de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.NodeHelper

All Implemented Interfaces:: Comparable<GraphElement>, Attributable, GraphElement, Node, HelperClass

public class NodeHelper
extends Object
implements Node, HelperClass

Constructor Summary

Constructors

Constructor Description

NodeHelper(Node workNode)

NodeHelper(Node n, boolean isLastNode)

Method Summary

Modifier and Type	Method	Description
`void`	`addAttribute(Attribute attr, String path)`	Adds `attr` to the attributes at position indicated by path.
`void`	`addBoolean(String path, String id, boolean value)`	Adds a `BooleanAttribute` with the given value and id to a `CollectionAttribute` at `path`.
`void`	`addByte(String path, String id, byte value)`	Adds an ByteAttribute with the given value and id to a `CollectionAttribute` at `path`.
`void`	`addDataMapping(SubstanceInterface mappingData)`
`void`	`addDataMapping(Collection<DataSetRow> datasetRows, String substanceName)`
`void`	`addDouble(String path, String id, double value)`	Adds a `DoubleAttribute` with the given value and `id` to a `CollectionAttribute` at `path`.
`void`	`addFloat(String path, String id, float value)`	Adds a `FloatAttribute` with the given value and `id` to a `CollectionAttribute` at `path`.
`void`	`addInteger(String path, String id, int value)`	Adds an IntegerAttribute with the given value and `id` to a `CollectionAttribute` at `path`.
`void`	`addLong(String path, String id, long value)`	Adds an LongAttribute with the given value and id to a `CollectionAttribute` at `path`.
`void`	`addShort(String path, String id, short value)`	Adds an ShortAttribute with the given value and id to a `CollectionAttribute` at `path`.
`void`	`addString(String path, String id, String value)`	Adds an StringAttribute with the given value and id to a `CollectionAttribute` at `path`.
`void`	`changeBoolean(String path, boolean value)`	Changes the `Attribute` at the given path to the given value.
`void`	`changeByte(String path, byte value)`	Changes the `Attribute` at the given path to the given value.
`void`	`changeDouble(String path, double value)`	Changes the `Attribute` at the given path to the given value.
`void`	`changeFloat(String path, float value)`	Changes the `Attribute` at the given path to the given value.
`void`	`changeInteger(String path, int value)`	Changes the `Attribute` at the given path to the given value.
`void`	`changeLong(String path, long value)`	Changes the `Attribute` at the given path to the given value.
`void`	`changeShort(String path, short value)`	Changes the `Attribute` at the given path to the given value.
`void`	`changeString(String path, String value)`	Changes the `Attribute` at the given path to the given value.
`int`	`compareTo(GraphElement o)`
`Collection<Edge>`	`getAllInEdges()`	Union of `getDirectedInEdges()` and `getUndirectedEdges()` .
`Collection<Node>`	`getAllInNeighbors()`	Union of `getInNeighbors()` and `getUndirectedNeighbors()` .
`HashSet<Node>`	`getAllOutChildNodes()`
`Collection<Edge>`	`getAllOutEdges()`	Union of `getDirectedOutEdges()` and `getUndirectedEdges()` .
`Collection<Node>`	`getAllOutNeighbors()`	Union of `getOutNeighbors()` and `getUndirectedNeighbors()`.
`ArrayList<String>`	`getAlternativeIDs()`	Enumerate alternative identifiers, assigned to the mapped xml substance data.
`ArrayList<String>`	`getAlternativeIDsWithIdx(int index)`	Enumerate alternative identifiers, assigned to the mapped xml substance data.
`Attribute`	`getAttribute(String path)`	Returns the `Attribute` located at the given path.
`CollectionAttribute`	`getAttributes()`	Returns the attributes of the current object in the base hierarchie in a `CollectionAttribute`.
`Object`	`getAttributeValue(String path, String name, Object returnIfNull, Object returnType)`
`double`	`getAverage()`
`boolean`	`getBoolean(String path)`	Returns the value of the `Attribute` at the given path.
`Color`	`getBorderColor()`
`double`	`getBorderWidth()`
`byte`	`getByte(String path)`	Returns the value of the `Attribute` at the given path.
`String`	`getClusterID(String ifNoCluster)`
`ExperimentInterface`	`getDataMappings()`
`DataSetTable`	`getDatasetTable()`
`int`	`getDegree()`	Returns the degree of a node
`Collection<Edge>`	`getDirectedInEdges()`	Returns a collection containing the directed ingoing edges of the `Node`.
`Iterator<Edge>`	`getDirectedInEdgesIterator()`	Returns an iterator containing the directed ingoing edges of the `Node`.
`Collection<Edge>`	`getDirectedOutEdges()`	Returns a collection containing the outgoing directed edges of the `Node`.
`Iterator<Edge>`	`getDirectedOutEdgesIterator()`	Returns an iterator containing the outgoing directed edges of the `Node`.
`double`	`getDouble(String path)`	Returns the value of the `Attribute` at the given path.
`Collection<Edge>`	`getEdges()`	Returns a collection containing all the ingoing and outgoing directed and undirected edges of the current `Node`.
`Iterator<Edge>`	`getEdgesIterator()`	Returns an iterator containing all the ingoing and outgoing directed and undirected edges of the current `Node`.
`Color`	`getFillColor()`
`float`	`getFloat(String path)`	Returns the value of the `Attribute` at the given path.
`Graph`	`getGraph()`	Returns the Graph the GraphElement belongs to.
`Node`	`getGraphNode()`
`double`	`getHeight()`
`long`	`getID()`
`TreeMap<DataMappingId,Stack<Double>>`	`getIdsAndAverageValues()`
`TreeMap<DataMappingId,Stack<Double>>`	`getIdsAndValues(Integer overrideReplicateId)`
`int`	`getInDegree()`	Returns the in-degree of the current `Node`.
`Set<Node>`	`getInNeighbors()`	Returns a collection containing the neighbor nodes belonging to incoming edges.
`Iterator<Node>`	`getInNeighborsIterator()`	Returns an iterator over the neighbor nodes belonging to incoming edges.
`int`	`getInteger(String path)`	Returns the value of the `Attribute` at the given path.
`String`	`getLabel()`
`String`	`getLabel(boolean htmlEncoded)`
`ListenerManager`	`getListenerManager()`	Returns the `ListenerManager` asscociated to this `Attributable`.
`long`	`getLong(String path)`	Returns the value of the `Attribute` at the given path.
`ArrayList<SampleAverageInterface>`	`getMappedAverageSampleData()`
`double`	`getMappedMaxSampleAvgValue()`
`ArrayList<Double>`	`getMappedMeanValuesForTimePoint(int timeValue)`
`double`	`getMappedMinSampleAvgValue()`
`ArrayList<NumericMeasurementInterface>`	`getMappedSampleData()`
`ArrayList<NumericMeasurementInterface>`	`getMappedSampleDataForTimePoint(int timeValue)`
`ArrayList<ConditionInterface>`	`getMappedSeriesData()`
`Set<String>`	`getMappedSeriesNames()`
`Set<Integer>`	`getMappedTimePointsCoveredByAllLines()`
`Set<Integer>`	`getMappedUniqueTimePoints()`
`ExperimentInterface`	`getMappingDataDocument(String substanceName, String measurementUnit, String experimentStart, String experimentName, String coordinator, String optRemark, String optSequence)`
`ArrayList<SubstanceInterface>`	`getMappings()`
`Set<Node>`	`getNeighbors()`	Returns a collection containing all the neighbor nodes of the current `Node`.
`Iterator<Node>`	`getNeighborsIterator()`	Returns an interator over the neighbor nodes of the current `Node`.
`static List<NodeHelper>`	`getNodeHelperList(Collection<Node> nodes)`
`int`	`getOutDegree()`	Returns the out-degree of the current `Node`.
`Set<Node>`	`getOutNeighbors()`	Returns a collection containing all the neighbors of the current `Node` which are connected by an outgoing `Edge`.
`Iterator<Node>`	`getOutNeighborsIterator()`	Returns an iterator containing all the neighbors of the current `Node` which are connected by an outgoing `Edge`.
`String`	`getPathwayReference()`
`Point2D`	`getPosition()`
`ArrayList<NodeHelper>`	`getReachableLeafNodes()`
`double`	`getRounding()`
`String`	`getShape()`
`short`	`getShort(String path)`	Returns the value of the `Attribute` at the given path.
`String`	`getString(String path)`	Returns the value of the `Attribute` at the given path.
`String`	`getTooltip()`
`Collection<Edge>`	`getUndirectedEdges()`	Returns a collection containing the undirected ingoing and outgoing edges of the `Node`.
`Iterator<Edge>`	`getUndirectedEdgesIterator()`	Returns an iterator containing all undirected edges of the `Node`.
`Collection<Node>`	`getUndirectedNeighbors()`	Returns a collection containing all the neighbors which are connected to the current `Node` by an undirected `Edge`.
`Iterator<Node>`	`getUndirectedNeighborsIterator()`
`String`	`getURL()`
`int`	`getViewID()`
`double`	`getWidth()`
`double`	`getX()`
`double`	`getY()`
`boolean`	`hasDataMapping()`
`boolean`	`isLastNode()`
`void`	`labelWordWrap()`
`boolean`	`memAddDataMapping(String substanceName, String measurementUnit, String experimentStart, String experimentName, String coordinator, String optRemark, String optSequence)`
`int`	`memGetPlantID(String species, String genotype, String optVariety, String optGrowthConditions, String optTreatment)`
`boolean`	`memSample(double value, int replicate, int plantID, String unit, String optTimeUnit, Integer optTimeValueForComparision)`
`void`	`mergeMultipleMappings()`
`int`	`removeAdditionalDataMappingIDs()`
`Attribute`	`removeAttribute(String path)`	Deletes the `Attribute` located at the given path from the attributes.
`void`	`removeDataMapping()`
`void`	`setAttributeValue(String path, String name, Object value)`
`void`	`setBoolean(String path, boolean value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setBorderColor(Color c)`
`void`	`setBorderWidth(double w)`
`void`	`setByte(String path, byte value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setChartRange(double minValue, double maxValue)`	Shortcut method to modify the range axis minimum and maximum value.
`void`	`setChartSettingUseCustomRange(boolean set)`	Shortcut method to enable or disable the display of a custom range.
`void`	`setChartType(GraffitiCharts chartType0123456)`
`void`	`setClusterID(String clusterID)`
`void`	`setDouble(String path, double value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setFillColor(Color c)`
`void`	`setFloat(String path, float value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setGraph(Graph graph)`
`void`	`setID(long id)`
`void`	`setInteger(String path, int value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setLabel(String label)`
`void`	`setLabelAlignment(int index, AlignmentSetting align)`	Set Label Position relative to the node.
`void`	`setLabelFontSize(int size, boolean wordWrap)`
`void`	`setLong(String path, long value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setPathwayReference(String ref)`
`void`	`setPosition(double x, double y)`
`void`	`setPosition(Point2D position)`
`void`	`setRounding(double r)`
`void`	`setShort(String path, short value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setSize(double width, double height)`
`void`	`setString(String path, String value)`	Sets the `Attribute` at the given path to the given value.
`void`	`setTooltip(String tooltip)`
`void`	`setURL(String url)`
`void`	`setViewID(int id)`
`boolean`	`writeDatasetTable(String fileName, boolean useAverage)`

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- NodeHelper
  
  public NodeHelper(Node n, boolean isLastNode)
- NodeHelper
  
  public NodeHelper(Node workNode)
Method Details
- getAlternativeIDs
  
  public ArrayList<String> getAlternativeIDs()
  
  Enumerate alternative identifiers, assigned to the mapped xml substance data.
  
  Returns:
  
  A list of alternative names, assigned to a node and its mapping data.
- getAlternativeIDsWithIdx
  
  public ArrayList<String> getAlternativeIDsWithIdx(int index)
  
  Enumerate alternative identifiers, assigned to the mapped xml substance data. Only the specified index value is processed.
  
  Returns:
  
  A list of alternative names, assigned to a node and its mapping data.
- memSample
  
  public boolean memSample(double value, int replicate, int plantID, String unit, String optTimeUnit, Integer optTimeValueForComparision)
- memGetPlantID
  
  public int memGetPlantID(String species, String genotype, String optVariety, String optGrowthConditions, String optTreatment)
- memAddDataMapping
  
  public boolean memAddDataMapping(String substanceName, String measurementUnit, String experimentStart, String experimentName, String coordinator, String optRemark, String optSequence)
- addDataMapping
  
  public void addDataMapping(Collection<DataSetRow> datasetRows, String substanceName)
- getMappingDataDocument
  
  public ExperimentInterface getMappingDataDocument(String substanceName, String measurementUnit, String experimentStart, String experimentName, String coordinator, String optRemark, String optSequence)
- writeDatasetTable
  
  public boolean writeDatasetTable(String fileName, boolean useAverage)
- getGraphNode
  
  public Node getGraphNode()
- setFillColor
  
  public void setFillColor(Color c)
- getFillColor
  
  public Color getFillColor()
- isLastNode
  
  public boolean isLastNode()
- getBorderColor
  
  public Color getBorderColor()
- setBorderColor
  
  public void setBorderColor(Color c)
- setSize
  
  public void setSize(double width, double height)
- getWidth
  
  public double getWidth()
- getHeight
  
  public double getHeight()
- getClusterID
  
  public String getClusterID(String ifNoCluster)
- setClusterID
  
  public void setClusterID(String clusterID)
- setPosition
  
  public void setPosition(double x, double y)
- getX
  
  public double getX()
- getY
  
  public double getY()
- getURL
  
  public String getURL()
- setURL
  
  public void setURL(String url)
- getPathwayReference
  
  public String getPathwayReference()
- setPathwayReference
  
  public void setPathwayReference(String ref)
- setAttributeValue
  
  public void setAttributeValue(String path, String name, Object value)
- getAttributeValue
  
  public Object getAttributeValue(String path, String name, Object returnIfNull, Object returnType)
- getTooltip
  
  public String getTooltip()
- setTooltip
  
  public void setTooltip(String tooltip)
- setLabel
  
  public void setLabel(String label)
- getLabel
  
  public String getLabel()
- getBorderWidth
  
  public double getBorderWidth()
- setBorderWidth
  
  public void setBorderWidth(double w)
- setRounding
  
  public void setRounding(double r)
- getRounding
  
  public double getRounding()
- getDataMappings
  
  public ExperimentInterface getDataMappings()
- getMappings
  
  public ArrayList<SubstanceInterface> getMappings()
- getMappedSeriesNames
  
  public Set<String> getMappedSeriesNames()
- getMappedSeriesData
  
  public ArrayList<ConditionInterface> getMappedSeriesData()
- getMappedSampleData
  
  public ArrayList<NumericMeasurementInterface> getMappedSampleData()
- getMappedAverageSampleData
  
  public ArrayList<SampleAverageInterface> getMappedAverageSampleData()
- getMappedSampleDataForTimePoint
  
  public ArrayList<NumericMeasurementInterface> getMappedSampleDataForTimePoint(int timeValue)
- getMappedMeanValuesForTimePoint
  
  public ArrayList<Double> getMappedMeanValuesForTimePoint(int timeValue)
- getMappedTimePointsCoveredByAllLines
  
  public Set<Integer> getMappedTimePointsCoveredByAllLines()
- getMappedUniqueTimePoints
  
  public Set<Integer> getMappedUniqueTimePoints()
- setChartType
  
  public void setChartType(GraffitiCharts chartType0123456)
- getAverage
  
  public double getAverage()
- getAllInEdges
  
  public Collection<Edge> getAllInEdges()
  
  Description copied from interface: Node
  
  Union of getDirectedInEdges() and getUndirectedEdges() .
  
  Specified by:
  
  getAllInEdges in interface Node
  
  Returns:
  
  Collection
- getAllInNeighbors
  
  public Collection<Node> getAllInNeighbors()
  
  Description copied from interface: Node
  
  Union of getInNeighbors() and getUndirectedNeighbors() .
  
  Specified by:
  
  getAllInNeighbors in interface Node
  
  Returns:
  
  Collection
- getAllOutEdges
  
  public Collection<Edge> getAllOutEdges()
  
  Description copied from interface: Node
  
  Union of getDirectedOutEdges() and getUndirectedEdges() .
  
  Specified by:
  
  getAllOutEdges in interface Node
  
  Returns:
  
  Collection
- getAllOutNeighbors
  
  public Collection<Node> getAllOutNeighbors()
  
  Description copied from interface: Node
  
  Union of getOutNeighbors() and getUndirectedNeighbors().
  
  Specified by:
  
  getAllOutNeighbors in interface Node
  
  Returns:
  
  Collection
- getDirectedInEdges
  
  public Collection<Edge> getDirectedInEdges()
  
  Description copied from interface: Node
  
  Returns a collection containing the directed ingoing edges of the Node.
  
  Specified by:
  
  getDirectedInEdges in interface Node
  
  Returns:
  
  a collection containing the directed ingoing edges of the Node.
- getDirectedInEdgesIterator
  
  public Iterator<Edge> getDirectedInEdgesIterator()
  
  Description copied from interface: Node
  
  Returns an iterator containing the directed ingoing edges of the Node.
  
  Specified by:
  
  getDirectedInEdgesIterator in interface Node
  
  Returns:
  
  an iterator containing the directed ingoing edges of the Node.
- getDirectedOutEdges
  
  public Collection<Edge> getDirectedOutEdges()
  
  Description copied from interface: Node
  
  Returns a collection containing the outgoing directed edges of the Node.
  
  Specified by:
  
  getDirectedOutEdges in interface Node
  
  Returns:
  
  a collection containing the outgoing directed edges of the Node.
- getDirectedOutEdgesIterator
  
  public Iterator<Edge> getDirectedOutEdgesIterator()
  
  Description copied from interface: Node
  
  Returns an iterator containing the outgoing directed edges of the Node.
  
  Specified by:
  
  getDirectedOutEdgesIterator in interface Node
  
  Returns:
  
  an iterator containing the outgoing directed edges of the Node.
- getEdges
  
  public Collection<Edge> getEdges()
  
  Description copied from interface: Node
  
  Returns a collection containing all the ingoing and outgoing directed and undirected edges of the current Node. Ingoing and outgoing edges will not be separated and there will be no ordering on the collection.
  
  Specified by:
  
  getEdges in interface Node
  
  Returns:
  
  a collection containing all ingoing and outgoing directed and undirected edges of the current Node.
- getEdgesIterator
  
  public Iterator<Edge> getEdgesIterator()
  
  Description copied from interface: Node
  
  Returns an iterator containing all the ingoing and outgoing directed and undirected edges of the current Node. Ingoing and outgoing edges will not be separated and there will be no ordering on the collection.
  
  Specified by:
  
  getEdgesIterator in interface Node
  
  Returns:
  
  an iterator containing all ingoing and outgoing directed and undirected edges of the current Node.
- getInDegree
  
  public int getInDegree()
  
  Description copied from interface: Node
  
  Returns the in-degree of the current Node. The in-degree is defined as the number of ingoing, directed edges plus the number of undirected edges.
  
  Specified by:
  
  getInDegree in interface Node
  
  Returns:
  
  the in-degree of the current Node.
- getInNeighbors
  
  public Set<Node> getInNeighbors()
  
  Description copied from interface: Node
  
  Returns a collection containing the neighbor nodes belonging to incoming edges. Note that the number of Elements returned by this function might be less than the number returned by getInDegree(), due to the fact that multiple edges between the same two nodes are possible but the corresponding Node is only inserted once.
  
  Specified by:
  
  getInNeighbors in interface Node
  
  Returns:
  
  a collection containing the neighbor nodes belonging to incoming edges.
- getInNeighborsIterator
  
  public Iterator<Node> getInNeighborsIterator()
  
  Description copied from interface: Node
  
  Returns an iterator over the neighbor nodes belonging to incoming edges.
  
  Specified by:
  
  getInNeighborsIterator in interface Node
  
  Returns:
  
  a Iterator over the neighbor nodes belonging to incoming edges.
- getNeighbors
  
  public Set<Node> getNeighbors()
  
  Description copied from interface: Node
  
  Returns a collection containing all the neighbor nodes of the current Node. A neighbor Node is either the source or the target of either an ingoing or an outgoing or an undirected Edge.
  
  Specified by:
  
  getNeighbors in interface Node
  
  Returns:
  
  a collection containing all the neighbor nodes of the current Node.
- getNeighborsIterator
  
  public Iterator<Node> getNeighborsIterator()
  
  Description copied from interface: Node
  
  Returns an interator over the neighbor nodes of the current Node. A neighbor Node is either the source or the target of either an ingoing or outgoing or undirected Edge.
  
  Specified by:
  
  getNeighborsIterator in interface Node
  
  Returns:
  
  an iterator over the neighbor nodes of the current Node.
- getOutDegree
  
  public int getOutDegree()
  
  Description copied from interface: Node
  
  Returns the out-degree of the current Node. The out-degree is defined as the number of outgoing, directed edges plus the number of undirected edges.
  
  Specified by:
  
  getOutDegree in interface Node
  
  Returns:
  
  the out-degree of the current Node.
- getOutNeighbors
  
  public Set<Node> getOutNeighbors()
  
  Description copied from interface: Node
  
  Returns a collection containing all the neighbors of the current Node which are connected by an outgoing Edge. Note that the number of elements returned by this function might be less than the number returned by getOutDegree(), due to the fact that multiple edges between the same two nodes are possible but the corresponding Node is only inserted once.
  
  Specified by:
  
  getOutNeighbors in interface Node
  
  Returns:
  
  a collection containing all the neighbor nodes of the current Node connected by an outgoing Edge.
- getOutNeighborsIterator
  
  public Iterator<Node> getOutNeighborsIterator()
  
  Description copied from interface: Node
  
  Returns an iterator containing all the neighbors of the current Node which are connected by an outgoing Edge.
  
  Specified by:
  
  getOutNeighborsIterator in interface Node
  
  Returns:
  
  an iterator containing all the neighbor Nodes of the current Node connected by an outgoing Edge.
- getUndirectedNeighborsIterator
  
  public Iterator<Node> getUndirectedNeighborsIterator()
  
  Specified by:
  
  getUndirectedNeighborsIterator in interface Node
- getUndirectedEdges
  
  public Collection<Edge> getUndirectedEdges()
  
  Description copied from interface: Node
  
  Returns a collection containing the undirected ingoing and outgoing edges of the Node.
  
  Specified by:
  
  getUndirectedEdges in interface Node
  
  Returns:
  
  a collection containing the undirected ingoing and outgoing edges of the Node.
- getUndirectedEdgesIterator
  
  public Iterator<Edge> getUndirectedEdgesIterator()
  
  Description copied from interface: Node
  
  Returns an iterator containing all undirected edges of the Node.
  
  Specified by:
  
  getUndirectedEdgesIterator in interface Node
  
  Returns:
  
  an iterator containing all undirected edges of the Node.
- getUndirectedNeighbors
  
  public Collection<Node> getUndirectedNeighbors()
  
  Description copied from interface: Node
  
  Returns a collection containing all the neighbors which are connected to the current Node by an undirected Edge.
  
  Specified by:
  
  getUndirectedNeighbors in interface Node
  
  Returns:
  
  a collection containing all the neighbors which are connected to the current Node by an undirected Edge.
- setGraph
  
  public void setGraph(Graph graph)
  
  Specified by:
  
  setGraph in interface Node
- getGraph
  
  public Graph getGraph()
  
  Description copied from interface: GraphElement
  
  Returns the Graph the GraphElement belongs to.
  
  Specified by:
  
  getGraph in interface GraphElement
  
  Returns:
  
  the Graph the GraphElement belongs to.
- setID
  
  public void setID(long id)
  
  Specified by:
  
  setID in interface GraphElement
- getID
  
  public long getID()
  
  Specified by:
  
  getID in interface GraphElement
- getViewID
  
  public int getViewID()
  
  Specified by:
  
  getViewID in interface GraphElement
- setViewID
  
  public void setViewID(int id)
  
  Specified by:
  
  setViewID in interface GraphElement
- getAttribute
  
  public Attribute getAttribute(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the Attribute located at the given path.
  
  Specified by:
  
  getAttribute in interface Attributable
  
  Parameters:
  
  path - the path to the Attribute.
  
  Returns:
  
  DOCUMENT ME!
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the location specified by path.
- getAttributes
  
  public CollectionAttribute getAttributes()
  
  Description copied from interface: Attributable
  
  Returns the attributes of the current object in the base hierarchie in a CollectionAttribute.
  
  Specified by:
  
  getAttributes in interface Attributable
  
  Returns:
  
  the attributes of the current object.
- setBoolean
  
  public void setBoolean(String path, boolean value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The Attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setBoolean in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getBoolean
  
  public boolean getBoolean(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getBoolean in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- setByte
  
  public void setByte(String path, byte value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The Attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setByte in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getByte
  
  public byte getByte(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getByte in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- setDouble
  
  public void setDouble(String path, double value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setDouble in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getDouble
  
  public double getDouble(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getDouble in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- setFloat
  
  public void setFloat(String path, float value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setFloat in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getFloat
  
  public float getFloat(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getFloat in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- setInteger
  
  public void setInteger(String path, int value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The Attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setInteger in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getInteger
  
  public int getInteger(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getInteger in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- getListenerManager
  
  public ListenerManager getListenerManager()
  
  Description copied from interface: Attributable
  
  Returns the ListenerManager asscociated to this Attributable.
  
  Specified by:
  
  getListenerManager in interface Attributable
  
  Returns:
  
  the ListenerManager asscociated to this Attributable.
- setLong
  
  public void setLong(String path, long value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The Attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setLong in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getLong
  
  public long getLong(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getLong in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- setShort
  
  public void setShort(String path, short value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The Attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setShort in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getShort
  
  public short getShort(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getShort in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- setString
  
  public void setString(String path, String value)
  
  Description copied from interface: Attributable
  
  Sets the Attribute at the given path to the given value. The Attribute is created at the given location, if it does not yet exist.
  
  Specified by:
  
  setString in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
- getString
  
  public String getString(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Returns the value of the Attribute at the given path.
  
  Specified by:
  
  getString in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  Returns:
  
  the value of the Attribute at the given path.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- addAttribute
  
  public void addAttribute(Attribute attr, String path) throws AttributeExistsException, NoCollectionAttributeException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  Adds attr to the attributes at position indicated by path. Informs the ListenerManager about the change: calls preAttributeAdded and postAttributeAdded in the ListenManager. Also sets the parent and the attributable of attr.
  Implementation Notes: path specifies the location of the CollectionAttribute or (in case path is the empty string) the Attributable attr should be added to. Usage should look as follows:
  
  Graph g = new Graph(..); CollectionAttribute ca = new CollectionAttribute("root"); //add ca to the attributable g as root attribute g.addAttribute(ca, ""); IntegerAttribute ia = Integer.valueOfAttribute("int", 10); //add ia as child of root g.addAttribute(ia, "root");
  
  Given there already exists an Attribute with the same id and cannot be overwritten, then an AttributeExistsException will be thrown.
  Specified by:
  
  addAttribute in interface Attributable
  
  Parameters:
  
  attr - the Attribute to be added.
  
  Throws:
  
  AttributeExistsException - if there is already an Attribute with the same id as attr at location path.
  
  NoCollectionAttributeException - if the Attribute at location path is not a CollectionAttribute.
  
  FieldAlreadySetException
- addBoolean
  
  public void addBoolean(String path, String id, boolean value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds a BooleanAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addBoolean in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new IntegerAttribute should be added to.
  
  id - the id of the newly created Attribute.
  
  value - the value of the newly created Attribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- addByte
  
  public void addByte(String path, String id, byte value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds an ByteAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addByte in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new ByteAttribute should be added to.
  
  id - the id of the new ByteAttribute.
  
  value - the value of the new ByteAttribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- addDouble
  
  public void addDouble(String path, String id, double value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds a DoubleAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addDouble in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new IntegerAttribute should be added to.
  
  id - the id of the newly created Attribute.
  
  value - the value of the newly created Attribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- addFloat
  
  public void addFloat(String path, String id, float value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds a FloatAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addFloat in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new IntegerAttribute should be added to.
  
  id - the id of the newly created Attribute.
  
  value - the value of the newly created Attribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- addInteger
  
  public void addInteger(String path, String id, int value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds an IntegerAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addInteger in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new IntegerAttribute should be added to.
  
  id - the id of the Integer.valueOfAttribute.
  
  value - the value of the Integer.valueOfAttribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- addLong
  
  public void addLong(String path, String id, long value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds an LongAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addLong in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new LongAttribute should be added to.
  
  id - the id of the new LongAttribute.
  
  value - the value of the new LongAttribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- addShort
  
  public void addShort(String path, String id, short value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds an ShortAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addShort in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new ShortAttribute should be added to.
  
  id - the id of the new ShortAttribute.
  
  value - the value of the new ShortAttribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- addString
  
  public void addString(String path, String id, String value) throws NoCollectionAttributeException, AttributeExistsException, FieldAlreadySetException
  
  Description copied from interface: Attributable
  
  Adds an StringAttribute with the given value and id to a CollectionAttribute at path.
  
  Specified by:
  
  addString in interface Attributable
  
  Parameters:
  
  path - the path to the CollectionAttribute the new IntegerAttribute should be added to.
  
  id - the id of the newly created Attribute.
  
  value - the value of the newly created Attribute.
  
  Throws:
  
  NoCollectionAttributeException - if the Attribute at the location specified by path is no CollectionAttribute.
  
  AttributeExistsException - if there is already an Attribute with the given id at the given path.
  
  FieldAlreadySetException
- changeBoolean
  
  public void changeBoolean(String path, boolean value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeBoolean in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- changeByte
  
  public void changeByte(String path, byte value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeByte in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- changeDouble
  
  public void changeDouble(String path, double value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeDouble in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- changeFloat
  
  public void changeFloat(String path, float value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeFloat in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- changeInteger
  
  public void changeInteger(String path, int value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeInteger in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- changeLong
  
  public void changeLong(String path, long value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeLong in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- changeShort
  
  public void changeShort(String path, short value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeShort in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- changeString
  
  public void changeString(String path, String value) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Changes the Attribute at the given path to the given value.
  
  Specified by:
  
  changeString in interface Attributable
  
  Parameters:
  
  path - the path to search for the Attribute.
  
  value - the value to set to the Attribute to.
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the specified location.
- removeAttribute
  
  public Attribute removeAttribute(String path) throws AttributeNotFoundException
  
  Description copied from interface: Attributable
  
  Deletes the Attribute located at the given path from the attributes. Informs the ListenerManager about the change: calls pre-/postAttributeRemoved in the ListenerManager.
  
  Specified by:
  
  removeAttribute in interface Attributable
  
  Parameters:
  
  path - the path of the Attribute to be removed.
  
  Returns:
  
  the removed attribute
  
  Throws:
  
  AttributeNotFoundException - if there is no Attribute at the location specified by path.
- removeDataMapping
  
  public void removeDataMapping()
- addDataMapping
  
  public void addDataMapping(SubstanceInterface mappingData)
- mergeMultipleMappings
  
  public void mergeMultipleMappings()
- getDegree
  
  public int getDegree()
  
  Description copied from interface: Node
  
  Returns the degree of a node
  
  Specified by:
  
  getDegree in interface Node
  
  Returns:
  
  Returns the number of incoming directed edges + outgooing directed edges + number of connected undirected edges.
- getNodeHelperList
  
  public static List<NodeHelper> getNodeHelperList(Collection<Node> nodes)
- setPosition
  
  public void setPosition(Point2D position)
- getPosition
  
  public Point2D getPosition()
- setChartRange
  
  public void setChartRange(double minValue, double maxValue)
  
  Shortcut method to modify the range axis minimum and maximum value. Besides setting the minimum and maximum value, this method enables the use of the custom values. You may disable the use of the custom range with the method setChartSettingUseCustomRange.
  
  Parameters:
  
  minValue -
  
  maxValue -
- setChartSettingUseCustomRange
  
  public void setChartSettingUseCustomRange(boolean set)
  
  Shortcut method to enable or disable the display of a custom range. (see also setChartRange) Implementation: setAttributeValue("charting", "useCustomRange", Boolean.valueOf(set));
- getMappedMinSampleAvgValue
  
  public double getMappedMinSampleAvgValue()
- getMappedMaxSampleAvgValue
  
  public double getMappedMaxSampleAvgValue()
- getDatasetTable
  
  public DataSetTable getDatasetTable()
- getAllOutChildNodes
  
  public HashSet<Node> getAllOutChildNodes()
- hasDataMapping
  
  public boolean hasDataMapping()
- getIdsAndValues
  
  public TreeMap<DataMappingId,Stack<Double>> getIdsAndValues(Integer overrideReplicateId)
- getIdsAndAverageValues
  
  public TreeMap<DataMappingId,Stack<Double>> getIdsAndAverageValues()
- setLabelFontSize
  
  public void setLabelFontSize(int size, boolean wordWrap)
- setLabelAlignment
  
  public void setLabelAlignment(int index, AlignmentSetting align)
  
  Set Label Position relative to the node.
  
  Parameters:
  
  index - Use "-1" to set position of main label, use values 0 to 99 to set annotation label positions.
  
  align - The node label alignment setting.
- labelWordWrap
  
  public void labelWordWrap()
- removeAdditionalDataMappingIDs
  
  public int removeAdditionalDataMappingIDs()
- getShape
  
  public String getShape()
- getLabel
  
  public String getLabel(boolean htmlEncoded)
- compareTo
  
  public int compareTo(GraphElement o)
  
  Specified by:
  
  compareTo in interface Comparable<GraphElement>
- getReachableLeafNodes
  
  public ArrayList<NodeHelper> getReachableLeafNodes()
  
  Returns:
  
  List of leaf-nodes, reachable from this node.

Constructor	Description
`NodeHelper(Node workNode)`
`NodeHelper(Node n, boolean isLastNode)`

Class NodeHelper

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

NodeHelper

NodeHelper

Method Details

getAlternativeIDs

getAlternativeIDsWithIdx

memSample

memGetPlantID

memAddDataMapping

addDataMapping

getMappingDataDocument

writeDatasetTable

getGraphNode

setFillColor

getFillColor

isLastNode

getBorderColor

setBorderColor

setSize

getWidth

getHeight

getClusterID

setClusterID

setPosition

getX

getY

getURL

setURL

getPathwayReference

setPathwayReference

setAttributeValue

getAttributeValue

getTooltip

setTooltip

setLabel

getLabel

getBorderWidth

setBorderWidth

setRounding

getRounding

getDataMappings

getMappings

getMappedSeriesNames

getMappedSeriesData

getMappedSampleData

getMappedAverageSampleData

getMappedSampleDataForTimePoint

getMappedMeanValuesForTimePoint

getMappedTimePointsCoveredByAllLines

getMappedUniqueTimePoints

setChartType

getAverage

getAllInEdges

getAllInNeighbors

getAllOutEdges

getAllOutNeighbors

getDirectedInEdges

getDirectedInEdgesIterator

getDirectedOutEdges

getDirectedOutEdgesIterator

getEdges

getEdgesIterator

getInDegree

getInNeighbors

getInNeighborsIterator

getNeighbors

getNeighborsIterator

getOutDegree

getOutNeighbors

getOutNeighborsIterator

getUndirectedNeighborsIterator

getUndirectedEdges

getUndirectedEdgesIterator

getUndirectedNeighbors

setGraph

getGraph