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apollo.dataadapter.das.simple
Class DASFeatureContentHandler
java.lang.Objectorg.xml.sax.helpers.DefaultHandler
- All Implemented Interfaces:
- org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler
- public class DASFeatureContentHandler
- extends org.xml.sax.helpers.DefaultHandler
I am the ContentHandler used when SimpleDASServer parses
the result of a 'features' call to a das data source (with a specified
dsn and segment).
I am DAS 1.0 compliant.
During the parse, I create a list, stored on myself, of the returned
features. This list is retrieved by calling getFeaturess after the parse
is complete
If any of the features retrieved during my run contain subparts or are
reference features (have children), then I store them away.
When I am done with my parse, I
re-invoke the SimpleDASServer with another getFeatures call,
passing in all the segments that have children.
which creates another instance of me(!) and starts a another parse of
the child-features. This is how I assemble all features for a given parent.
| Constructor Summary | |
DASFeatureContentHandler()
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DASFeatureContentHandler(apollo.dataadapter.das.DASServerI theServer,
apollo.dataadapter.das.DASDsn theDsn,
java.util.HashMap theSegments,
java.util.HashMap theParentFeatures,
long theGlobalStart,
long theGlobalEnd)
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| Methods inherited from class org.xml.sax.helpers.DefaultHandler |
endDocument, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
mode
private java.lang.String mode
modeStack
private java.util.Stack modeStack
featureArray
private java.util.List featureArray
DASGFF
private java.lang.String DASGFF
SEGMENT
private java.lang.String SEGMENT
FEATURE
private java.lang.String FEATURE
TYPE
private java.lang.String TYPE
METHOD
private java.lang.String METHOD
START
private java.lang.String START
END
private java.lang.String END
SCORE
private java.lang.String SCORE
ORIENTATION
private java.lang.String ORIENTATION
PHASE
private java.lang.String PHASE
NOTE
private java.lang.String NOTE
GROUP
private java.lang.String GROUP
TARGET
private java.lang.String TARGET
GROUPTARGET
private java.lang.String GROUPTARGET
LABEL
private java.lang.String LABEL
ID
private java.lang.String ID
SEGMENT_ID
private java.lang.String SEGMENT_ID
SEGMENT_START
private java.lang.String SEGMENT_START
SEGMENT_STOP
private java.lang.String SEGMENT_STOP
METHOD_ID
private java.lang.String METHOD_ID
TYPE_ID
private java.lang.String TYPE_ID
TYPE_CATEGORY
private java.lang.String TYPE_CATEGORY
TYPE_REFERENCE
private java.lang.String TYPE_REFERENCE
TYPE_SUBPARTS
private java.lang.String TYPE_SUBPARTS
TARGET_ID
private java.lang.String TARGET_ID
TARGET_START
private java.lang.String TARGET_START
TARGET_STOP
private java.lang.String TARGET_STOP
GROUP_ID
private java.lang.String GROUP_ID
GROUP_TARGET_START
private java.lang.String GROUP_TARGET_START
GROUP_TARGET_STOP
private java.lang.String GROUP_TARGET_STOP
currentFeature
private apollo.dataadapter.das.DASFeature currentFeature
currentSegment
private apollo.dataadapter.das.DASSegment currentSegment
server
public apollo.dataadapter.das.DASServerI server
parentFeatures
public java.util.HashMap parentFeatures
segments
public java.util.HashMap segments
dsn
public apollo.dataadapter.das.DASDsn dsn
segmentsToBeRequested
public java.util.HashMap segmentsToBeRequested
parentFeaturesOfSegmentsToBeRequested
public java.util.HashMap parentFeaturesOfSegmentsToBeRequested
private static boolean print
globalStart
private long globalStart
globalEnd
private long globalEnd
| Constructor Detail |
DASFeatureContentHandler
public DASFeatureContentHandler()
DASFeatureContentHandler
public DASFeatureContentHandler(apollo.dataadapter.das.DASServerI theServer, apollo.dataadapter.das.DASDsn theDsn, java.util.HashMap theSegments, java.util.HashMap theParentFeatures, long theGlobalStart, long theGlobalEnd)
| Method Detail |
getGlobalStart
private long getGlobalStart()
getGlobalEnd
private long getGlobalEnd()
getServer
private apollo.dataadapter.das.DASServerI getServer()
getSegments
private java.util.HashMap getSegments()
getDSN
private apollo.dataadapter.das.DASDsn getDSN()
setSegments
private void setSegments(java.util.HashMap theSegments)
setDSN
private void setDSN(apollo.dataadapter.das.DASDsn theDSN)
getSegmentsToBeRequested
private java.util.HashMap getSegmentsToBeRequested()
getParentFeaturesOfSegmentsToBeRequested
private java.util.HashMap getParentFeaturesOfSegmentsToBeRequested()
getParentFeatures
private java.util.HashMap getParentFeatures()
getCurrentFeature
private apollo.dataadapter.das.DASFeature getCurrentFeature()
setCurrentFeature
private void setCurrentFeature(apollo.dataadapter.das.DASFeature theFeature)
getCurrentSegment
private apollo.dataadapter.das.DASSegment getCurrentSegment()
setCurrentSegment
private void setCurrentSegment(apollo.dataadapter.das.DASSegment theSegment)
addFeature
private void addFeature(apollo.dataadapter.das.DASFeature theFeature)
getFeatures
public java.util.List getFeatures()
getModeStack
private java.util.Stack getModeStack()
setMode
private void setMode(java.lang.String theMode)
getMode
private java.lang.String getMode()
closeMode
private void closeMode()
startElement
public void startElement(java.lang.String namespaceURI, java.lang.String localName, java.lang.String qualifiedName, org.xml.sax.Attributes attributes) throws org.xml.sax.SAXException
- Description copied from class:
org.xml.sax.helpers.DefaultHandler - Receive notification of the start of an element.
By default, do nothing. Application writers may override this method in a subclass to take specific actions at the start of each element (such as allocating a new tree node or writing output to a file).
mapCurrentFeatureCoordinatesToParentFeature
private void mapCurrentFeatureCoordinatesToParentFeature(apollo.dataadapter.das.DASFeature theCurrentFeature, apollo.dataadapter.das.DASFeature theParentFeature, apollo.dataadapter.das.DASSegment theParentSegment)
- Convert this feature's coordinates and orientation
_globally_ - that is, with respect to the
root feature of the set (a chromosome, say). The global start,
end and orientation of the set. The parent feature passed into
this MUST have start/end and orientation expressed GLOBALLY!
endElement
public void endElement(java.lang.String namespaceURI, java.lang.String localName, java.lang.String qualifiedName) throws org.xml.sax.SAXException
- Description copied from class:
org.xml.sax.helpers.DefaultHandler - Receive notification of the end of an element.
By default, do nothing. Application writers may override this method in a subclass to take specific actions at the end of each element (such as finalising a tree node or writing output to a file).
characters
public void characters(char[] text,
int start,
int length)
throws org.xml.sax.SAXException
- Description copied from class:
org.xml.sax.helpers.DefaultHandler - Receive notification of character data inside an element.
By default, do nothing. Application writers may override this method to take specific actions for each chunk of character data (such as adding the data to a node or buffer, or printing it to a file).
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SUMMARY: JAVADOC | SOURCE | DOWNLOAD | NESTED | FIELD | CONSTR | METHOD |
DETAIL: FIELD | CONSTR | METHOD | ||||||||