NotesToAnnotation (jsbml-fbc 1.5 API)

java.lang.Object
- org.sbml.jsbml.ext.fbc.converters.NotesToAnnotation

```
public class NotesToAnnotation
extends Object
```
NotesToAnnotation transfers information from the Cobra style notes to the annotations.

Since:

1.5

Author:

Thomas Hamm

See Also:

transfer(SBMLDocument, String[])

Constructor Summary

Constructors
Constructor and Description

NotesToAnnotation()

Constructors
Constructor and Description
`NotesToAnnotation()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`SBMLDocument`	`transfer(SBMLDocument sbmlDocument, String[] keys)` Transfers information from the Cobra style notes of species and reactions to the annotations (see example below).

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

Constructor Detail
- NotesToAnnotation
```
public NotesToAnnotation()
```

Method Detail

transfer

public SBMLDocument transfer(SBMLDocument sbmlDocument,
                             String[] keys)
                      throws IOException

Transfers information from the Cobra style notes of species and reactions to the annotations (see example below).

 Example:
 
 Cobra style note of a species:
   <notes>
     <body xmlns="http://www.w3.org/1999/xhtml">
       <p>KEGG Compound: C00004</p>
     </body>
   </notes>
         
 New annotation of the species (after the transfer of the information):
    <annotation>
      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
        <rdf:Description rdf:about="#cfa155dc-e6ed-4d90-8b0b-ad4cb8a88d6b">
          <bqbiol:is>
            <rdf:Bag>
              <rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00004" />
            </rdf:Bag>
          </bqbiol:is>
        </rdf:Description>
      </rdf:RDF>
    </annotation>

Parameters:: sbmlDocument - the SBMLDocument where the information should be transfered from the notes; keys - a string array with the keys from the elements of the notes that should be transfered
Returns:: the new SBMLDocument with transfered information in the annotations
Throws:: IOException - if an error occurs

Class NotesToAnnotation

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

NotesToAnnotation

Method Detail

transfer