air java_Aird-SDK-Java

Aird-SDK-Java

Best Practise

### Aird Index File Suffix: .json

### Aird Data File Suffix: .aird

Aird Index File and Aird Data File show be stored in the same directory with the same file name but with different suffix, so

that AirdScanUtil.class can scan both of the two files with the same file name;

when dealing with Spectra, we advice that you should process with Swath Window one by one so that we can control the Memory

#Main API Class

AirdInfo:Main Info Class that contains all the aird index file(json format) information

SwathIndex: Contains all the information about one Swath Window

AirdScanUtil : Scan for a directory for all the aird index file

AirdParser: parse Spectrum with rt or parse Spectrums with Swath Window

Detail Description

##AirdInfo

Name

Type

Required

Description

compressors

List

True

The compression strategies for m/z and intensity array

rangeList

List

False

The precursor m/z window ranges which have been adjusted with experiment overlap. This field is targeted for DIA and PRM type format

indexList

List

True

The index for mass spectrometry data

instruments

List

True

General information about the MS instrument

dataProcessings

List

False

Description of any manipulation (from the first conversion to Aird format until the creation of the current Aird instance document) applied to the data

softwares

List

False

Software used to convert the data. If data has been processed (e.g. profile > centroid) by any additional progs these should be added too

parentFiles

List

False

Path to all the ancestor files (up to the native acquisition file) used to generate the current Aird document

version

String

True

Aird format version

versionCode

Integer

True

Aird format version code

type

String

True

Aird Type. There are four types now: DIA, DDA, PRM, COMMON

fileSize

Long

True

The file size for Aird file and JSON file

totalScanCount

Long

True

Total spectrums count

airdPath

String

False

The .aird file path

creator

String

False

The file creator, this field can be set up in the AirdPro

createDate

String

False

The create date for the aird file

ignoreZeroIntensityPoint

Boolean

True

Whether ignore the point which intensity is 0

features

String

False

Some other features stored with “key:value;key:value” format

##Compressor

Name

Type

Required

Description

----

----

----

----

target

String

True

mz, intensity

methods

List

True

zlib, pFor, log10

precision

Integer

False

10^N, the N means N decimal places for the final data

byteOrder

String

True

LITTLE_ENDIAN, BIG_ENDIAN

##WindowRange

Name

Type

Required

Description

----

----

----

----

start

Double

True

Precursor m/z start

end

Double

True

Precursor m/z end

mz

Double

True

Precursor m/z

features

String

False

Some other features stored with “key:value;key:value” format

##BlockIndex

Name

Type

Required

Description

----

----

----

----

level

Integer

True

1:MS1, 2:MS2

startPtr

Long

True

The start point for the block

endPtr

Long

True

The endpoint for the block

num

Integer

False

The scan number in the vendor file. If a block has a list of MS2, this field is the related MS1’s number

rangeList

List

False

The precursor m/z window ranges which have been adjusted with experiment overlap. This field is targeted for DIA and PRM type format

nums

List

False

Scan numbers in the block

rts

List

True

All the retention times in the block

mzs

List

True

COMMON: the start position for every m/z bytes. Others: the size for every m/z bytes size

ints

List

True

COMMON: the start position for every m/z bytes. Others: the size for every m/z bytes size

features

String

False

Some other features stored with “key:value;key:value” format

##Instrument

Name

Type

Required

Description

----

----

----

----

manufacturer

String

False

Instrument manufacturer: ”ABSciex”,”Thermo Fisher”

ionization

String

False

Ionization

resolution

String

False

Resolution

model

String

False

Instrument model

source

List

False

Source: ”electrospray ionization”, ”electrospray inlet”

analyzer

List

False

Analyzer: “quadrupole”, “orbitrap”

detector

List

False

Detector: ”inductive detector”

features

String

False

Some other features stored with “key:value;key:value” format

##DataProcessing

Name

Type

Required

Description

----

----

----

----

processingOperations

List

False

Any additional manipulation not included elsewhere in the dataProcessing element

##Software

Name

Type

Required

Description

----

----

----

----

name

String

True

The software name

version

String

False

The software version

##ParentFile

Name

Type

Required

Description

----

----

----

----

name

String

True

The filename

location

String

False

The file location

type

String

False

The file type

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