| Modifier and Type | Method and Description |
|---|---|
void |
LCMSData.load(LCMSDataSubset subset)
Will load scan meta-info and spectra for the specified subset.
|
void |
LCMSData.load(LCMSDataSubset subset,
Object user)
Will load scan meta-info and spectra for the specified subset.
|
| Modifier and Type | Method and Description |
|---|---|
ISpectrum |
IScan.fetchSpectrum()
Get the spectrum, possibly preloading it from disk.
|
| Modifier and Type | Method and Description |
|---|---|
ISpectrum |
ScanDefault.fetchSpectrum() |
| Modifier and Type | Method and Description |
|---|---|
static void |
ScanCollectionHelper.finalizeScanCollection(IScanCollection scans)
Sets relationships between parent/child scans based on scan numbering.
|
void |
IScanCollection.loadData(LCMSDataSubset subset)
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Loads spectra for a subset of scans, or all of them, depending on the configuration.
|
void |
IScanCollection.loadData(LCMSDataSubset subset,
StorageStrategy storageStrategy)
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Loads spectra for a subset of scans, or all of them, depending on the configuration.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ScanCollectionDefault.loadData(LCMSDataSubset subset) |
void |
ScanCollectionDefault.loadData(LCMSDataSubset subset,
StorageStrategy storageStrategy) |
| Modifier and Type | Class and Description |
|---|---|
class |
RunHeaderBoundsNotFound
Created by Dmitry Avtonomov on 2015-10-26.
|
class |
RunHeaderParsingException
Used in areas, where run header info is parsed.
|
| Modifier and Type | Method and Description |
|---|---|
T |
LCMSDataSource.fetchIndex()
Returns the index, or parses it from the original file and caches for future reuse.
|
LCMSRunInfo |
LCMSDataSource.fetchRunInfo()
Gets the run info, parsing it if it yet hasn't been, and caches for reuse.
|
LCMSRunInfo |
AbstractLCMSDataSource.fetchRunInfo() |
List<IScan> |
LCMSDataSource.parse(LCMSDataSubset subset)
Parse a range of scan numbers.
|
List<IScan> |
LCMSDataSource.parse(List<Integer> scanNums)
The storage strategy should always be
StorageStrategy.STRONG,
the receiver then can set it to whatever it needs. |
T |
LCMSDataSource.parseIndex() |
LCMSRunInfo |
LCMSDataSource.parseRunInfo() |
IScan |
LCMSDataSource.parseScan(int num,
boolean parseSpectrum)
Parse a single scan from file on disk by it's number.
|
ISpectrum |
LCMSDataSource.parseSpectrum(int num)
Parse a single spectrumRef from file on disk by it's number.
|
| Modifier and Type | Method and Description |
|---|---|
umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml |
GPMDBFile.parse() |
static umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml |
GPMDBParser.parse(Path path) |
| Modifier and Type | Method and Description |
|---|---|
static umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType |
MzIdentMLParser.parse(Path path)
Will parse the whole file.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
MzIdentMlReadWriteExample.main(String[] args) |
static void |
MzIdentMlExample.main(String[] args) |
| Modifier and Type | Method and Description |
|---|---|
static MZMLPeaksDecoder.DecodedData |
MZMLPeaksDecoder.decode(byte[] bytesIn,
int lengthIn,
Integer precision,
int numPoints,
EnumSet<PeaksCompression> compressions)
Converts a base64 encoded mz or intensity string used in mzML files to an array of doubles.
|
MZMLIndex |
MZMLFile.fetchIndex() |
MZMLRunInfo |
MZMLFile.fetchRunInfo() |
protected int |
MZMLIndexParser.findScanLength(long offset)
Finds the length of a scan entry in the original file by reading it,
starting at the provided offset and looking for an "end of scan" tag.
|
int |
MZMLMultiSpectraParser.findThisStreamFirstScanLen()
Intended use: find the length of the last scan entry in the file.
|
protected int |
MZMLMultiSpectraParser.mapIdRefToInternalScanNum(javolution.text.CharArray id)
Given a scan ID goes to the index and tries to find a mapping.
|
protected int |
MZMLMultiSpectraParser.mapRawNumToInternalScanNum(int spectrumIndex)
Given a scan internal number (spectrum index) goes to the index and tries to find a mapping.
|
MZMLIndex |
MZMLIndexParser.parse() |
MZMLIndex |
MZMLFile.parseIndex() |
MZMLRunInfo |
MZMLFile.parseRunInfo() |
| Constructor and Description |
|---|
MZMLMultiSpectraParser(InputStream is,
LCMSDataSubset subset,
MZMLFile source) |
| Modifier and Type | Method and Description |
|---|---|
static MZXMLPeaksDecoder.DecodedData |
MZXMLPeaksDecoder.decode(byte[] bytesIn,
int lengthIn,
int precision,
PeaksCompression compression)
Converts a base64 encoded mz-intensity string from used in mzXML and mzML
files to an array of doubles.
|
static MZXMLPeaksDecoder.DecodedData |
MZXMLPeaksDecoder.decode(byte[] bytesIn,
int precision,
PeaksCompression compression)
Convenience shortcut, which assumes the whole
bytesIn array is useful data. |
protected javolution.text.CharArray |
MZXMLMultiSpectraParser.fetchAttribute(javolution.xml.sax.Attributes attrs,
MZXMLMultiSpectraParser.ATTR attr) |
MZXMLIndex |
MZXMLFile.fetchIndex() |
protected int |
MZXMLIndexParser.findScanLength(long offset)
Finds the length of a scan entry in the original file by reading it,
starting at the provided offset and looking for an "end of scan" tag.
|
MZXMLIndex |
MZXMLIndexParser.parse() |
MZXMLIndex |
MZXMLFile.parseIndex() |
LCMSRunInfo |
MZXMLFile.parseRunInfo() |
| Modifier and Type | Method and Description |
|---|---|
static void |
Example4.main(String[] args) |
static void |
Example3.main(String[] args) |
static void |
Example2.main(String[] args) |
static void |
Example.main(String[] args) |
| Modifier and Type | Method and Description |
|---|---|
static Iterator<umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary> |
PepXmlParser.parse(InputStream is)
This is helpful for huge combined pepxml files where identification results from several runs are
merged together.
|
static umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis |
PepXmlParser.parse(Path path)
The simplest method to parse the whole MsmsPipelineAnalysis from a file.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
PepXmlSimpleExample.main(String[] args) |
| Modifier and Type | Method and Description |
|---|---|
static umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary |
ProtXmlParser.parse(Path path) |
| Modifier and Type | Method and Description |
|---|---|
static void |
ProtXmlSimpleExample.main(String[] args) |
| Modifier and Type | Method and Description |
|---|---|
ThermoRawIndex |
ThermoRawFile.fetchIndex() |
List<IScan> |
ThermoRawFile.parse(LCMSDataSubset subset) |
List<IScan> |
ThermoRawFile.parse(List<Integer> scanNums) |
ThermoRawIndex |
ThermoRawFile.parseIndex() |
LCMSRunInfo |
ThermoRawFile.parseRunInfo() |
IScan |
ThermoRawFile.parseScan(int num,
boolean parseSpectrum) |
ISpectrum |
ThermoRawFile.parseSpectrum(int num) |
| Modifier and Type | Method and Description |
|---|---|
I |
AbstractXMLBasedDataSource.buildIndex(I idx)
Be careful with this method, it will go over the whole file, building index from scans that it can find.
|
List<IScan> |
AbstractXMLBasedDataSource.parse(LCMSDataSubset subset) |
List<IScan> |
AbstractXMLBasedDataSource.parse(List<Integer> scanNums)
Deprecated.
this method has not been updated to the new parsing version
|
IScan |
AbstractXMLBasedDataSource.parseScan(int num,
boolean parseSpectrum) |
ISpectrum |
AbstractXMLBasedDataSource.parseSpectrum(int num) |
| Modifier and Type | Method and Description |
|---|---|
static ByteArrayHolder |
ZlibInflater.zlibUncompressBuffer(byte[] compressed,
Integer uncompressedLen)
Convenience method for
ZlibInflater.zlibUncompressBuffer(byte[], int, Integer). |
static ByteArrayHolder |
ZlibInflater.zlibUncompressBuffer(byte[] bytes,
int length,
Integer uncompressedLen)
Inflates zLib compressed byte[].
|
| Modifier and Type | Method and Description |
|---|---|
void |
Base64ContextPooled.close() |
void |
Base64Context.close()
should be called when context becomes useless
|
Base64Context |
Base64.decode(byte[] pArray,
Base64Context ctx)
Decodes a byte[] containing characters in the Base-N alphabet.
|
Base64Context |
Base64.decode(byte[] pArray,
int offset,
int length,
Base64Context ctx)
Decodes a byte[] containing characters in the Base-N alphabet.
|
Base64Context |
Base64.decode(char[] pArray,
Base64Context ctx)
Decodes a char[] containing characters in the Base-N alphabet.
|
Base64Context |
Base64.decode(char[] pArray,
int offset,
int length,
Base64Context ctx)
Decodes a char[] containing characters in the Base-N alphabet.
|
byte[] |
Base64ContextPooled.ensureBufferHasCapacityLeft(int size) |
byte[] |
Base64Context.ensureBufferHasCapacityLeft(int size)
Ensure, that the output data buffer has enough space left for
size mode bytes. |
| Modifier and Type | Method and Description |
|---|---|
static OffsetLength |
XmlUtils.locate(String tag1,
TAG_TYPE tag1Type,
POSITION tag1Loc,
String tag2,
TAG_TYPE tag2Type,
POSITION tag2Loc,
long maxOffset,
InputStream is)
Deprecated.
Try using
XmlUtils.locate(List, List, InputStream, long).
This method uses an XML parser internally, so it's 1) slower than the other method
2) it's reporting of locations is in Characters, not Bytes! |
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