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java.lang.Object | +--jadex.xml.XMLUtilities
This is a utility class for processing XML files in Sequence View. Some frequently used methods for XML processing are here. All these methods are static to keep methods calling simple. The element data structure used here is JDOM format.
Constructor Summary | |
XMLUtilities()
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Method Summary | |
static int |
getLayer(org.jdom.Element sequence)
Get the layer of a element in XML document from root element, i.e., Chromosome. |
static MapRange |
getMapRange(org.jdom.Element sequence)
Extract the maprange information from sequence element |
static MapRange |
getMapRange(org.jdom.Element sequence,
org.jdom.Namespace ns)
Extract the maprange information from sequence element |
static java.lang.String |
getName(org.jdom.Element sequence)
Get the name of the sequence from its attribute. |
static org.jdom.Namespace |
getNamespace()
Deprecated. please don't use this method anymore. |
static long[] |
getPositions(org.jdom.Element sequence)
Get the position of the sequence element. |
static long[] |
getPositions(org.jdom.Element sequence,
org.jdom.Namespace ns)
Get the position of the sequence element. |
static java.util.List |
getSubSequences(org.jdom.Element sequence)
Get the subsequences from a sequence element or a chromosome (root). |
static java.util.List |
getSubSequences(org.jdom.Element sequence,
org.jdom.Namespace ns)
Get the subsequences from a sequenc element. |
static boolean |
isOdd(org.jdom.Element sequence)
See the position of the sequence element in the subsequenc list is Odd or even. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public XMLUtilities()
Method Detail |
public static org.jdom.Namespace getNamespace()
public static long[] getPositions(org.jdom.Element sequence, org.jdom.Namespace ns)
sequence
- the sequence element to be parsed.ns
- the Namespace this sequence elemenet used.public static long[] getPositions(org.jdom.Element sequence)
sequence
- the sequenc elemnet too be parsed.public static MapRange getMapRange(org.jdom.Element sequence, org.jdom.Namespace ns)
sequence
- elementpublic static MapRange getMapRange(org.jdom.Element sequence)
sequence
- elementpublic static java.util.List getSubSequences(org.jdom.Element sequence)
sequence
- the element to be parsed.public static java.util.List getSubSequences(org.jdom.Element sequence, org.jdom.Namespace ns)
sequence
- the sequence element to be parsed.ns
- the name space this sequence element is in.public static java.lang.String getName(org.jdom.Element sequence)
sequence
- the sequenc element.public static int getLayer(org.jdom.Element sequence)
sequence
- the sequence element to be analyzed.public static boolean isOdd(org.jdom.Element sequence)
sequence
- the sequence element to be analyzed.
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