Author: slotia
Date: 2012-08-22 17:45:36 -0700 (Wed, 22 Aug 2012)
New Revision: 30256
Added:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CyTable-CyRows-CyColumns.png
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
Log:
Changed CyTable overview documentation
Added:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CyTable-CyRows-CyColumns.png
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(Binary files differ)
Property changes on:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CyTable-CyRows-CyColumns.png
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Added: svn:mime-type
+ application/octet-stream
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
2012-08-22 23:29:46 UTC (rev 30255)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
2012-08-23 00:45:36 UTC (rev 30256)
@@ -1,23 +1,57 @@
/**
This package contains the core interfaces that define the basic network and
-table data types that constitute the foundation of Cytoscape. Cytoscape
supports
-two basic types of data: network data {@link org.cytoscape.model.CyNetwork}
and table data
-{@link org.cytoscape.model.CyTable}. For the most part, these can be thought
of as
-independent, but Cytoscape provides a way to index table rows using network
object ids,
-thus providing a linkage between them. In fact, Cytoscape uses this linkage
internally
-to store network metadata in the tables.
+table data structures that are foundational to Cytoscape. Cytoscape supports
+two basic, separate types of data: network data {@link
org.cytoscape.model.CyNetwork} and table data
+{@link org.cytoscape.model.CyTable}.
+
+<p>
+For the most part, the table and network data structures are
+independent. However, Cytoscape can link them together by indexing table rows
using network object ids.
+In fact, Cytoscape uses this linkage internally to store network metadata in
the tables.
+</p>
+
<h3>CyTable</h3>
A {@link org.cytoscape.model.CyTable} is Cytoscape's representation of tabular
data. A {@link org.cytoscape.model.CyTable}
consists of a series of columns ({@link org.cytoscape.model.CyColumn}) and
rows ({@link org.cytoscape.model.CyRow}).
-Columns are typed and the type of the column must be defined when it is
created. All data access is through the
-{@link org.cytoscape.model.CyRow}, which has a primary key. The column for
the primary key is created when the
-table is created (see {@link org.cytoscape.model.CyTableFactory}). Cytoscape
provides an extention to the standard
-table model that allows a column in one table to refer to a column in another
table. These so-called "virtual" columns
-provide a mechanism for tables to share data. This is used extensively by
Cytoscape to provide shared data between networks.
-When tables are created by Cytoscape, they are provided with a unique
identifier (SUID). This SUID may be used to
+
+<p>
+Columns are typed. A column has a single type that is only defined when it is
created.
+A column would have the <i>string type</i> if it stores text. Or it could have
the <i>integer type</i>
+if it stores whole numbers. Besides strings and integers, columns can have
other types.
+</p>
+
+<p>
+Cell values in the table are accessed through a
+{@link org.cytoscape.model.CyRow}. Each row has a <i>primary key</i>.
+A primary key is the row's unique identifier. No two rows in the
+same table have the same primary key.
+In each table, there is one column designated for storing the primary keys of
each row.
+The column for the primary key is created when the
+table is created (see {@link org.cytoscape.model.CyTableFactory}).
+</p>
+
+<p align="center">
+<img src="doc-files/CyTable-CyRows-CyColumns.png">
+</p>
+
+<h4>Virtual Columns</h4>
+<p>
+Cytoscape allows a column in one table to refer to
+the contents of a column in another table. These are called <i>virtual
columns</i>.
+They allow tables to share data.
+If cell values change in one virtual column, all other tables with
+that virtual column will change too.
+Virtual columns are used extensively by Cytoscape to provide shared data
between networks.
+</p>
+
+<h4>Unique Identifiers (SUIDs)</h4>
+<p>
+Each table in Cytoscape has a unique identifier (SUID). This SUID may be used
to
uniquely identify the table. {@link org.cytoscape.model.CyNetwork}s, {@link
org.cytoscape.model.CyNode}s, and
{@link org.cytoscape.model.CyEdge}s also have SUIDs that uniquely identify
them. They all inherit from the same
base interface, {@link org.cytoscape.model.CyIdentifiable}.
+</p>
+
<h4>Creating a CyTable ({@link org.cytoscape.model.CyTableFactory})</h4>
Usually, App developers would not create new {@link
org.cytoscape.model.CyTable}s, but would utilize the default
tables created for each network (see below). However, there are some
circumstances where it might be desirable
@@ -36,6 +70,10 @@
where <code>bc</code> is the OSGi BundleContext.
</p>
+<p id="CyTable-Footnote1">
+[1] Each row in a table has a unique identifier, called the <i>primary key</i>.
+No two rows in the same table have the same primary key.
+</p>
<h3>CyNetwork</h3>
In Cytoscape, a network ({@link org.cytoscape.model.CyNetwork}) is
conceptually a collection
of nodes ({@link org.cytoscape.model.CyNode}) and the edges ({@link
org.cytoscape.model.CyEdge}) that connect them.
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