Author: slotia
Date: 2012-08-23 18:00:53 -0700 (Thu, 23 Aug 2012)
New Revision: 30263
Added:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CySubNetwork-vs-CyNetwork.png
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CyTable-virtual-column.png
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
Log:
Updated more model docs
Added:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CySubNetwork-vs-CyNetwork.png
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Property changes on:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CySubNetwork-vs-CyNetwork.png
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Added: svn:mime-type
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Added:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CyTable-virtual-column.png
===================================================================
(Binary files differ)
Property changes on:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/doc-files/CyTable-virtual-column.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
2012-08-23 22:59:23 UTC (rev 30262)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
2012-08-24 01:00:53 UTC (rev 30263)
@@ -15,7 +15,7 @@
consists of a series of columns ({@link org.cytoscape.model.CyColumn}) and
rows ({@link org.cytoscape.model.CyRow}).
<p>
-Columns are typed. A column has a single type that is only defined when it is
created.
+Columns have unique names and 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>
@@ -36,14 +36,39 @@
<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.
+Cytoscape allows the contents of a column in one table to
+be shared with another table. These are called <i>virtual columns</i>.
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>
+<p>
+To add a virtual column, you will have to specify a couple things:
+ <ul>
+ <li>
+ <i>Target table</i>: the table into which you want to put the virtual
column.
+ </li>
+ <li>
+ <i>Target column</i>: the name of the virtual column you want in the
target table.
+ </li>
+ <li>
+ <i>Source table</i>: the table from which you want to get your virtual
column's contents.
+ </li>
+ <li>
+ <i>Source column</i>: the column in the source table from which you want
to get your virtual column's contents.
+ </li>
+ <li>
+ <i>Target join key</i>: the column in the target table whose cells match
the source table's primary key column.
+ This is used to match up the rows between the source and target tables.
+ </li>
+ </ul>
+</p>
+
+<p align="center">
+<img src="doc-files/CyTable-virtual-column.png">
+</p>
+
<h4>Unique Identifiers (SUIDs)</h4>
<p>
Each table in Cytoscape has a unique identifier (SUID). This SUID may be used
to
@@ -53,47 +78,69 @@
</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
-to maintain a separate table for the purposes of maintaining a large shared
data store that is not directly related
-to nodes and edges in a network.
-<p>There are two ways of creating a new CyTable, depending on the type of App
that you are developing. If
-your App inherits from {@link org.cytoscape.app.swing.AbstractCySwingApp} or
{@link org.cytoscape.app.AbstractCyApp}
-then you have direct access to the {@link org.cytoscape.model.CyTableFactory}
through the
-{@link org.cytoscape.app.CyAppAdapter#getCyTableFactory} method. If you are
implementing an OSGi bundle, then
-you can find the {@link org.cytoscape.model.CyTableFactory} service by adding
to your CyActivator
-(see {@link org.cytoscape.service.util.AbstractCyActivator}):
-<dl>
-<dd>
-<code>CyTableFactory tableFactory = getService(bc,
CyTableFactory.class);</code>
-</dd></dl>
-where <code>bc</code> is the OSGi BundleContext.
+Usually, App developers do not need to create {@link
org.cytoscape.model.CyTable}s. Instead, they would use the default
+tables created for each network (see below). However, it is sometimes needed
to create {@code CyTable}s for apps
+that need separate tables for storing tabular data that is not directly
related to nodes and edges in a network.
+
+<p>Creating a new CyTable depends on the type of App that you are developing.
+ <ul>
+ <li>
+ <i>If your App is a simple app</i>
+ <p>
+ You have a class that inherits from {@link
org.cytoscape.app.swing.AbstractCySwingApp} or {@link
org.cytoscape.app.AbstractCyApp}.
+ These classes have direct access to the {@link
org.cytoscape.model.CyTableFactory} through the
+ {@link org.cytoscape.app.CyAppAdapter#getCyTableFactory} method.
+ </p>
+ </li>
+ <li>
+ <i>If your App is an OSGi bundle</i>
+ <p>
+ You can get the {@link org.cytoscape.model.CyTableFactory} service by
adding this to your {@code CyActivator}
+ (see {@link org.cytoscape.service.util.AbstractCyActivator}):
+ <dl><dd>
+ <code>CyTableFactory tableFactory = getService(bc,
CyTableFactory.class);</code>
+ </dd></dl>
+ where {@code bc} is the OSGi {@code BundleContext}.
+ </p>
+ </li>
+ </ul>
</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.
+A network ({@link org.cytoscape.model.CyNetwork}) is a collection
+of nodes ({@link org.cytoscape.model.CyNode}) and the edges ({@link
org.cytoscape.model.CyEdge}) that connect nodes together.
It's important to note that because an edge is defined as a link between two
nodes, both
-nodes must exist in the network for the edge to exist. Technically,
Cytoscape's network model represents
-a <a href="http://www.wikipedia.org/wiki/Multigraph";>multigraph</a>,
-which means that two nodes can be connected by more than one edge. Cytoscape
does not support
-a <a href="hhtp://www.wikipedia.org/wiki/Hypergraph">hypergraph</a>
-(so edges can't connect more than two nodes), nor does Cytoscape directly
support a network hierarchy, although
-one can be implemented using the Cytoscape model by combining network pointers
and subnetworks (see the discussion in
+nodes must exist in the network for the edge to exist. {@code CyNetwork}
supports
+<a href="http://www.wikipedia.org/wiki/Multigraph";>multigraphs</a>,
+which means that two nodes can be connected together by more than one edge.
{@code CyNetwork} does not support
+<a href="hhtp://www.wikipedia.org/wiki/Hypergraph">hypergraphs</a>, so edges
cannot connect more than two nodes.
+
+<p>
+Cytoscape does not directly support a network hierarchy, although
+it can be implemented using the Cytoscape model by combining network pointers
and subnetworks (see the discussion in
the next section).
+</p>
+
<h4>CyRootNetwork and CySubNetwork ({@link
org.cytoscape.model.subnetwork})</h4>
-Cytoscape's network model is actually a little more complicated than what is
implied by looking solely in the
-{@link org.cytoscape.model} package. Cytoscape actually implements a "forest"
of networks, where each "tree" in
-the forest has a "root" ({@link org.cytoscape.model.subnetwork.CyRootNetwork})
and a series of
-branches ({@link org.cytoscape.model.subnetwork.CySubNetwork}). This is
generally hidden since most App implementers don't need
-to know about the root network, and a {@link
org.cytoscape.model.subnetwork.CySubNetwork} is also a
-{@link org.cytoscape.model.CyNetwork} with a couple of extra methods. Even
though this isn't
-commonly used by App implementers, there are some nice features that this
provides.
-Since all nodes and edges will exist in the root network, it means that they
are shared amongst all of the subnetworks. This
+Cytoscape's network model is a little more complicated than what a cursory
glance at the
+{@link org.cytoscape.model} package suggests. Cytoscape has multiple <i>root
networks</i>
+({@link org.cytoscape.model.subnetwork.CyRootNetwork}). Each root network has
multiple
+<i>subnetworks</i> ({@link org.cytoscape.model.subnetwork.CySubNetwork}).
+This structure is hidden since most App implementers don't need
+to know about the root network.
+When you are working with a {@link org.cytoscape.model.CyNetwork}, you're
really working with a
+{@link org.cytoscape.model.subnetwork.CySubNetwork}. {@code CySubNetwork}s are
just {@code CyNetwork}s
+with a couple additional methods.
+
+<p align="center">
+<img src="doc-files/CySubNetwork-vs-CyNetwork.png">
+</p>
+
+<p>
+This hierarchy provides some nice features.
+All nodes and edges really exist in the root network, not the subnetwork.
+The subnetwork is merely refers to a subset of nodes and edges in the root
network.
+This implies that nodes and edges are shared amongst all of the subnetworks.
This
allows Cytoscape to set up shared tables so that data values in one subnetwork
(say for a node) are shared with the
same node in another subnetwork. This can be very useful when importing a lot
of data (e.g. large expression data sets).
The other advantage is that it provides a place to "save" nodes and edges that
we might use later. This is used extensively
@@ -112,6 +159,8 @@
{@link org.cytoscape.model.subnetwork.CyRootNetwork} provides methods to
create and add new subnetworks
(see {@link org.cytoscape.model.subnetwork.CyRootNetwork#addSubNetwork} for
example).
</p>
+
+
<h4>CyNetworks and CyTables</h4>
When a {@link org.cytoscape.model.CyNetwork} is created, Cytoscape also
creates a series of {@link org.cytoscape.model.CyTable}s
to contain information about the network and its nodes and edges. Some of
these tables are public (visible to the user) but local
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