| 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.
|
static void |
MZMLFile.main(String[] args) |
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.
|
int |
MZXMLMultiSpectraParser.findThisStreamFirstScanLen()
Intended use: find the length of the last scan entry in the file.
|
static void |
MZXMLFile.main(String[] args)
Use this for testing only
|
protected int |
MZXMLMultiSpectraParser.mapRawNumToInternalScanNum(int rawScanNum)
Given a scan internal number (spectrum index) goes to the index and tries to find a mapping.
|
MZXMLIndex |
MZXMLIndexParser.parse() |
MZXMLIndex |
MZXMLFile.parseIndex() |
LCMSRunInfo |
MZXMLFile.parseRunInfo() |
protected int |
MZXMLMultiSpectraParser.tagPrecursorStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader) |
protected void |
MZXMLMultiSpectraParser.tagScanStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader) |
| Constructor and Description |
|---|
MZXMLMultiSpectraParser(InputStream is,
LCMSDataSubset subset,
MZXMLFile source) |
| 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 |
|---|---|
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 |
|---|---|
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 |
|---|---|
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. |
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