IonAnnotation (MSDK - Mass Spectrometry Development Kit 0.0.20 API)

All Known Implementing Classes:

SimpleIonAnnotation, SiriusIonAnnotation
```
public interface IonAnnotation
```
Annotation of a detected feature with a chemical structure, formula, or textual description.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`URL`	`getAccessionURL()` getAccessionURL.
`String`	`getAnnotationId()` getAnnotationId.
`org.openscience.cdk.interfaces.IAtomContainer`	`getChemicalStructure()` getChemicalStructure.
`String`	`getDatabase()` getDatabase
`String`	`getDescription()` getDescription.
`Double`	`getExpectedMz()` getExpectedMz.
`Float`	`getExpectedRetentionTime()` getRetentionTime.
`org.openscience.cdk.interfaces.IMolecularFormula`	`getFormula()` Chemical formula annotation should include charge, e.g.
`String`	`getIdentificationMethod()` getIdentificationMethod.
`String`	`getInchiKey()` getInchiKey
`IonType`	`getIonType()` getIonType.
`Integer`	`getReliability()` Returns the reliability of the identification.
`String`	`getSpectraRef()` getSpectraRef

- Method Detail
  - getChemicalStructure
```
@Nullable
org.openscience.cdk.interfaces.IAtomContainer getChemicalStructure()
```
    getChemicalStructure.
    
    Returns:
    
    Chemical structure of this annotation.
  - getFormula
```
@Nullable
org.openscience.cdk.interfaces.IMolecularFormula getFormula()
```
    Chemical formula annotation should include charge, e.g. C6H13O6+ or [C34H58N5O35P3]2-.
    
    Returns:
    
    Chemical formula of this annotation.
  - getIonType
```
@Nullable
IonType getIonType()
```
    getIonType.
    
    Returns:
    
    Ionization type for this annotation.
  - getExpectedMz
```
@Nullable
Double getExpectedMz()
```
    getExpectedMz.
    
    Returns:
    
    Expected m/z value of this annotation.
  - getExpectedRetentionTime
```
@Nullable
Float getExpectedRetentionTime()
```
    getRetentionTime.
    
    Returns:
    
    RT
    
    Since:
    
    0.0.8
  - getAnnotationId
```
String getAnnotationId()
```
    getAnnotationId.
    
    Returns:
    
    a String object.
  - getDescription
```
@Nullable
String getDescription()
```
    getDescription.
    
    Returns:
    
    Textual description of this annotation.
  - getIdentificationMethod
```
@Nullable
String getIdentificationMethod()
```
    getIdentificationMethod.
    
    Returns:
    
    Identification method (e.g. database name) of this annotation.
  - getAccessionURL
```
@Nullable
URL getAccessionURL()
```
    getAccessionURL.
    
    Returns:
    
    Accession URL for a database, if this annotation comes from a database.
  - getInchiKey
```
@Nullable
String getInchiKey()
```
    getInchiKey
    
    Returns:
    
    InChI key of this annotation.
  - getDatabase
```
@Nullable
String getDatabase()
```
    getDatabase
    
    Returns:
    
    Textual database description of this annotation.
  - getSpectraRef
```
@Nullable
String getSpectraRef()
```
    getSpectraRef
    
    Returns:
    
    Textual reference to a spectrum in a spectrum file for this annotation.
  - getReliability
```
@Nullable
Integer getReliability()
```
    Returns the reliability of the identification. This must be reported as an integer between 1-4: 1: Identified metabolites 2: Putatively annotated compounds 3: Putatively characterized compound classes 4: Unknown compounds
    
    Returns:
    
    The reliability of the ion annotation identification.

Interface IonAnnotation

Method Summary

Method Detail

getChemicalStructure

getFormula

getIonType

getExpectedMz

getExpectedRetentionTime

getAnnotationId

getDescription

getIdentificationMethod

getAccessionURL

getInchiKey

getDatabase

getSpectraRef

getReliability