public class CobraUtil
extends java.lang.Object
| Modifier and Type | Field and Description |
|---|---|
private static org.apache.log4j.Logger |
logger |
| Constructor and Description |
|---|
CobraUtil() |
| Modifier and Type | Method and Description |
|---|---|
static java.util.Properties |
parseCobraNotes(SBase sbase)
Parses the notes of the given
SBase element. |
public static java.util.Properties parseCobraNotes(SBase sbase)
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>
sbase - 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.