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java.lang.ObjectGene
@ThreadSafe public final class Gene
Utilities for working with genes.
Field Summary | |
---|---|
static String |
EMBEDDABLE_STUB_LOCAL_NAME
Local name of stub elements that represent contained genes in embeddable forms. |
static int |
G_INDEX_FLAG_DOUBLE_DASH
G-index flag indicating a 'g' attribute value that begins '--'. |
static int |
G_INDEX_FLAG_NONE
G-index flag indicating that a node has no 'g' attribute. |
static int |
G_INDEX_FLAG_SINGLE_DASH
G-index flag indicating a 'g' attribute value that begins with a single '-'. |
static int |
G_INDEX_FLAG_UNKNOWN
G-index flag indicating an unrecognized 'g' attribute value. |
Method Summary | |
---|---|
static void |
abstract_embeddable(Element sequence,
List<Element> gList)
Tranforms a genetic-form sequence into an abstract form suitable for embeddable encoding. |
static void |
adjustLeftPadding(Element element,
int delta,
StringBuilder b)
Adjusts the left padding (leading space content) of an element. |
static Element |
createG(String locus,
Element gg,
StringBuilder b)
Creates an unattached gene meta-data ('g') element. |
static Element |
createGG(Element metaData,
StringBuilder b)
Creates an unattached 'g' list ('gg') element. |
static Element |
ensureGG(Element metaData,
StringBuilder b)
Returns a document's 'gg' element; if necessary creating it. |
static void |
escape_embeddable(StringBuilder b)
Tranforms an embeddable sequence from unescaped to escaped form. |
static Element |
findGG(Element metaData)
Finds a document's 'gg' element. |
static boolean |
gIndexIsGene(int gIndex)
Returns true iff gIndexOf >= 0, indicating a gene. |
static boolean |
gIndexIsNonGenetic(int gIndex)
Returns true iff gIndexOf indicates a non-genetic element; either G_INDEX_FLAG_SINGLE_DASH or G_INDEX_FLAG_DOUBLE_DASH. |
static int |
gIndexOf(Element element)
Returns the g-index of an element, derived from its 'g' attribute value. |
static int |
gIndexOf(String g)
Returns the g-index of a 'g' attribute value. |
static int |
gIndexOfNode(Node node)
Returns the g-index of a node. |
static String |
gOf(int gIndex)
Returns the g-index encoded as a string suitable for a 'g' attribute value. |
static String |
gROf(Element element)
Returns the effective 'gR' attribute of an element. |
static boolean |
hasChildGene(Node node)
Returns true iff the node has a child gene. |
static boolean |
isGene(Element element)
Returns true if the element is a gene. |
static int |
linkG(Element g,
Element sequenceElement,
Element gg,
int gIndex,
StringBuilder b)
Links a gene meta-data ('g') element into the document. |
static Element |
selfOrAncestorAsGene(Node node)
Returns the node if it is a gene; otherwise the nearest ancestor that is a gene. |
static void |
unescape_embeddable(StringBuilder b)
Tranforms an embeddable sequence from escaped to unescaped form. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final String EMBEDDABLE_STUB_LOCAL_NAME
public static final int G_INDEX_FLAG_NONE
gIndexOf(Element)
,
Constant Field Valuespublic static final int G_INDEX_FLAG_UNKNOWN
gIndexOf(String)
,
Constant Field Valuespublic static final int G_INDEX_FLAG_SINGLE_DASH
gIndexOf(String)
,
gIndexIsNonGenetic(int)
,
Constant Field Valuespublic static final int G_INDEX_FLAG_DOUBLE_DASH
gIndexOf(String)
,
gIndexIsNonGenetic(int)
,
Constant Field ValuesMethod Detail |
---|
public static void abstract_embeddable(Element sequence, List<Element> gList)
sequence
- genetic-form sequencegList
- list of gene meta-data ('g') elements in the documentpublic static void adjustLeftPadding(Element element, int delta, StringBuilder b)
element
- whose padding to adjustdelta
- number of space characters to remove (negative)
or add (positive)b
- string builder to use, overwriting its existing contentpublic static Element createG(String locus, Element gg, StringBuilder b)
locus
- of the genegg
- the meta-data 'gg' element,
to which caller will attach new 'g' elementb
- string builder to use, overwriting its existing contentpublic static Element createGG(Element metaData, StringBuilder b)
metaData
- the document's
meta-data element,
to which caller will attach new 'gg' elementb
- string builder to use, overwriting its existing contentensureGG(Element,StringBuilder)
public static Element ensureGG(Element metaData, StringBuilder b)
metaData
- the document's
meta-data elementb
- string builder to use, overwriting its existing contentcreateGG(Element,StringBuilder)
,
findGG(Element)
public static void escape_embeddable(StringBuilder b)
b
- string builder containing the unescaped sequenceunescape_embeddable(StringBuilder)
,
d/gene/note.xht#Escapingpublic static Element findGG(Element metaData)
metaData
- the document's
meta-data element
ensureGG(Element,StringBuilder)
public static boolean gIndexIsNonGenetic(int gIndex)
public static boolean gIndexIsGene(int gIndex)
public static int gIndexOf(Element element)
gIndexOfNode(Node)
public static int gIndexOfNode(Node node)
public static int gIndexOf(String g)
gIndexOf(Element)
,
gOf(int)
public static String gOf(int gIndex)
gIndexOf(String)
public static String gROf(Element element)
element
- e.g. a meta-data 'gg' or ancestor 'a' element
public static boolean hasChildGene(Node node)
public static boolean isGene(Element element)
gIndexOf(Element)
public static int linkG(Element g, Element sequenceElement, Element gg, int gIndex, StringBuilder b)
g
- gene meta-data elementsequenceElement
- element that will become the gene;
it should itself be attached in the document,
or the namespace prefix lookup may failgg
- the meta-data 'gg' elementgIndex
- prior count of 'g' elements,
and offset for the newly created 'g' element, in 'gg' listb
- string builder to use, overwriting its existing content
createG(String,Element,StringBuilder)
public static Element selfOrAncestorAsGene(Node node)
node
- reference node, which may be null
public static void unescape_embeddable(StringBuilder b)
b
- string builder containing the escaped sequenceescape_embeddable(StringBuilder)
,
d/gene/note.xht#Escaping
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