Ms2Query (pgatk-io 1.0.1-SNAPSHOT API)

java.lang.Object
- io.github.bigbio.pgatk.io.mgf.Ms2Query

All Implemented Interfaces:

Spectrum, Serializable
```
public class Ms2Query
extends Object
implements Spectrum
```
This class reads the MS2 information in the MGF.

Author:

ypriverol

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description
`Ms2Query(boolean disableCommentSupport)` Default constructor generating an empty Ms2Query
`Ms2Query(String mgfQuery, int index, boolean disableCommentSupport, boolean ignoreWrongPeaks)` Generates a Ms2Query from a mgf part representing an Ms2Query (including "BEGIN IONS" and "END IONS")

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addErrorTag(String errorTolerantTag)` Adds an error tolerant tag.
`void`	`addETag(String errorTolerantTag)` Adds an error tolerant tag.
`void`	`addPeak(Double mz, Double intensity)` Adds a peak to the spectrum.
`void`	`addSequenceQualifier(String sequenceQualifier)` Ads a sequence qualifier.
`void`	`addTag(String tag)` Adds a tag.
`Collection<? extends Param>`	`getAdditional()` Get Attributes as `CvParam`
`String`	`getChargeState()`
`String`	`getComposition()`
`List<String>`	`getErrorTolerantTags()`
`String`	`getId()` Gets the ID.
`Long`	`getIndex()` Internal Spectrum in the corresponding file MGF or mzXML or mzML, starting from 1, incrementing by one for each consecutive spectrum.
`String`	`getInstrument()`
`Integer`	`getMsLevel()` Returns the msLevel of the spectrum.
`Map<Double,Double>`	`getPeakList()` Returns the spectrum's peak list as a HashMap with the m/z values as keys and the corresponding intensities as values.
`Double`	`getPeptideIntensity()`
`Double`	`getPeptideMass()`
`Integer`	`getPrecursorCharge()` Gets the precursor charge.
`Double`	`getPrecursorIntensity()` Returns the precursor's intensity or null in case it it not available.
`Double`	`getPrecursorMZ()` Returns the precursor's m/z or null in case the precursor's m/z is not available.
`String`	`getRetentionTime()`
`String`	`getScan()`
`List<String>`	`getSequenceQualifiers()`
`List<String>`	`getTags()`
`String`	`getTitle()`
`Double`	`getTolerance()`
`MgfUtils.PeptideToleranceUnit`	`getToleranceUnit()`
`Map<Integer,String>`	`getUserTags()`
`String`	`getVariableModifications()`
`void`	`saveAttribute(String name, String value)` Stores the attribute in the respective member variable.
`void`	`setChargeState(String chargeState)`
`void`	`setComposition(String composition)`
`void`	`setErrorTolerantTags(List<String> errorTolerantTags)`
`void`	`setIndex(long index)`
`void`	`setInstrument(String instrument)`
`void`	`setPeakList(Map<Double,Double> peakList)`
`void`	`setPeptideIntensity(Double peptideIntensity)`
`void`	`setPeptideMass(Double peptideMass)`
`void`	`setRetentionTime(String retentionTime)`
`void`	`setScan(String scan)`
`void`	`setSequenceQualifiers(List<String> sequenceQualifiers)`
`void`	`setTags(List<String> tags)`
`void`	`setTitle(String title)`
`void`	`setTolerance(Double tolerance)`
`void`	`setToleranceUnit(MgfUtils.PeptideToleranceUnit toleranceUnit)`
`void`	`setUserTags(Map<Integer,String> userTags)`
`void`	`setVariableModifications(String variableModifications)`
`String`	`toString()` Compiles all the information from this Ms2Query object.

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

- Constructor Detail
  - Ms2Query
```
public Ms2Query(boolean disableCommentSupport)
```
    Default constructor generating an empty Ms2Query
  - Ms2Query
```
public Ms2Query(String mgfQuery,
                int index,
                boolean disableCommentSupport,
                boolean ignoreWrongPeaks)
         throws PgatkIOException
```
    Generates a Ms2Query from a mgf part representing an Ms2Query (including "BEGIN IONS" and "END IONS")
    
    Parameters:
    
    mgfQuery - the mgf part to parse
    
    index - RAW Original scan Number
    
    disableCommentSupport - true to disable comment support, false otherwise
    
    Throws:
    
    PgatkIOException - any problems parsing the mgf part
- Method Detail
  - saveAttribute
```
public void saveAttribute(String name,
                          String value)
```
    Stores the attribute in the respective member variable.
    
    Parameters:
    
    name - The attribute's name
    
    value - The attribute's value
    
    Throws:
    
    PgatkIOException - any problems saving the attribute
  - addPeak
```
public void addPeak(Double mz,
                    Double intensity)
```
    Adds a peak to the spectrum.
    
    Parameters:
    
    mz - the mz value
    
    intensity - the intensity value
  - addSequenceQualifier
```
public void addSequenceQualifier(String sequenceQualifier)
```
    Ads a sequence qualifier.
    
    Parameters:
    
    sequenceQualifier - the sequence qualifier to put.
  - addTag
```
public void addTag(String tag)
```
    Adds a tag.
    
    Parameters:
    
    tag - the tag to put.
  - addETag
```
public void addETag(String errorTolerantTag)
```
    Adds an error tolerant tag.
    
    Parameters:
    
    errorTolerantTag - the error tolerant tag
  - addErrorTag
```
public void addErrorTag(String errorTolerantTag)
```
    Adds an error tolerant tag.
    
    Parameters:
    
    errorTolerantTag - the error tolerant tag
  - getTitle
```
public String getTitle()
```
  - setTitle
```
public void setTitle(String title)
```
  - getChargeState
```
public String getChargeState()
```
  - setChargeState
```
public void setChargeState(String chargeState)
```
  - getTolerance
```
public Double getTolerance()
```
  - setTolerance
```
public void setTolerance(Double tolerance)
```
  - getToleranceUnit
```
public MgfUtils.PeptideToleranceUnit getToleranceUnit()
```
  - setToleranceUnit
```
public void setToleranceUnit(MgfUtils.PeptideToleranceUnit toleranceUnit)
```
  - getComposition
```
public String getComposition()
```
  - setComposition
```
public void setComposition(String composition)
```
  - getTags
```
public List<String> getTags()
```
  - setTags
```
public void setTags(List<String> tags)
```
  - getRetentionTime
```
public String getRetentionTime()
```
  - setRetentionTime
```
public void setRetentionTime(String retentionTime)
```
  - getInstrument
```
public String getInstrument()
```
  - setInstrument
```
public void setInstrument(String instrument)
```
  - getSequenceQualifiers
```
public List<String> getSequenceQualifiers()
```
  - setSequenceQualifiers
```
public void setSequenceQualifiers(List<String> sequenceQualifiers)
```
  - getErrorTolerantTags
```
public List<String> getErrorTolerantTags()
```
  - setErrorTolerantTags
```
public void setErrorTolerantTags(List<String> errorTolerantTags)
```
  - getScan
```
public String getScan()
```
  - setScan
```
public void setScan(String scan)
```
  - getVariableModifications
```
public String getVariableModifications()
```
  - setVariableModifications
```
public void setVariableModifications(String variableModifications)
```
  - getPeakList
```
public Map<Double,Double> getPeakList()
```
    Description copied from interface: Spectrum
    
    Returns the spectrum's peak list as a HashMap with the m/z values as keys and the corresponding intensities as values.
    
    Specified by:
    
    getPeakList in interface Spectrum
    
    Returns:
  - setPeakList
```
public void setPeakList(Map<Double,Double> peakList)
```
  - getPeptideMass
```
public Double getPeptideMass()
```
  - setPeptideMass
```
public void setPeptideMass(Double peptideMass)
```
  - getPeptideIntensity
```
public Double getPeptideIntensity()
```
  - setPeptideIntensity
```
public void setPeptideIntensity(Double peptideIntensity)
```
  - getUserTags
```
public Map<Integer,String> getUserTags()
```
  - setUserTags
```
public void setUserTags(Map<Integer,String> userTags)
```
  - toString
```
public String toString()
```
    Compiles all the information from this Ms2Query object.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    a String of all the information from this object.
  - getIndex
```
public Long getIndex()
```
    Description copied from interface: Spectrum
    
    Internal Spectrum in the corresponding file MGF or mzXML or mzML, starting from 1, incrementing by one for each consecutive spectrum. This is the number is used in the mzIdentML and mzTab files to reference the Spectrum.
    
    Specified by:
    
    getIndex in interface Spectrum
  - getId
```
public String getId()
```
    Gets the ID.
    
    Specified by:
    
    getId in interface Spectrum
    
    Returns:
    
    the ID. If none is set, null is returned,
  - setIndex
```
public void setIndex(long index)
```
  - getPrecursorCharge
```
public Integer getPrecursorCharge()
```
    Gets the precursor charge.
    
    Specified by:
    
    getPrecursorCharge in interface Spectrum
    
    Returns:
    
    the precursor charge. If there is no charge state, or if there are multiple charge states then null is returned.
  - getPrecursorMZ
```
public Double getPrecursorMZ()
```
    Description copied from interface: Spectrum
    
    Returns the precursor's m/z or null in case the precursor's m/z is not available.
    
    Specified by:
    
    getPrecursorMZ in interface Spectrum
    
    Returns:
  - getPrecursorIntensity
```
public Double getPrecursorIntensity()
```
    Description copied from interface: Spectrum
    
    Returns the precursor's intensity or null in case it it not available.
    
    Specified by:
    
    getPrecursorIntensity in interface Spectrum
    
    Returns:
  - getMsLevel
```
public Integer getMsLevel()
```
    Description copied from interface: Spectrum
    
    Returns the msLevel of the spectrum. NULL in case the MS level is not available or unknown.
    
    Specified by:
    
    getMsLevel in interface Spectrum
    
    Returns:
  - getAdditional
```
public Collection<? extends Param> getAdditional()
```
    Get Attributes as CvParam
    
    Specified by:
    
    getAdditional in interface Spectrum
    
    Returns:
    
    the additional paramgroup.

Class Ms2Query

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Ms2Query

Ms2Query

Method Detail

saveAttribute

addPeak

addSequenceQualifier

addTag

addETag

addErrorTag

getTitle

setTitle

getChargeState

setChargeState

getTolerance

setTolerance

getToleranceUnit

setToleranceUnit

getComposition

setComposition

getTags

setTags

getRetentionTime

setRetentionTime

getInstrument

setInstrument

getSequenceQualifiers

setSequenceQualifiers

getErrorTolerantTags

setErrorTolerantTags

getScan

setScan

getVariableModifications

setVariableModifications

getPeakList

setPeakList

getPeptideMass

setPeptideMass

getPeptideIntensity

setPeptideIntensity

getUserTags

setUserTags

toString

getIndex

getId

setIndex

getPrecursorCharge

getPrecursorMZ

getPrecursorIntensity

getMsLevel

getAdditional