| Package | Description |
|---|---|
| uk.ac.ebi.arrayexpress2.magetab.datamodel |
Classes for constructing an in-memory datamodel of the data contained in IDF and
SDRF files, as specified by the MAGE-TAB specification.
|
| uk.ac.ebi.arrayexpress2.magetab.datamodel.layout | |
| uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node |
Classes that model nodes in the SDRF graph datastructure, as described by the
MAGE-TAB specification.
|
| uk.ac.ebi.arrayexpress2.magetab.handler.sdrf |
SDRF specific handler classes.
|
| uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node |
Specific handlers for SDRF node data items, as defined in the MAGE-TAB
specification.
|
| uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.attribute |
SDRF Handler implementations that are capable of handling data items that
represent attributes attached to a node, as defined by the MAGE-TAB
specification.
|
| uk.ac.ebi.arrayexpress2.magetab.handler.visitor |
Visitor classes that can be used to visit and inspect MAGE-TAB handlers.
|
| uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor |
| Modifier and Type | Method and Description |
|---|---|
<T extends SDRFNode> |
SDRF.lookupNode(String nodeName,
Class<T> nodeType)
Deprecated.
since version 1.1, use
AbstractGraph.getNode(String, Class) instead |
<T extends SDRFNode> |
SDRF.lookupNodes(Class<T> nodeType)
Deprecated.
since version 1.1, use
AbstractGraph.getNodes(Class) instead |
| Modifier and Type | Method and Description |
|---|---|
SDRFNode |
SDRF.lookupNode(String nodeName,
String nodeType)
Deprecated.
since version 1.1, use
AbstractGraph.getNode(String, String) instead |
| Modifier and Type | Method and Description |
|---|---|
Collection<? extends SDRFNode> |
SDRF.lookupNodes(String nodeType)
Deprecated.
since version 1.1, use
AbstractGraph.getNodes(String) instead |
| Modifier and Type | Method and Description |
|---|---|
void |
SDRF.removeNodeFromGraph(SDRFNode node)
Deprecated.
since version 1.1, use
AbstractGraph.removeNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node)
instead |
void |
SDRF.storeNode(SDRFNode node)
Deprecated.
since version 1.1, use
AbstractGraph.addNode(uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node)
instead |
| Modifier and Type | Method and Description |
|---|---|
boolean |
SDRF.hasBeenHandled(String nodeName,
Class<? extends SDRFNode> nodeType)
Determine whether a given node has been handled already, and exists in the graph.
|
| Modifier and Type | Method and Description |
|---|---|
SDRFNode |
SDRFLayout.getNode(Location location) |
| Modifier and Type | Method and Description |
|---|---|
void |
SDRFLayout.addNodeLocation(SDRFNode node,
Location location) |
Collection<Location> |
SDRFLayout.getLocationsForNode(SDRFNode node) |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractSDRFNode
An abstract top-level implementation of an SDRFNode.
|
class |
ArrayDataMatrixNode
An array data matrix node in the graph.
|
class |
ArrayDataNode
An array data node in the graph.
|
class |
ArrayDesignNode
Deprecated.
since version 1.1
|
class |
AssayNode
An Assay Node, in the SDRF graph.
|
class |
DerivedArrayDataMatrixNode
A derived array data matrix node in the graph.
|
class |
DerivedArrayDataNode
A derived array data node in the graph.
|
class |
ExtractNode
An extract node in the graph.
|
class |
HybridizationNode
A hybridization node in the graph.
|
class |
ImageNode
An image node in the graph.
|
class |
LabeledExtractNode
A labeled extract node in the graph.
|
class |
NormalizationNode
A normalization node in the graph.
|
class |
ProtocolApplicationNode
A protocol "node" in the graph.
|
class |
SampleNode
A sample node in the graph.
|
class |
ScanNode
A scan node in the graph.
|
class |
SourceNode
A source node in the graph.
|
| Modifier and Type | Method and Description |
|---|---|
protected <T extends SDRFNode> |
SDRFReadInContextHandler.fetchUpstreamNode(SDRF sdrf,
String nodeName,
Class<T> nodeClass)
Used for adding nodes that are upstream of the current node in the SDRF graph.
|
| Modifier and Type | Method and Description |
|---|---|
protected SDRFNode |
SDRFReadInContextHandler.handleUpstreamNode(SDRF sdrf,
String nodeName,
String nodeType,
int lineNumber,
int columnNumber)
Used for adding nodes that are upstream of the current node in the SDRF graph.
|
| Modifier and Type | Method and Description |
|---|---|
static String |
SDRFReadUtils.getNodeColName(SDRFNode node,
String headerName) |
protected int |
SDRFReadHandler.readAttribute(SDRFAttributeReader reader,
String[] header,
String[] data,
SDRF sdrf,
SDRFNode parentNode,
int lineNumber,
int columnNumber,
int startIndex) |
protected void |
SDRFReadHandler.updateChildNode(String[] header,
String[] data,
SDRFNode node,
int valueIndex) |
| Modifier and Type | Class and Description |
|---|---|
class |
SDRFNodeConversionHandler<D extends SDRFNode,O>
An abstract implementation of a ConversionHandler for writing data from an
SDRFNode
to some external output resource. |
| Modifier and Type | Method and Description |
|---|---|
protected abstract boolean |
SDRFNodeConversionHandler.canConvertData(SDRFNode data)
Performs specific checks on the SDRFNode to determine if this handler can convert it.
|
| Modifier and Type | Method and Description |
|---|---|
void |
PerformerAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber) |
void |
MaterialTypeAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber) |
void |
TechnologyTypeAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber) |
void |
LabelAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber) |
void |
ArrayDesignAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode parentNode,
int lineNumber,
int columnNumber) |
void |
ParameterValueAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber) |
void |
ProviderAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber) |
void |
SDRFAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber)
Reads the attributes from the data and sets them on the supplied SDRFNode
|
void |
FactorValueAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode sdrfNode,
int lineNumber,
int columnNumber) |
void |
CharacteristicsAttributeReader.readAttributes(String[] header,
String[] data,
SDRF sdrf,
SDRFNode parentNode,
int lineNumber,
int columnNumber) |
| Modifier and Type | Method and Description |
|---|---|
Set<Point> |
LocationTracker.getSDRFLocations(SDRFNode sdrfNode)
Deprecated.
since version 1.1, use SDRF.getLayout().getLocationsForNode() instead
|
| Modifier and Type | Class and Description |
|---|---|
class |
SDRFNodeWrapper<T extends SDRFNode>
Class needed for graph2tab algorithm
Creates wrappers for the SDRF graph's nodes
|
| Modifier and Type | Method and Description |
|---|---|
protected SDRFNodeWrapper |
WrapperNodeFactory.createNewNode(SDRFNode base) |
| Constructor and Description |
|---|
ModelTableBuilder(Collection<? extends SDRFNode> nodes,
WrapperNodeFactory factory) |
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