Author: slotia
Date: 2012-08-24 13:00:01 -0700 (Fri, 24 Aug 2012)
New Revision: 30269
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
Log:
Fixed some more language
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
2012-08-24 19:14:18 UTC (rev 30268)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/package-info.java
2012-08-24 20:00:01 UTC (rev 30269)
@@ -1,18 +1,18 @@
/**
-This package contains the core interfaces that define the basic network and
+This package has the core interfaces that define the basic network and
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}.
+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.
+independent. However, Cytoscape can link them together by matching table rows
with network object identifiers.
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}).
+{@link org.cytoscape.model.CyTable} is Cytoscape's data structure for tabular
data. A {@link org.cytoscape.model.CyTable}
+consists of columns ({@link org.cytoscape.model.CyColumn}) and rows ({@link
org.cytoscape.model.CyRow}).
<p>
Columns have unique names and are typed. A column has a single type that is
only defined when it is created.
@@ -36,11 +36,11 @@
<h4>Virtual Columns</h4>
<p>
-Cytoscape allows the contents of a column in one table to
-be shared with another table. These are called <i>virtual columns</i>.
+You can share the contents of a column in one table
+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.
+Virtual columns are used a lot by Cytoscape to shared data between networks.
</p>
<p>
@@ -71,18 +71,19 @@
<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
+Each table in Cytoscape has a unique identifier (SUID).
+{@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}.
+interface, {@link org.cytoscape.model.CyIdentifiable}.
</p>
<h4>Creating a CyTable ({@link org.cytoscape.model.CyTableFactory})</h4>
-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.
+Usually, App developers do not need to create {@link
org.cytoscape.model.CyTable}s. Instead, they use
+tables created for each network (see below). However, apps sometimes need to
create separate {@code CyTable}s
+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.
+<p>
+Creating a new {@code CyTable} depends on the type of App that you are
developing.
<ul>
<li>
<i>If your App is a simple app</i>
@@ -108,7 +109,7 @@
<h3>CyNetwork</h3>
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.
+of nodes ({@link org.cytoscape.model.CyNode}) and 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. {@code CyNetwork}
supports
<a href="http://www.wikipedia.org/wiki/Multigraph";>multigraphs</a>,
@@ -117,7 +118,7 @@
<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
+it can be implemented using the Cytoscape model by combining network pointers
and subnetworks (see
the next section).
</p>
@@ -127,9 +128,9 @@
({@link org.cytoscape.model.subnetwork.CyRootNetwork}). Each root network has
multiple
<i>subnetworks</i> ({@link org.cytoscape.model.subnetwork.CySubNetwork}).
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
+{@link org.cytoscape.model.subnetwork.CySubNetwork}. After all, {@code
CySubNetwork}s are just {@code CyNetwork}s
with a couple additional methods.
-This structure is hidden since most App implementers don't need
+This structure is hidden since most App developers don't need
to know about the root network.
<p align="center">
@@ -137,10 +138,10 @@
</p>
<p>
-All nodes and edges really exist in the root network.
-The subnetwork is merely a subset of nodes and edges in the root network.
+All nodes and edges exist in the root network.
+The subnetwork merely refers to a subset of nodes and edges in the root
network.
+Nodes and edges are shared amongst all of the subnetworks with a common root
network.
The purpose of this structure is so that you can share table data across
networks.
-Nodes and edges are shared amongst all of the subnetworks with a common root
network.
You can 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 is useful for importing a lot of data
(e.g. large expression data sets).
You can also "save" nodes and edges for later use by keeping them in the root
network and removing them
@@ -150,7 +151,7 @@
<p>
When the first network is created by the {@link
org.cytoscape.model.CyNetworkFactory}, a new
-{@link org.cytoscape.model.subnetwork.CyRootNetwork} is actually created. Each
root network has a <i>base network</i>,
+{@link org.cytoscape.model.subnetwork.CyRootNetwork} is first created. Each
root network has a <i>base network</i>,
which is a {@link org.cytoscape.model.subnetwork.CySubNetwork} that contains
everything in the root network. The base network is
is returned by {@link org.cytoscape.model.CyNetworkFactory#createNetwork}.
</p>
@@ -165,10 +166,12 @@
<dd><code>CyRootNetwork rootNetwork =
((CySubNetwork)network).getRootNetwork();</code></dd>
</dl>
{@link org.cytoscape.model.subnetwork.CyRootNetwork} provides methods to
create and add new subnetworks
-(see {@link org.cytoscape.model.subnetwork.CyRootNetwork#addSubNetwork} for
example).
+(see {@link org.cytoscape.model.subnetwork.CyRootNetwork#addSubNetwork}).
</p>
<h3>CyNetworks and CyTables</h3>
+
+<h4>Types of tables</h4>
When a {@link org.cytoscape.model.CyNetwork} is created, Cytoscape creates
three types of {@link org.cytoscape.model.CyTable}s
that store information about the network, its nodes, and its edges:
<ol>
@@ -188,13 +191,12 @@
</li>
</ol>
-<p>
-Having separate local and shared tables provides lots
-of flexibility for certain applications. However, the App developer will often
want to get all of the public information
-about a network, node, or edge, regardless of whether it's shared or local.
Cytoscape provides a <i>default table</i>
-that has all of the local and shared data for a given
-network, node, or edge.
-</p>
+<h5>The default table</h5>
+Local and shared tables provide flexibility for certain scenarios.
+However, App developers usually does not care whether data is local or shared.
+They will often want to get all of the visible information
+about a network, node, or edge, regardless of whether it's shared or local.
<i>Default tables</i>
+has all of the local and shared data for networks, nodes, and edges.
<p>
App implementers should be aware that when a new column is created in the
default
@@ -204,8 +206,7 @@
local to only this network.
</p>
-<p>
-To obtain one of these tables:
+<h4>Getting a table associated with a network</h4>
<table border="1" cellpadding="10">
<tr>
<td></td>
@@ -260,11 +261,11 @@
<td valign="top">{@code cyNetwork.getTable(CyEdge.class,} {@link
org.cytoscape.model.CyNetwork#HIDDEN_ATTRS}{@code )}</td>
</tr>
</table>
-</p>
+<h4>Getting node and edge data</h4>
<p>
There are two ways of getting node and edge data from one of the tables listed
above.
-<ul>
+<ol>
<li>
First, get the table as shown above. Then use {@link
org.cytoscape.model.CyTable#getRow} method.
Here's an example for getting the hidden attribtues of an edge:
@@ -284,9 +285,10 @@
}</pre>
<p>Instead of passing in the SUID, you just pass in the edge itself.</p>
</li>
-</ul>
+</ol>
<h4>Managing CyNetworks ({@link org.cytoscape.model.CyNetworkManager}) and
CyTables ({@link org.cytoscape.model.CyTableManager})</h4>
+
A generalized graph or network is a very useful data construct that can be
usefully used by algorithms and Apps for
purposes other than providing a user with a network visualization. Since a
lot of Apps will need to know about
the creation of new networks the user might want to manipulate, Cytoscape
provides a mechanism to "register"
@@ -315,11 +317,11 @@
<ul>
<li>
- If the App is an OSGi bundle, this may be done in the {@code CyActivator}
class provided by the bundle.
+ If the App is an OSGi bundle, register the listener in the {@code
CyActivator} class.
</li>
<li>
- If the App is a Simple App (inherits from {@link
org.cytoscape.app.AbstractCyApp}) then
-the App implementer should use the following code:
+ If the App is a Simple App, which has a class that inherits from {@link
org.cytoscape.app.AbstractCyApp}, then
+the App developer should use the following code:
<dl>
<dd><pre><code>
ServiceRegistrar serviceRegistrar = getCyServiceRegistrar(); // This comes
from CyAppAdapter
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