Mini-Retreat One

Topics for Discussion

Meeting Notes

pre-meeting comments


Goal is to discuss these core layers and target an API for this core to allow more rapid, distributed porting and development

Minimal set of core layers to focus on:


public interface CyDataTable {

         * A public CyDataTable is a table that is accessible to the user
         * through the user interface.  Private or non-public CyDataTables will
         * not be visible to the user from the normal user interface, although
         * they will be accessible to plugin writers through the API.
         * @return Whether or not this CyDataTable should be publicly accessible.
        public boolean isPublic();

         * @return The session unique identifier.
        public long getSUID();

         * @return A human readable name for the CyDataTable.
        public String getTitle();

         * @param title The human readable title for the CyDataTable
         * suitable for use in a user interface.
        public void setTitle(String title);

         * The keySet of this map defines all columns in the CyDataTable and the
         * the values of this map define the types of the columns.
         * @return A map of column names to the {@link Class} objects that defines
         * the column type.
        public Map<String,Class<?>> getColumnTypeMap();

         * @param columnName The name identifying the attribute.
        public void deleteColumn(String columnName);

         * @param columnName The name identifying the column.
         * @param type The type associated with the column. 
         * @param unique Whether the entries in the column are unique. 
        public <T> void createColumn(String columnName, Class<? extends T> type, boolean unique); 

         * Unique columns can be used to map the values from one CyDataTable to another.
         * @return A list of column names where the values within the column are
         * guaranteed to be unique. 
        public List<String> getUniqueColumns();

         * @param columnName The name identifying the column to return.
         * @param type The type of the column to return.
         * @return The list of values of type T that exist in the column specified by
         * the columnName.
        public <T> List<? extends T> getColumnValues(String columnName, Class<? extends T> type);

         * @param primaryKey The primary key index of the row to return.
         * @return The {@link CyRow} identified by the specified index.
        public CyRow getRow(long primaryKey);

         * @return A new {@link CyRow} object for this CyDataTable. 
        public CyRow addRow();

         * By default all {@link CyRow}s created have a primary key column of
         * type {@link Integer} that gets created at initialization which is
         * identified by this string.
         * If the CyDataTable is created and immediately bound to a {@link CyNetwork}
         * then the primary key attribute is populated with the SUID of the 
         * {@link GraphObject}.
        public static final String PRIMARY_KEY = "AID";

CyDataTable Data Types and Serialization Proposal


Tackled CyGroups: Selection/Filters/NamedSelection(Groups)


ViewModel / Presentation Requirements

Plans and Decisions

Outdated_Cytoscape_3.0/MiniRetreatOne (last edited 2011-02-24 15:36:50 by PietMolenaar)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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