Finnigan - Thermo/Finnigan mass spec data decoder River stage zero No dependents

"Finnigan" is a non-functional package whose only purpose is to pull in all other packages in the module into its namespace. It does no work; all work is done in the sub-modules. Each submodule has its own documentation; please see the "SUBMODULES" s...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::Error - a decoder for Error, an error log record River stage zero No dependents

Error is a varibale-length structure containing timestamped error messages. It implicitly links an error message to a scan using the retention time. METHODS decode($stream) The constructor method time Get the entry's timestamp (retention time) messag...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::Peak - a full-featured decoder for a single (M/z, abundance) pair, an element of the PeakList structure River stage zero No dependents

This decoder is useless in normal life. It is a full-featured decoder for the pair of floating-point numbers representing the centroid _M/z_ and intensity of a peak. The data it generates contain the seek addresses, sizes and types of both attributes...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::Peaks - a decoder for PeaksList, the list of peak centroids River stage zero No dependents

This decoder reads the stream of floating-point numbers into a list of Finnigan::Peak objects, each containing an (M/z, abundance) pair. It is a simple but full-featured decoder for the PeakList structure, part of ScanDataPacket. The data it generate...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::SeqRow - a decoder for one row of the sequencer table River stage zero No dependents

This structure contains an instance of Finnigan::InjectionData and a bunch of text tags, with one long integer buried among them. Those strings whose meaning is obvious identify the sample and its provenance. Finnigan::InjectionData contains injectio...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::InstID - a decoder for InstID, a set of instrument identifiers River stage zero No dependents

InstID is a static (fixed-size) structure containing several instrument identifiers and some unknown data. The identifiers include the model name, the serial number and the software version. METHODS decode($stream) The constructor method model Get th...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::CASInfo - a decoder for autosampler data River stage zero No dependents

CASInfo is a structure with uncertain purpose that contains a binary preamble with autosampler co-ordinates (CASInfoPreamble), followed by a text string. The text string is apparently a comment; in one instance where it was non-null, it contained thi...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::Scan - a lightweight scan data decoder River stage zero No dependents

This decoder reads the entire ScanDataPacket, discarding the location and type meta-data. It is a more efficient alternative to the full-featured combination decoders using the Finnigan::Profile, Finnigan::Peaks and Finnigan::Peak modules. METHODS de...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::OLE2FAT - a decoder for FAT Sector, a block allocation structure in OLE2 River stage zero No dependents

This is an auxiliary decoder used by Finnigan::OLE2File; it is of no use on its own. It reads a specified number of 4-byte intergers into an array that is to be interpreted as a sector allocation table by the caller of the sect method. METHODS decode...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::OLE2DIF - a decoder for Double-Indirect FAT, a block allocation structure in Microsoft OLE2 River stage zero No dependents

This is an auxiliary decoder used by Finnigan::OLE2File; it is of no use otherwise. It reads a specified number of 4-byte intergers into an array that is to be interpreted as a sector allocation table by the caller of the sect method. DIF == Double-I...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::Reaction - a decoder for Reaction, the container for precursor mass and fragmentation energy River stage zero No dependents

This object contains a couple of double-precision floating point numbers that define the precursor ion M/z and the energy of the fragmentation reaction. There are other elements that currently remain unknown: a double (set to 1.0 in all observations)...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::AuditTag - a decoder for AuditTag, a substructure found in the Finnigan file headers River stage zero No dependents

AuditTag is a structure with uncertain purpose that contains a timestamp in Windows format and a pair of text tags. These tags seem to carry the user ID of the person who created the files. Additionally, there is a long integer, possibly carrying the...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::Profile - a full-featured decoder for Finnigan scan profiles River stage zero No dependents

Finningan::Profile is a full-featured decoder for Finnigan scan profiles. The data it generates contain the seek addresses, sizes and types of all decoded elements, no matter how small. That makes it very handy in the exploration of the file format a...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::Decoder - a generic binary structure decoder River stage zero No dependents

This class is not inteded to be used directly; it is a parent class for all Finnigan decoders. The fields to decode are passed to the decoder's read() method in a list reference, where every even item specifies the key the item will be known as in th...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::OLE2File - a decoder for Microsoft structured data files (OLE2 a.k.a. CDF) River stage zero No dependents

Thermo uses the Microsoft OLE2 container to store the instrument method files. This container has a hirerachical structure based on a FAT filesystem. It seems like there are always two levels of hierarchy used in the method container: one directory n...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::FileHeader - a decoder for Finnigan file headers River stage zero No dependents

The key information contained in the Finnigan header is the file version number. Since the file structure varies from one version to another, the decoders must be aware of it. METHODS decode($stream) The constructor method version Get the file versio...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::RunHeader - a decoder for RunHeader, the primary file index structure River stage zero No dependents

Decodes RunHeader, the static (fixed-size) structure containing data stream lengths and addresses, as well as some unidentified data. Every data stream in the file has its address stored in RunHeader or in its historical antecedent SampleInfo, which ...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::MethodFile - a decoder for the outer MethodFile container River stage zero No dependents

This object decodes the outer container for a Windows OLE2 directory which in turn contains a set of method files for various instruments, both in binary and text representations. The outer container also contains a name translation table mapping the...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::ScanEvent - a decoder for ScanEvent, a detailed scan descriptor River stage zero No dependents

This is a variable-layout (but otherwise static) structure, contaning several key details about the scan. Most of those details are concentrated in its head element, ScanEventPreamble. The layout depends on the number of precursor ions and is governe...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC

Finnigan::SampleInfo - a decoder for SampleInfo, the primary file index structure River stage zero No dependents

SampleInfo is a static (fixed-size) binary preamble to RunHeader containing data stream lengths and addresses, as well as some unidentified data. All data streams in the file, except for the list of ScanHeader records and TrailerScanEvent stream have...

SELKOVJR/Finnigan-0.0206d - 12 May 2012 00:17:37 UTC
38 results (0.026 seconds)