CobraUtil (IDARE [idare] 1.0 API)

java.lang.Object
- idare.ThirdParty.CobraUtil

```
public class CobraUtil
extends Object
```
Contains some useful methods to manipulate 'COBRA SBML'

Since:

1.1

Version:

$Rev: 2390 $

Author:

Nicolas Rodriguez

- Constructor Summary
  
  Constructors
  Constructor and Description
  
  CobraUtil()
- Method Summary
  
  All Methods Static Methods Concrete Methods
  Modifier and Type Method and Description
  
  static Properties parseCobraNotes(SBase sbase)
  Parses the notes of the given SBase element.
  - Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructors
Constructor and Description
`CobraUtil()`

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static Properties`	`parseCobraNotes(SBase sbase)` Parses the notes of the given `SBase` element.

Constructor Detail
- CobraUtil
```
public CobraUtil()
```

Method Detail

parseCobraNotes

public static Properties parseCobraNotes(SBase sbase)

Parses the notes of the given SBase element.

The notes are expecting to have some 'p' elements with a content of the form 'KEY: VALUE'. The key will be used for the property name and the value will be the property value. The key is inserted even is the value is an empty String.

Below are examples for a species and a reaction:

  <body xmlns="http://www.w3.org/1999/xhtml">
    <p>FORMULA: H4N</p>
    <p>CHARGE: 1</p>
    <p>HEPATONET_1.0_ABBREVIATION: HC00765</p>
    <p>EHMN_ABBREVIATION: C01342</p>
    <p>INCHI: InChI=1S/H3N/h1H3/p+1</p>
  </body>

  <body xmlns="http://www.w3.org/1999/xhtml">
    <p>GENE_ASSOCIATION: 1594.1</p>
    <p>SUBSYSTEM: Vitamin D metabolism</p>
    <p>EC Number: </p>
    <p>Confidence Level: 4</p>
    <p>AUTHORS: PMID:14671156,PMID:9333115</p>
    <p>NOTES: based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, 1st ed (book) pg.196 IT</p>
  </body>

Parameters:: sbase - the SBase object
Returns:: a Properties object that store all the KEY/VALUE pair found in the notes. If the given SBase has no notes or if the notes are not of the expected format, an empty Properties object is returned.

Class CobraUtil

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CobraUtil

Method Detail

parseCobraNotes