Package de.unijena.cheminf.scaffolds

Class GraphStreamUtility

java.lang.Object
de.unijena.cheminf.scaffolds.GraphStreamUtility
public class GraphStreamUtility extends Object
Contains functionalities to visualise CDK-Scaffold-generated scaffold networks and trees in a very basic way, employing the open GraphStream graph library. Please note that this is a very basic functionality primarily meant for visual inspection and debugging. GraphStream might also throw errors in some cases where the problem lies with the library, not this functionality here.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final boolean
    DEFAULT_ARE_NODES_LABELLED
    Default setting value for whether to label nodes with their index and level in the created graphs.
    static final org.openscience.cdk.depict.DepictionGenerator
    DEFAULT_CDK_DEPICTION_GENERATOR
    Default CDK depiction generator used to create structure images for the graph nodes
    static final String
    DEFAULT_GRAPH_ID
    Default ID given to the created graphs if no ID is given.
    static final String
    DEFAULT_GRAPH_STYLE_SHEET
    Default style sheet that is used for the created graphs if no custom style is defined.
    static final String
    DEFAULT_GRAPHSTREAM_UI
    Default graph viewer used for visualisation.
    static final String
    GRAPH_NODE_PROPERTY_KEY_SCAFFOLD_NODE_BASE_INSTANCE
    the cdk-scaffold ScaffoldNodeBase instances represented by a node in the created graph is stored under this property key.

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream.
    static void
    displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream.
    static void
    displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aDepictionGenerator)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream.
    static void
    displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aDepictionGenerator, String aStyleSheet)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream.
    static void
    displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aDepictionGenerator, String aStyleSheet, String aGraphStreamUIProperty)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream.
    static org.graphstream.graph.Graph
    generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds.
    static org.graphstream.graph.Graph
    generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds.
    static org.graphstream.graph.Graph
    generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds.
    static org.graphstream.graph.Graph
    generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator, String aStyleSheet)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds.
    static org.graphstream.graph.Graph
    generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator, String aStyleSheet, String aGraphID)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds.
    static org.graphstream.graph.Graph
    generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator, String aStyleSheet, org.graphstream.graph.Graph aGraph)
    The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds.
    static File
    getGraphStreamDisplayFolder()
    Folder to store screenshots, temporary image files, etc.
    static File
    getTempFolder()
    Folder for temporary files like the node structure depictions.
    static void
    screenshotGraph(org.graphstream.graph.Graph aGraph, String aFilePath)
    Creates a screenshot of the given graph using the "ui.screenshot" attribute.
    static void
    screenshotGraphHighQuality(org.graphstream.graph.Graph aGraph, String aFilePath)
    Creates a high quality screenshot of the given graph using the FileSinkImages method writeAll().
    static void
    screenshotGraphHighQuality(org.graphstream.graph.Graph aGraph, String aFilePath, org.graphstream.stream.file.FileSinkImages aFileSinkImages)
    Creates a high quality screenshot of the given graph using the FileSinkImages method writeAll().
    static void
    setGraphStreamDisplayFolder(File aDirectory)
    Sets the folder to store screenshots, temporary image files, etc.
    static void
    setTempFolder(File aDirectory)
    Sets the folder for temporary files like the node structure depictions.

    Methods inherited from class java.lang.Object

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

  • Field Details

    • DEFAULT_GRAPH_STYLE_SHEET

      public static final String DEFAULT_GRAPH_STYLE_SHEET
      Default style sheet that is used for the created graphs if no custom style is defined.
      See Also:

    • DEFAULT_GRAPH_ID

      public static final String DEFAULT_GRAPH_ID
      Default ID given to the created graphs if no ID is given.
      See Also:

    • DEFAULT_GRAPHSTREAM_UI

      public static final String DEFAULT_GRAPHSTREAM_UI
      Default graph viewer used for visualisation.
      See Also:

    • DEFAULT_ARE_NODES_LABELLED

      public static final boolean DEFAULT_ARE_NODES_LABELLED
      Default setting value for whether to label nodes with their index and level in the created graphs.
      See Also:

    • DEFAULT_CDK_DEPICTION_GENERATOR

      public static final org.openscience.cdk.depict.DepictionGenerator DEFAULT_CDK_DEPICTION_GENERATOR
      Default CDK depiction generator used to create structure images for the graph nodes

    • GRAPH_NODE_PROPERTY_KEY_SCAFFOLD_NODE_BASE_INSTANCE

      public static final String GRAPH_NODE_PROPERTY_KEY_SCAFFOLD_NODE_BASE_INSTANCE
      the cdk-scaffold ScaffoldNodeBase instances represented by a node in the created graph is stored under this property key.
      See Also:

  • Method Details

    • getGraphStreamDisplayFolder

      public static File getGraphStreamDisplayFolder()
      Folder to store screenshots, temporary image files, etc.
      Returns:
      output folder

    • setGraphStreamDisplayFolder

      public static void setGraphStreamDisplayFolder(File aDirectory) throws NullPointerException, IllegalArgumentException
      Sets the folder to store screenshots, temporary image files, etc.
      Parameters:
      aDirectory - folder directory where the JRE can write and read
      Throws:
      NullPointerException - if the given folder is null
      IllegalArgumentException - if the JRE is unable to read and write in the given folder

    • getTempFolder

      public static File getTempFolder()
      Folder for temporary files like the node structure depictions.
      Returns:
      folder for temporary files

    • setTempFolder

      public static void setTempFolder(File aDirectory) throws NullPointerException, IllegalArgumentException
      Sets the folder for temporary files like the node structure depictions.
      Parameters:
      aDirectory - folder directory where the JRE can write and read
      Throws:
      NullPointerException - if the given folder is null
      IllegalArgumentException - if the JRE is unable to read and write in the given folder

    • displayWithGraphStream

      public static void displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection) throws NullPointerException, IllegalArgumentException, IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream.
      NOTE: It is not recommended displaying multiple graphs at the same time using this method because of multithreading issues.
      Parameters:
      aScaffoldNodeCollection - displayed scaffold graph
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • displayWithGraphStream

      public static void displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled) throws NullPointerException, IllegalArgumentException, IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      NOTE: It is not recommended displaying multiple graphs at the same time using this method because of multithreading issues.
      Parameters:
      aScaffoldNodeCollection - displayed scaffold graph
      areNodesLabelled - adds a label with node level and node index if true
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • displayWithGraphStream

      public static void displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aDepictionGenerator) throws NullPointerException, IllegalArgumentException, IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      NOTE: It is not recommended displaying multiple graphs at the same time using this method because of multithreading issues.
      Parameters:
      aScaffoldNodeCollection - displayed scaffold graph
      areNodesLabelled - adds a label with node level and node index if true
      aDepictionGenerator - CDK depiction generator used for generating the structure images on the graph nodes
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • displayWithGraphStream

      public static void displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aDepictionGenerator, String aStyleSheet) throws NullPointerException, IllegalArgumentException, IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      NOTE: It is not recommended displaying multiple graphs at the same time using this method because of multithreading issues.
      Parameters:
      aScaffoldNodeCollection - displayed scaffold graph
      areNodesLabelled - adds a label with node level and node index if true
      aDepictionGenerator - CDK depiction generator used for generating the structure images on the graph nodes
      aStyleSheet - style sheet property for the graph
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • displayWithGraphStream

      public static void displayWithGraphStream(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aDepictionGenerator, String aStyleSheet, String aGraphStreamUIProperty) throws NullPointerException, IllegalArgumentException, IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is displayed in an application window using GraphStream. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph. The GraphStream UI property defines which graphics library is employed, Java Swing (more reliable) or JavaFX (more experimental).
      NOTE: It is not recommended displaying multiple graphs at the same time using this method because of multithreading issues.
      Parameters:
      aScaffoldNodeCollection - displayed scaffold graph
      areNodesLabelled - adds a label with node level and node index if true
      aDepictionGenerator - CDK depiction generator used for generating the structure images on the graph nodes
      aStyleSheet - style sheet property for the graph
      aGraphStreamUIProperty - "swing" or "javafx" (make sure to have installed the respective dependencies)
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • generateGraphFromScaffoldNodeCollection

      public static org.graphstream.graph.Graph generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection) throws IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds.
      Parameters:
      aScaffoldNodeCollection - scaffold graph (scaffold tree or network) to parse
      Returns:
      GraphStream Graph instance representing the given scaffold graph with structure depictions of the scaffolds on its nodes
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • generateGraphFromScaffoldNodeCollection

      public static org.graphstream.graph.Graph generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled) throws IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      Parameters:
      aScaffoldNodeCollection - scaffold graph (scaffold tree or network) to parse
      areNodesLabelled - adds a label with node level and node index if true
      Returns:
      GraphStream Graph instance representing the given scaffold graph with structure depictions of the scaffolds on its nodes
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • generateGraphFromScaffoldNodeCollection

      public static org.graphstream.graph.Graph generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator) throws IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      Parameters:
      aScaffoldNodeCollection - scaffold graph (scaffold tree or network) to parse
      areNodesLabelled - adds a label with node level and node index if true
      aCDKDepictionGenerator - CDK depiction generator used for generating the structure images on the graph nodes
      Returns:
      GraphStream Graph instance representing the given scaffold graph with structure depictions of the scaffolds on its nodes
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • generateGraphFromScaffoldNodeCollection

      public static org.graphstream.graph.Graph generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator, String aStyleSheet) throws IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      Parameters:
      aScaffoldNodeCollection - scaffold graph (scaffold tree or network) to parse
      areNodesLabelled - adds a label with node level and node index if true
      aCDKDepictionGenerator - CDK depiction generator used for generating the structure images on the graph nodes
      aStyleSheet - style sheet property for the graph
      Returns:
      GraphStream Graph instance representing the given scaffold graph with structure depictions of the scaffolds on its nodes
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • generateGraphFromScaffoldNodeCollection

      public static org.graphstream.graph.Graph generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator, String aStyleSheet, String aGraphID) throws IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      Parameters:
      aScaffoldNodeCollection - scaffold graph (scaffold tree or network) to parse
      areNodesLabelled - adds a label with node level and node index if true
      aCDKDepictionGenerator - CDK depiction generator used for generating the structure images on the graph nodes
      aStyleSheet - style sheet property for the graph
      aGraphID - id given to the newly created Graph instance
      Returns:
      GraphStream Graph instance representing the given scaffold graph with structure depictions of the scaffolds on its nodes
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • generateGraphFromScaffoldNodeCollection

      public static org.graphstream.graph.Graph generateGraphFromScaffoldNodeCollection(org.openscience.cdk.tools.scaffold.ScaffoldNodeCollectionBase aScaffoldNodeCollection, boolean areNodesLabelled, org.openscience.cdk.depict.DepictionGenerator aCDKDepictionGenerator, String aStyleSheet, org.graphstream.graph.Graph aGraph) throws NullPointerException, IllegalArgumentException, IOException
      The ScaffoldNodeCollectionBase (scaffold network or tree) is parsed into a GraphStream Graph object with nodes depicting the scaffolds. The optional numbering of the nodes reflects their respective indices in the exported adjacency matrix and their level in the graph.
      Parameters:
      aScaffoldNodeCollection - scaffold graph (scaffold tree or network) to parse
      areNodesLabelled - adds a label with node level and node index if true
      aCDKDepictionGenerator - CDK depiction generator used for generating the structure images on the graph nodes
      aStyleSheet - style sheet property for the graph
      aGraph - empty(!) Graph instance (convenience here, e.g. to connect a file sink image instance to the graph before it is constructed)
      Returns:
      GraphStream Graph instance representing the given scaffold graph with structure depictions of the scaffolds on its nodes
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if image files cannot be written for the depicted scaffold structures

    • screenshotGraph

      public static void screenshotGraph(org.graphstream.graph.Graph aGraph, String aFilePath) throws NullPointerException, IllegalArgumentException, IOException
      Creates a screenshot of the given graph using the "ui.screenshot" attribute.
      Parameters:
      aGraph - graph to screenshot
      aFilePath - file path were the screenshot should be created (existing files will be overridden)
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if an I/O error occurs while writing

    • screenshotGraphHighQuality

      public static void screenshotGraphHighQuality(org.graphstream.graph.Graph aGraph, String aFilePath) throws NullPointerException, IllegalArgumentException, IOException
      Creates a high quality screenshot of the given graph using the FileSinkImages method writeAll().
      NOTE: It is not recommended screenshotting multiple graphs at the same time using this method because of multithreading issues.
      Parameters:
      aGraph - graph to screenshot
      aFilePath - file path were the screenshot should be created (existing files will be overridden)
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if an I/O error occurs while writing

    • screenshotGraphHighQuality

      public static void screenshotGraphHighQuality(org.graphstream.graph.Graph aGraph, String aFilePath, org.graphstream.stream.file.FileSinkImages aFileSinkImages) throws NullPointerException, IllegalArgumentException, IOException
      Creates a high quality screenshot of the given graph using the FileSinkImages method writeAll().
      NOTE: It is not recommended screenshotting multiple graphs at the same time using this method because of multithreading issues.
      Parameters:
      aGraph - graph to screenshot
      aFilePath - file path were the screenshot should be created (existing files will be overridden)
      aFileSinkImages - FileSinkImages instance with custom configuration to create the screenshot
      Throws:
      NullPointerException - if any parameter is null
      IllegalArgumentException - if any parameter does not fulfil its requirements
      IOException - if an I/O error occurs while writing