| 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.
If you don't want the index to be cached, you can call LCMSDataSource.parseIndex() instead. |
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.
Assuming every LCMS file interface must be able to do that. The storage strategy should always be StorageStrategy.STRONG,
the receiver then can set it to whatever it needs. |
ISpectrum |
LCMSDataSource.parseSpectrum(int num)
Parse a single spectrumRef from file on disk by it's number.
Assuming every LCMS file interface must be able to do that. |
| Modifier and Type | Method and Description |
|---|---|
Bioml |
GPMDBFile.parse() |
static Bioml |
GPMDBParser.parse(Path path) |
| Modifier and Type | Method and Description |
|---|---|
static MzIdentMLType |
MzIdentMLParser.parse(Path path)
Will parse the whole file.
|
| Modifier and Type | Method and Description |
|---|---|
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() |
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() |
protected void |
MZMLIndexParser.parseIndexEntries(byte[] bytes,
TreeMap<Integer,MZMLIndexParser.OffsetId> map) |
LCMSRunInfo |
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() |
protected void |
MZXMLIndexParser.parseIndexEntries(byte[] bytes,
TreeMap<Integer,Long> map) |
LCMSRunInfo |
MZXMLFile.parseRunInfo() |
protected int |
MZXMLIndexParser.parseScanNumFromIndex(javolution.text.CharArray scanIdentifier) |
protected int |
MZXMLMultiSpectraParser.tagPeaksStart(javolution.xml.internal.stream.XMLStreamReaderImpl reader,
int eventType) |
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 MsmsPipelineAnalysis |
PepXmlParser.parse(Path path) |
| Modifier and Type | Method and Description |
|---|---|
static void |
PepXmlSimpleExample.main(String[] args) |
| Modifier and Type | Method and Description |
|---|---|
static 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).Inflates zLib compressed byte[]. |
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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