this stream.
|
protected InputStream |
MZXMLRunHeaderParser.getRunHeaderInputStream(OffsetLength msRunLocation)
Reads the whole msRun header portion from the file, appending a closing
</msRun> tag to the end,
so that it could be unmarshalled using JAXB without errors. |
protected <T> T |
XmlBasedRunHeaderParser.parseHeaderWithJAXB(Class<T> clazz,
OffsetLength msRunLocation) |
| Constructor and Description |
|---|
MZXMLIndexElement(int num,
int numRaw,
OffsetLength offlen) |
| Modifier and Type | Field and Description |
|---|---|
protected OffsetLength |
AbstractXMLBasedIndexElement.offlen
The offset and length of scan entry in the XML file.
|
| Modifier and Type | Method and Description |
|---|---|
OffsetLength |
XMLBasedIndexElement.getOffsetLength() |
OffsetLength |
AbstractXMLBasedIndexElement.getOffsetLength() |
| Modifier and Type | Method and Description |
|---|---|
void |
XMLBasedIndexElement.setOffsetLength(OffsetLength offlen)
This mutator is needed to facilitate "fixing" of index after it was created.
|
void |
AbstractXMLBasedIndexElement.setOffsetLength(OffsetLength offlen)
Use carefully, the only intended use for this mutator is to extend the already existing offset-length pairs
if the original length was not extending all the way up to the next "scan" tag.
|
| Modifier and Type | Method and Description |
|---|---|
protected int[] |
AbstractXMLBasedDataSource.distributeParseLoad(int numWorkers,
ArrayList<OffsetLength> readTasks) |
protected byte[] |
AbstractXMLBasedDataSource.readContinuousBatchOfSpectra(Iterator<? extends Map.Entry<Integer,? extends XMLBasedIndexElement>> entries,
RandomAccessFile file,
byte[] readBuf,
ArrayList<OffsetLength> readTasks,
int maxScansToReadInBatch) |
protected byte[] |
AbstractXMLBasedDataSource.readListOfSpectra(ListIterator<Integer> scanNumsIter,
int maxScansToReadInBatch,
ArrayList<OffsetLength> readTasks,
NavigableMap<Integer,? extends XMLBasedIndexElement> index,
RandomAccessFile file,
byte[] readBuf)
Reads up to (@code maxScansToRead) scans from the iterator, checking for continuity of scans in the
original file, so it could do sequential reads.
|
protected ArrayList<Future<List<IScan>>> |
AbstractXMLBasedDataSource.submitParseTasks(LCMSDataSubset subset,
LCMSRunInfo info,
int numWorkers,
ExecutorService exec,
byte[] readBuf1,
ArrayList<OffsetLength> readTasks,
int[] workerScanCounts,
boolean areScansContinuous) |
| Constructor and Description |
|---|
AbstractXMLBasedIndexElement(int num,
int numRaw,
OffsetLength offlen) |
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