LCMSDataSubset (MSFTBX 1.8.5 API)

java.lang.Object
- umich.ms.datatypes.LCMSDataSubset

All Implemented Interfaces:

Serializable
```
public class LCMSDataSubset
extends Object
implements Serializable
```
Represents a subset of a ScanCollection.

Author:

Dmitry Avtonomov

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static LCMSDataSubset`	`MS1_WITH_SPECTRA` Sets up the parsing parameters to parse all scans, but spectra only for MS1 scans.
`static LCMSDataSubset`	`MS2_WITH_SPECTRA` Sets up the parsing parameters to parse all scans, but spectra only for MS2 scans.
`static LCMSDataSubset`	`STRUCTURE_ONLY` Sets up the parsing parameters to parse only scans for the whole run, no spectra.
`static LCMSDataSubset`	`WHOLE_RUN` Sets up the parsing parameters to parse all the scans and spectra in a run.

Constructor Summary

Constructors
Constructor and Description
`LCMSDataSubset()`
`LCMSDataSubset(Integer scanNumLo, Integer scanNumHi, Set<Integer> msLvls, List<DoubleRange> mzRanges)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`contains(LCMSDataSubset other)` Checks if data ranges described by this subset fully contain ranges specified in another set.
`boolean`	`equals(Object o)`
`Set<Integer>`	`getMsLvls()`
`List<DoubleRange>`	`getMzRanges()`
`Integer`	`getScanNumHi()`
`Integer`	`getScanNumLo()`
`int`	`hashCode()`
`boolean`	`isInSubset(IScan scan)` In some cases we don't have the lower/upper mz window (for MS1 this requires either this data to be in scan meta info, or the spectrumRef to be parsed).
`LCMSDataSubset`	`merge(LCMSDataSubset other)` Doesn't modify original values, always returns a new one.
`void`	`setMsLvls(Set<Integer> msLvls)`
`void`	`setMzRanges(List<DoubleRange> mzRanges)`
`void`	`setScanNumHi(Integer scanNumHi)`
`void`	`setScanNumLo(Integer scanNumLo)`
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - WHOLE_RUN
```
public static final LCMSDataSubset WHOLE_RUN
```
    Sets up the parsing parameters to parse all the scans and spectra in a run.
  - MS1_WITH_SPECTRA
```
public static final LCMSDataSubset MS1_WITH_SPECTRA
```
    Sets up the parsing parameters to parse all scans, but spectra only for MS1 scans.
  - MS2_WITH_SPECTRA
```
public static final LCMSDataSubset MS2_WITH_SPECTRA
```
    Sets up the parsing parameters to parse all scans, but spectra only for MS2 scans.
  - STRUCTURE_ONLY
```
public static final LCMSDataSubset STRUCTURE_ONLY
```
    Sets up the parsing parameters to parse only scans for the whole run, no spectra.
- Constructor Detail
  - LCMSDataSubset
```
public LCMSDataSubset()
```
  - LCMSDataSubset
```
public LCMSDataSubset(Integer scanNumLo,
                      Integer scanNumHi,
                      Set<Integer> msLvls,
                      List<DoubleRange> mzRanges)
```
    Parameters:
    
    scanNumLo - null means from the beginning
    
    scanNumHi - null means to the end
    
    msLvls - null means any MS-level. If you provide an empty set, then no scan can match this expression.
    
    mzRanges - null means any. If you provide an empty set, then no scan can match this expression.
- Method Detail
  - getScanNumLo
```
public Integer getScanNumLo()
```
  - setScanNumLo
```
public void setScanNumLo(Integer scanNumLo)
```
  - getScanNumHi
```
public Integer getScanNumHi()
```
  - setScanNumHi
```
public void setScanNumHi(Integer scanNumHi)
```
  - getMsLvls
```
public Set<Integer> getMsLvls()
```
  - setMsLvls
```
public void setMsLvls(Set<Integer> msLvls)
```
  - getMzRanges
```
public List<DoubleRange> getMzRanges()
```
  - setMzRanges
```
public void setMzRanges(List<DoubleRange> mzRanges)
```
  - isInSubset
```
public boolean isInSubset(IScan scan)
```
    In some cases we don't have the lower/upper mz window (for MS1 this requires either this data to be in scan meta info, or the spectrumRef to be parsed). In this case the method returns TRUE.
  - contains
```
public boolean contains(LCMSDataSubset other)
```
    Checks if data ranges described by this subset fully contain ranges specified in another set. According to this definition, for example WHOLE_RUN contains any other subset, including itself.
  - merge
```
public LCMSDataSubset merge(LCMSDataSubset other)
```
    Doesn't modify original values, always returns a new one.
    
    Returns:
    
    a new instance of LCMSDataSubset, even if this subset contains(umich.ms.datatypes.LCMSDataSubset) the other one.
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class LCMSDataSubset

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

WHOLE_RUN

MS1_WITH_SPECTRA

MS2_WITH_SPECTRA

STRUCTURE_ONLY

Constructor Detail

LCMSDataSubset

LCMSDataSubset

Method Detail

getScanNumLo

setScanNumLo

getScanNumHi

setScanNumHi

getMsLvls

setMsLvls

getMzRanges

setMzRanges

isInSubset

contains

merge

equals

hashCode

toString